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Long Reads

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

The human genome contains more than 200,000 gene isoforms. However, different isoforms can be highly similar, and with an average length of 1.5kb remain difficult to study with short read sequencing.

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Generation of iPSCs from endangered Grevy's zebra and comparative transcriptomic analysis of mammalian PSCs

Induced pluripotent stem cells (iPSCs) can provide a biological resource for functional and conservation research in various species. This expectation has led to generation of iPSCs from various species, including those identified as endangered species.

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Extent and complexity of RNA processing in the development of honey bee queen and worker castes revealed by Nanopore direct RNA sequencing

The distinct honey bee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity.

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Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis

Background

Experimental proof of gene function assignments in plants is based on mutant analyses.

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Full-length transcriptomic analysis reveals osmoregulatory mechanisms in Coilia nasus eyes reared under hypotonic and hyperosmotic stress

In recent years, sea-level rise, caused by global warming, will trigger salinity changes. This will threaten the survival of aquatic animals. Till now, the osmoregulatory mechanism of Coilia nasus eyes has not been yet explored.

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Complete genome sequence of a virulent African swine fever virus from a domestic pig in Ukraine

Here, we report the complete genome sequence of an African swine fever (ASF) virus (ASFV/Kyiv/2016/131) isolated from the spleen of a domesti

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Ultralong Oxford Nanopore reads enable the development of a reference-grade perennial ryegrass genome assembly

Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult.

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A rapid and cost-effective identification of invertebrate pests at the borders using MinION sequencing of DNA barcodes

The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations.

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From telomere to telomere: the transcriptional and epigenetic state of human repeat elements

Mobile elements and highly repetitive genomic regions are potent sources of lineage-specific genomic innovation and fingerprint individual genomes.

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Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses.

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Trycycler: consensus long-read assemblies for bacterial genomes

Assembly of bacterial genomes from long-read data (generated by Oxford Nanopore or Pacific Biosciences platforms) can often be complete: a single contig for each chromosome or plasmid in the genome.

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Single nuclei transcriptome of the Lesser Duckweed Lemna minuta reveals cell trajectories for an entire plant

The ability to trace every cell in some model organisms has led to the fundamental understanding of development and cellular function.

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A high-throughput multiplexing and selection strategy to complete bacterial genomes

Background Bacterial whole-genome sequencing based on short-read sequencing data often results in a draft assembly formed by contiguous sequences.

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Systematic dissection of a complex gut bacterial community

Efforts to model the gut microbiome have yielded important insights into the mechanisms of interspecies interactions, the impact of priority effects on ecosystem dynamics, and the role of diet and nutrient availability in determining community composition.

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In vivo augmentation of a complex gut bacterial community

Efforts to model the human gut microbiome in mice have led to important insights into the mechanisms of host-microbe interactions. However, the model communities studied to date have been defined or complex but not both, limiting their utility.

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Diverse mating phenotypes impact the spread of wtf meiotic drivers in S. pombe

Meiotic drivers are genetic loci that break Mendel’s law of segregation to be transmitted into more than half of the offspring produced by a heterozygote. The success of a driver relies on outcrossing because drivers gain their advantage in heterozygotes.

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Towards population-scale long-read sequencing

Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples.

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Complete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle

Saccharibacteria (formerly TM7) have reduced genomes, a small size, and appear to have a parasitic lifestyle dependent on a bacterial host.

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Dysgu: efficient structural variant calling using short or long reads

Structural variation (SV) plays a fundamental role in genome evolution and can underlie inherited or acquired diseases such as cancer.

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Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

Background

Whole genome sequencing of cultured pathogens is the state of the art public health response for the bioinformatic source tracking of illness outbreaks.

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Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing

We developed a method to tag telomeres and measure telomere length by nanopore sequencing in the yeast S.

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Jasmine: population-scale structural variant comparison and analysis

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare.

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Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings.

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Cell-free DNA analysis by whole-exome sequencing for hepatocellular carcinoma: a pilot study in Thailand

Liquid biopsy for cell-free DNA (cfDNA) is a non-invasive technique to characterize the genetic profile of a tumor. Despite being a valuable tool, there is no mutational profile of cfDNA from hepatocellular carcinoma (HCC) in patients from Thailand, where HCC is prevalent.

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MinION nanopore sequencing and assembly of a complete human papillomavirus genome

Background

The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consu

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Intronic haplotypes in the GBA gene do not predict age at diagnosis of Parkinson's Disease

Background

GBA mutations are a common risk factor for Parkinson's disease (PD).

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Widespread occurrence of hybrid internal-terminal exons in human transcriptomes

Alternative RNA processing is a major mechanism for diversifying the human transcriptome. Messenger RNA isoform differences are predominantly driven by alternative first exons, cassette internal exons and alternative last exons.

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Single-molecule, full-length transcript isoform sequencing reveals disease mutation-associated RNA isoforms in cardiomyocytes

Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult.

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The epiallelic nature of mouse rDNA

Ribosomal DNA (rDNA) displays substantial inter-individual genetic variation in human and mouse.

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Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first Telomere-to-Telomere (T2T) human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete

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Human Chr18 transcriptome dataset combined from the Illumina HiSeq, ONT MinION, and qPCR data

The chromosome-centric dataset was created by applying several technologies of transcriptome profiling. The described dataset is available at NCBI repository (BioProject ID PRJNA635536).

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WeFaceNano: a user-friendly pipeline for complete ONT sequence assembly and detection of antibiotic resistance in multi-plasmid bacterial isolates

Bacterial plasmids often carry antibiotic resistance genes and are a significant factor in the spread of antibiotic resistance.

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Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae

Genomic surveillance can inform effective public health responses to pathogen outbreaks. However, integration of non-local data is rarely done.

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High-quality Arabidopsis thaliana genome assembly with Nanopore and HiFi long reads

Here, we report a high-quality (HQ) and almost complete genome assembly with a single gap and quality value (QV) larger than 60 of the model plant Arabidopsis thaliana ecotype Columbia (Col-0), generated using combination of Oxford Nanopore Technology (ONT) ultra-long reads, hi

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Novel canine high-quality metagenome-assembled genomes, prophages, and host-associated plasmids by long-read metagenomics together with Hi-C proximity ligation

Long-read metagenomics facilitates the assembly of high-quality metagenome-assembled genomes (HQ MAGs) out of complex microbiomes. It provides highly contiguous assemblies by spanning repetitive regions, complete ribosomal genes, and mobile genetic elements.

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Single cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing

Transcript isoforms are mRNAs that arise from alternative splicing events. During RNA processing, different combinations of a gene's exons lead to a diverse set of isoforms. Polymorphisms or mutations at splice junctions can generate alternative splicing events.

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PlasLR enables adaptation of plasmid prediction for error-prone long reads

Plasmids are extra-chromosomal genetic elements commonly found in bacterial cells that support many functional aspects including environmental adaptations. The identification of these genetic elements is vital for the further study of function and behaviour of the organisms.

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Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive.

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Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts

Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2.

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Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020.

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A genomic link in China roses: and they all lived prickly but water deficient ever after?

Prickles act against herbivores, pathogens or mechanical injury, while also prevent water loss. However, whether prickles have new function and the molecular genetics of prickle patterning remains poorly explored.

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Human genome integration of SARS-CoV-2 contradicted by long-read sequencing

A recent study proposed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications.

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A new method for sequencing the mitochondrial genome by using long read technology

We describe a protocol to prepare a multiplexed mtDNA library from a blood sample for performing a long read sequencing of the mitochondrial genome. All steps are carefully described to get a high enrichment of mtDNA relative to total DNA extracted from the blood sample.

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Molecular characterization of multidrug-resistant Yersinia enterocolitica from foodborne outbreaks in Sweden

The foodborne pathogen Yersinia enterocolitica causes gastrointestinal infections worldwide.

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Characterising foot-and-mouth disease virus in clinical samples using nanopore sequencing

The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracing, and aiding the selection of the most appropriate vaccine for the circulating strains.

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Re-examination of two diatom reference genomes using long-read sequencing

Background

The marine diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum are valuable model organisms for exploring the evolution, diversity and ecology of this important algal group.

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Theory of local k-mer selection with applications to long-read alignment

Motivation Selecting a subset of k-mers in a string in a local manner is a common task in bioinformatics tools for speeding up computation.

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Coexistence of two bla CTX-M-14 genes in a bla NDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China

Objectives

The emergence of carbapenem-resistant Enterobacteriaceae has become a serious public-health threat.

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The draft genome sequence of Eucalyptus polybractea based on hybrid assembly with short- and long-reads reads

Eucalyptus polybractea is a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of the E. polybractea genome utilizing both short- and long-read technology.

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Extended-spectrum cephalosporin resistance in Escherichia coli from broiler chickens raised with or without antibiotics in Ontario, Canada

Extended-spectrum cephalosporin (ESC)-resistant Escherichia coli were isolated from fecal samples enriched in ESC-containing broth over two years from broiler chickens raised with and without therapeutic antimicrobials.

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Genomic and phylogenetic analysis of a multidrug-resistant Burkholderia contaminans strain isolated from a patient with ocular infection

Objectives

The genus Burkholderia comprises rod-shaped, non-spore-forming, obligately aerobic Gram-negative bacteria that is found across diverse ecological niches. Burkholderia contaminans, an emerging pathogen associat

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New full-length sequences of blastocystis subtypes generated via Nanopore sequencing allow for comparisons between full-length and partial sequences of the rRNA gene

Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subunit ribosomal (SSU rRNA) RNA gene.

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Dog10K_Boxer_Tasha_1.0: a long-read assembly of the dog reference genome

The domestic dog has evolved to be an important biomedical model for studies regarding the genetic basis of disease, morphology and behavior. Genetic studies in the dog have relied on a draft reference genome of a purebred female boxer dog named “Tasha” initially published in 2005.

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Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contigu

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Salmonella Paratyphi infection: use of nanopore sequencing as a vivid alternative for the identification of invading bacteria

In our study we present an overview of the use of Oxford Nanopore Technologies (ONT) sequencing technology on the background of Enteric fever.

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Targeted enrichment of rRNA Gene tandem arrays for ultra-long sequencing by selective restriction endonuclease digestion

Large regions of nearly identical repeats, such as the 45S ribosomal RNA (rRNA) genes of Nucleolus Organizer Regions (NORs), can account for major gaps in sequenced genomes.

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Differentiation of capripox viruses by nanopore sequencing

The genus capripoxvirus (CaPV), family Poxviridae, includes three virus species: goatpox virus (GPV), sheeppox virus (SPV) and lumpy skin disease virus (LSDV). CaPV causes disease outbreaks with consequent economic losses in Africa and the Middle East.

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The Lithuanian reference genome LT1 - a human de novo genome

We present LT1, the first high-quality human reference genome from the Baltic States. LT1 is a female de novo human reference genome assembly constructed using 57× of ultra-long nanopore reads and 47× of short paired-end reads.

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Phylogenomic evidence of reinfection and persistence of SARS-CoV-2: first report from Colombia

The continuing evolution of SARS-CoV-2 and the emergence of novel variants have raised concerns about possible reinfection events and potential changes in the coronavirus disease 2019 (COVID-19) transmission dynamics.

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Complete whole genome sequences of Escherichia coli surrogate strains and comparison of sequence methods with application to the food industry

In 2013, the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) began transitioning to whole genome sequencing (WGS) for foodborne disease outbreak- and recall-associated isolate identification of select bacterial species.

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Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: a case report

Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H.

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MINTyper: an outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads

For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a single-nucleotide polymorphisms-distance matrix from a set of sequencing reads.

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Polishing the Oxford Nanopore long-read assemblies of bacterial pathogens with Illumina short reads to improve genomic analyses

Oxford Nanopore sequencing has been widely used to achieve complete genomes of bacterial pathogens. However, the error rates of Oxford Nanopore long reads are high.

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Genome-wide Imputation Using the practical haplotype graph in the heterozygous crop cassava

Genomic applications such as genomic selection and genome-wide association have become increasingly common since the advent of genome sequencing.

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Anatomy promotes neutral coexistence of strains in the human skin microbiome

What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using 947 C.

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Nanopore sequencing and its application to the study of microbial communities

Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable technologies.

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Uncovering transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii

Background Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has colonized the main cities of Central Africa threatening vector control programs. The adaptation of An.

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An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics

Background

Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease.

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A chromosome-level genome assembly of the parasitoid wasp, Cotesia glomerata (Hymenoptera: Braconidae)

Hymenopterans make up about 20% of all animal species, but most are poorly known and lack high-quality genomic resources. One group of important, yet under-studied hymenopterans, are parasitoid wasps in the family Braconidae.

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Complex sequence organization of heterochromatin in the holocentric plant Cuscuta europaea elucidated by the computational analysis of nanopore reads

Repeat-rich regions of higher plant genomes are usually associated with constitutive heterochromatin, a specific type of chromatin that forms tightly packed nuclear chromocenters and chromosome bands.

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Illuminating the transposon insertion landscape in plants using Cas9-targeted Nanopore sequencing and a novel pipeline

Transposable elements (TEs), which occupy significant portions of most plant genomes, are a major source of genomic novelty, contributing to plant adaptation, speciation and new cultivar production.

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The human ribosomal RNA gene is composed of highly homogenized tandem clusters

The structure of the human ribosomal RNA gene clustering region (rDNA) has traditionally been hard to analyze due to its highly repetitive nature.

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The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads

Background Cherries are stone fruits and belong to the economically important plant family of Rosaceae with worldwide cultivation of different species. The ground cherry, Prunus fruticosa Pall.

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A reference-quality, fully annotated genome from a Puerto Rican individual

Until 2019, the human genome was available in only one fully-annotated version, which was the result of 18 years of continuous improvement and revision.

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The food additive xanthan gum drives adaptation of the human gut microbiota

The diets of industrialized countries reflect the increasing use of processed foods, often with the introduction of novel food additives. Xanthan gum is a complex polysaccharide with unique rheological properties that have established its use as a widespread stabilizer and thickening agent.

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Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion–deletion variant located in a region of complex genomic architecture

Targeted next generation sequencing (NGS) is the predominant methodology for the molecular genetic diagnosis of inherited conditions. In many laboratories, NGS-identified variants are routinely validated using a different method, to minimize the risk of a false-positive diagnosis.

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Telomere-to-telomere genome assembly of Phaeodactylum tricornutum

Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly.

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Inferring species compositions of complex fungal communities from long- and short-read sequence data

Background The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in culture.

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Comparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms

Background

The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities.

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The chromatin insulator CTCF regulates HPV18 transcript splicing and differentiation-dependent late gene expression

The ubiquitous host protein, CCCTC-binding factor (CTCF), is an essential regulator of cellular transcription and functions to maintain epigenetic boundaries, stabilise chromatin loops and regulate splicing of alternative exons.

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Linked machine learning classifiers improve species classification of fungi when using error-prone long-reads on extended metabarcodes

The increased usage of long-read sequencing for metabarcoding has not been matched with public databases suited for error-prone long-reads. We address this gap and present a proof-of-concept study for classifying fungal species using linked machine learning classifiers.

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Marker-assisted mapping enables effective forward genetic analysis in the arboviral vector Aedes aegypti, a species with vast recombination deserts

Aedes aegypti is a major vector of arboviruses that cause dengue, chikungunya, yellow fever and Zika.

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Segmental duplications and their variation in a complete human genome

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) have been among the last regions of the human reference genome (GRCh38) to be finished.

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The complete sequence of a human genome

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics.

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Sex chromosome transformation and the origin of a male-specific X chromosome in the creeping vole

The mammalian sex chromosome system (XX female/XY male) is ancient and highly conserved. The sex chromosome karyotype of the creeping vole (Microtus oregoni) represents a long-standing anomaly, with an X chromosome that is unpaired in females (X0) and exclusively maternally transmitted.

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Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Background: Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms recently implemented in Oxford Nanopore's own control software.

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Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Background

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

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Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Background

Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance.

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JAFFAL: Detecting fusion genes with long read transcriptome sequencing

Massively parallel short read transcriptome sequencing has greatly expanded our knowledge of fusion genes which are drivers of tumor initiation and progression. In cancer, many fusions are also important diagnostic markers and targets for therapy.

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Metaviromes reveal the dynamics of Pseudomonas host-specific phages cultured and uncultured by plaque assay

Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or the ones with highest ability to plaque on solid media is not well known.

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A comparative analysis of computational tools for the prediction of epigenetic DNA methylation from long-read sequencing data

Recent development of Oxford Nanopore long-read sequencing has opened new avenues of identifying epigenetic DNA methylation.

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Genome of the destructive oomycete Phytophthora cinnamomi provides insights into its pathogenicity and adaptive potential

Background

Phytophthora cinnamomi is an oomycete pathogen of global relevance. It is considered as one of the most invasive species, which has caused irreversible damage to natural ecosystems and horticultural crops.

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The SEQC2 epigenomics quality control (EpiQC) study: comprehensive characterization of epigenetic methods, reproducibility, and quantification

Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify cancer and other diseases.

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Direct nanopore sequencing of individual full Length tRNA Strands

We describe a method for direct tRNA sequencing using the Oxford Nanopore MinION. The principal technical advance is custom adapters that facilitate end-to-end sequencing of individual tRNA molecules. A second advance is a Nanopore sequencing pipeline optimized for tRNA.

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Spatially coordinated heterochromatinization of distal short tandem repeats in fragile X syndrome

Short tandem repeat (STR) instability is causally linked to pathologic transcriptional silencing in a subset of repeat expansion disorders. In fragile X syndrome (FXS), instability of a single CGG STR tract is thought to repress FMR1 via local DNA methylation.

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Redefining the PTEN promoter: identification of two upstream transcription start regions

Germline mutation of PTEN is causally observed in Cowden syndrome (CS) and is one of the most common genetic causes of autism spectrum disorder (ASD).

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Simultaneous hybrid genome sequencing of <i>Vermamoeba vermiformis</i> and its Dependentiae endosymbiont <i>Vermiphilus pyriformis</i>

A hybrid sequencing approach, using short and long reads sequencing, was employed for characterizing the genomes of the free-living amoeba host Vermamoeba vermiformis, along with its Dependentiae endosymbiont Vermiphilus pyriformis.

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Synergistic effect of short- and long-read sequencing on functional meta-omics

Real-world evaluations of metagenomic reconstructions are challenged by distinguishing reconstruction artefacts from genes and proteins present in situ.

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Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk

Dragline silk of golden orb-weaver spiders (Nephilinae) is noted for its unsurpassed toughness, combining extraordinary extensibility and tensile strength, suggesting industrial application as a sustainable biopolymer material.

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Genome of the estuarine oyster provides insights into climate impact and adaptive plasticity

Understanding the roles of genetic divergence and phenotypic plasticity in adaptation is central to evolutionary biology and important for assessing adaptive potential of species under climate change.

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The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?

Group B Streptococcus (GBS; Streptococcus agalactiae) is a major neonatal and opportunistic bacterial pathogen of humans and an important cause of mastitis in dairy cattle with significant impacts on food security.

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Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure

Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently.

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An annotated draft genome for the Andean bear, Tremarctos ornatus

The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America.

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Complete, closed and curated genome sequences of Photobacterium damselae subsp. piscicida isolates from Australia indicate mobilome-driven localized evolution and novel pathogenicity determinants

Despite the recent advances in sequencing technologies, the complete assembly of multi-chromosome genomes of the Vibrionaceae, often containing several plasmids, remains challenging.

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Personalized genome assembly for accurate cancer somatic mutation discovery using cancer-normal paired reference samples

The use of personalized genome assembly as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but never been systematically investigated.

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Shared and unique evolutionary trajectories to ciprofloxacin resistance in gram-negative bacterial pathogens

The resistance to broad-spectrum antibiotic ciprofloxacin is detected in high rates for a wide range of bacterial pathogens.

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Extensive OMICS resource for Sf21 and Tni cell lines

Insect-derived cell lines, from Spodoptera frugiperda (Sf21) and from Trichoplusia ni (Tni), are the two most widely used cell lines for recombinant protein expression in combination with the Baculoviral Expression Vector System (BEVS).

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Chromatin profiling reveals genome stability heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

Invasive Pulmonary aspergillosis is a life-threatening infection in immunosuppressed patients caused by the filamentous fungus Aspergillus fumigatus.

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Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Most cancers are characterized by the somatic acquisition of genomic rearrangements during tumour evolution that eventually drive the oncogenesis. There are different mutational mechanisms causing structural variation, some of which are specific to particular cancer types.

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Genome assembly of the popular Korean soybean cultivar Hwangkeum

Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome.

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Three bacterium-plasmid golden combinations facilitate the spread of ST11/CG258 carbapenemase-producing Klebsiella pneumoniae in China

Carbapenemase-producing Klebsiella pneumoniae (cpKP) poses serious threats to public health. Previous studies showed that only ST11/CG258-cpKP successfully disseminated in China, however, the underlying genetic bases are still unknown.

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Genomic analysis reveals the influence of climate change and currents on adaptation in an estuarine species

Understanding the evolutionary forces driving adaptive divergence and identifying the genomic variations, especially those mediating the plastic responses are critical to evaluate the adaptive capacity of species upon rapidly changing climate.

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The genome of the poecilogonous annelid Streblospio benedicti

Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution.

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Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea

Background Retrotransposons are genetic elements inducing mutations in all domains of life.

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Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa

New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa”, that we here define as clades for which <10% of all species are described and the estimated diversity exceeds 1000 species.

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Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Background Structural Variations (SVs) are very diverse genomic rearrangements. In the past, their detection was restricted to cytological approaches, then to NGS read size and partitionned assemblies.

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Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population

The pks island codes for the enzymes necessary for synthesis of the genotoxin colibactin, which contributes to the virulence of Escherichia coli strains and is suspected of promoting colorectal cancer. From a collection of 785 human and bovine E.

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Chromosome-level genome assembly and transcriptome- based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14

Rhodotorula toruloides is an oleaginous yeast with high biotechnological potential. In order to understand the molecular physiology of lipid synthesis in R. toruloides and to advance metabolic engineering, a high-resolution genome is required.

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Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters.

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Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Pseudomonas and Sphingomonas are among the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana. Relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants rem

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Association of Streptococcus mutans harboring bona-fide collagen binding proteins and Candida albicans with early childhood caries recurrence

Early childhood caries (ECC) recurrence occurs in approximately 40% of treated cases within one year. The association of Streptococcus mutans and Candida albicans with the onset of ECC is well known. Also, S.

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Epidemiological and genomic analysis of a Sydney hospital COVID-19 outbreak

Australia’s early COVID-19 experience involved clusters in northern Sydney, including hospital and aged-care facility (ACF) outbreaks.

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A novel SARS-CoV-2 variant of concern, B.1.526, identified in New York

Recent months have seen surges of SARS-CoV-2 infection across the globe along with considerable viral evolution.

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Genomics of aminoglycoside resistance in Pseudomonas aeruginosa bloodstream infections at a United States academic hospital

Pseudomonas aeruginosa is a frequent cause of antibiotic-resistant infections. Although P.

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Neutralising antibodies in spike mediated SARS-CoV-2 adaptation

SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated.

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Emergence and rising of ceftazidime-avibactam resistant KPC-producing Pseudomonas aeruginosa in China: a molecular epidemiology study

Background Infections by Carbapenem-resistant Pseudomonas aeruginosa (CRPA) are difficult to treat and novel antibiotics are desperately needed.

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Simultaneous detection and mutation surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by rapid field-deployable sequencing

Strategies for monitoring the COVID-19 infection are crucial for combating the pandemic. Here we describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes.

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Sequence analysis of 20,453 SARS-CoV-2 genomes from the Houston metropolitan area identifies the emergence of multiple isolates of all major variants of concern

Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the human immune response, or otherwise alter biologically important phenotypes.

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Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border

Background Uruguay is one of the few countries in the Americas that successfully contained the COVID-19 epidemic during the first half of 2020.

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Transcript- and annotation-guided genome assembly of the European starling

The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range.

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High-quality genome sequence resource for Fusarium andiyazi causing pokkah boeng disease of sugarcane in China

Sugarcane pokkah boeng disease (PBD) is emerging as a prevalent foliar disease in China. This airborne disease is caused by the Fusarium species complex.

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A chromosome-level assembly of a wild castor genome provides new insights into the adaptive evolution in a tropical desert

Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiations, strong lights and extremely dry conditions.

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Pervasive cis effects of variation in copy number of large tandem repeats on local DNA methylation and gene expression

Variable number tandem repeats (VNTRs) are composed of large tandemly repeated motifs, many of which are highly polymorphic in copy number. However, because of their large size and repetitive nature, they remain poorly studied.

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Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction

Hymenoptera is a hyperdiverse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environments, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance.

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Transcriptional activity and epigenetic regulation of transposable element in the symbiotic fungus Rhizophagus irregularis

Arbuscular mycorrhizal (AM) fungi form mutualistic relationships with most land plant species. AM fungi have long been considered as ancient asexuals.

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Exploiting synergistic interactions of Medicago sativa L. and Paraburkholderia tropica for enhanced biodegradation of diesel fuel hydrocarbons

The biotechnological application of microorganisms for rhizoremediation of contaminated sites requires the development of plant-microbe symbionts capable of plant growth promotion and hydrocarbon degradation.

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Comparison of long read sequencing technologies in interrogating bacteria and fly genomes

The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length.

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Genomic analysis of human noroviruses using hybrid Illumina-Nanopore data

Whole genome sequence (WGS) analysis of noroviruses is routinely performed by employing a metagenomic approach.

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Combined short and long-read sequencing reveals a complex transcriptomic Architecture of African swine fever virus

African swine fever virus (ASFV) is a large DNA virus belonging to the Asfarviridae family. Despite its agricultural importance, little is known about the fundamental molecular mechanisms of this pathogen.

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Complete sequencing of expanded SAMD12 repeats by long-read sequencing and Cas9-mediated enrichment

A pentanucleotide TTTCA repeat insertion into a polymorphic TTTTA repeat element in SAMD12 causes benign adult familial myoclonic epilepsy.

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Precise gene models using long-read sequencing reveal a unique poly(A) signal in Giardia lamblia

During pre-mRNA processing, the poly(A) signal is recognized by a protein complex that ensures precise cleavage and polyadenylation of the nascent transcript.

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ECNano: a cost-effective workflow for target enrichment sequencing and accurate variant calling on 4,800 clinically significant genes using a single MinION flowcell

Background: The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field.

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Structural variant selection for high-altitude adaptation using single-molecule long-read sequencing

Structural variants (SVs) can be important drivers of human adaptation with strong effects, but previous studies have focused primarily on common variants with weak effects.

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16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis

Research question:

Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read 16S rRNA gene sequencing with low initial investment costs that has been used for various microbiome studies but has not yet been investigated as an alterna

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Robust methylation-based classification of brain tumors using nanopore sequencing

DNA methylation-based classification of cancer provides a comprehensive molecular approach to diagnose tumors. In fact, DNA methylation profiling of human brain tumors already profoundly impacts clinical neuro-oncology.

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Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes

Identification of human leukocyte antigen (HLA) alleles from next-generation sequencing (NGS) data is challenging because of the high polymorphism and mosaic nature of HLA genes.

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Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13T

Background

There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface.

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Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

In this study, six bacterial isolates with variable GC, including Escherichia coli as mesophilic reference strain, were selected to compare hybrid assembly strategies based on next-generation sequencing (NGS) of short reads, single-tube long-fragment reads (stLFR) sequencing, a

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Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India

Emergence of distinct viral clades has been observed in SARS-CoV2 variants across the world and India. Identification of the genomic diversity and the phylodynamic profiles of the prevalent strains of the country are critical to understand the evolution and spread of the variants.

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Genomic architecture and evolutionary dynamics of a social niche polymorphism in the California harvester ant, Pogonomyrmex californicus

The societies of social insects are highly variable, including variation in the number of reproductives in a colony. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded by a single queen (haplometrosis, primary monogyny).

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Recovery of complete genomes and non-chromosomal replicons from activated sludge enrichment microbial communities with long read metagenome sequencing

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes from complex microbial communities.

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The GGC repeat expansion in NOTCH2NLC is associated with oculopharyngodistal myopathy type 3

Oculopharyngodistal myopathy (OPDM) is an adult-onset neuromuscular disease characterized by progressive ocular, facial, pharyngeal and distal limb muscle involvement.

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The genome of the Margined White butterfly (Pieris macdunnoughii): sex chromosome insights and the power of polishing with PoolSeq data

We report a chromosome-level assembly for Pieris macdunnoughii, a North American butterfly whose involvement in an evolutionary trap imposed by an invasive Eurasian mustard has made it an emerging model system for studying maladaptation in plant-insect interactions.

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Genomic taxonomic assignment of individual root-knot nematodes

Root-knot nematodes (RKN; genus Meloidogyne) are polyphagous plant pathogens of great economic importance to agriculturalists globally. These species are small, diverse, and can be challenging for accurate taxonomic identification.

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Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain

Pistachios have been implicated in two salmonellosis outbreaks and multiple recalls in the U.S.

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Evaluation of Salmonella serotype prediction with multiplex Nanopore sequencing

The use of whole genome sequencing (WGS) data generated by the long-read sequencing platform Oxford Nanopore Technologies (ONT) has been shown to provide reliable results for Salmonella serotype prediction in a previous study.

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Genome sequencing and morphometric analysis of alpine bumblebees experiencing climate change reveal ongoing phenotypic shifts and a lack of population structure

Populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms, in the last six decades.

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A squalene–hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol–independent anaerobic growth

Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated.

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Leakiness at the human-animal interface in Southeast Asia and implications for the spread of antibiotic resistance

International efforts to curb antimicrobial resistance have focused on drug development and limiting unnecessary use.

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A free-living protist that lacks canonical eukaryotic DNA replication and segregation systems

Cells must replicate and segregate their DNA with precision. In eukaryotes, these processes are part of a regulated cell-cycle that begins at S-phase with the replication of DNA and ends after M-phase.

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Genome sequences for two Acinetobacter baumannii strains obtained using the Unicycler hybrid assembly pipeline

Here, we report a complete genome sequence for Acinetobacter baumannii strain ATCC 17961, with plasmid sequences, and a high-quality (>98% complete) build for A. baumannii strain AB09-003.

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The genome of the European estuarine calanoid copepod Eurytemora affinis: potential use in molecular ecotoxicology

In this study, we sequenced and assembled the genome of a European estuarine calanoid copepod using Oxford Nanopore PromethION and Illumina HiSeq 2500 platforms. The length of the assembled genome was 776.1 Mb with N50 = 474.9 kb (BUSCO 85.9%), and the genome consisted of 2473 contigs.

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DNA preparation in Vitis vinifera L. for third generation sequencing

Background There have been several attempts to sequence the genome of Vitis vinifera L. (grapevine), utilizing low-resolution second-generation platforms.

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Deeplasmid: Deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes.

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Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes

RNA degradation is critical for control of gene expression, and endonucleolytic cleavage– dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the cytoplasm and identified using the CAGE method.

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Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long

Reconstructing the sequence of circular RNAs (circRNAs) from short RNA sequencing reads has proved challenging given the similarity of circRNAs and their corresponding linear messenger RNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length circRNAs.

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Alpha satellite insertions and the evolutionary landscape of centromeres

Human centromeres are composed of alpha satellite DNA hierarchically organized as higher-order repeats and epigenetically specified by CENP-A binding. Current evolutionary models assert that new centromeres are first epigenetically established and subsequently acquire an alphoid array.

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Genomic analysis of dibenzofuran-degrading Pseudomonas veronii strain Pvy reveals its biodegradative versatility

Certain industrial chemicals accumulate in the environment due to their recalcitrant properties. Bioremediation uses the capability of some environmental bacteria to break down these chemicals and attenuate the pollution.

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Genome Sequence Resource of Phytophthora vignae, the causal agent of stem and root rot of cowpea

The causal agent of stem and root rot of cowpea, Phytophthora vignae, is a widely distributed species of Phytophthora genus. Here, we generate a high-quality complete genome assembly of P.

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Chromosome-scale genome sequence of Alternaria alternata causing Alternaria brown spot of citrus

Alternaria brown spot (ABS) caused by Alternaria alternata is an economically important fungal disease of citrus worldwide. The ABS pathogen A.

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Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants

High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission.

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Mitochondrial genome sequencing of marine leukemias reveals cancer contagion between clam species in the seas of Southern Europe

Clonally transmissible cancers are tumour lineages that are transmitted between individuals via the transfer of living cancer cells. In marine bivalves, leukemia-like transmissible cancers, called hemic neoplasia, have demonstrated the ability to infect individuals from different species.

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Metapopulation structure of diatom-associated marine bacteria

Marine bacteria-phytoplankton interaction ultimately shapes ecosystem productivity. The biochemical mechanisms underlying their interactions become increasingly known, yet how these ubiquitous interactions drive bacterial evolution has not been illustrated.

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Chromosomal rearrangements but no change of genes and transposable elements repertoires in an invasive forest-pathogenic fungus

Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments.

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Oncogenic fusion protein anchors to histone acetyltransferase complex to the coding region of active genes

A chromosomal translocation found in cannibalistic acute myeloid leukemia (AML) leads to an in-frame fusion of the transcription elongation repressor ZMYND11 to MBTD1, a subunit of the NuA4/TIP60 histone acetyltransferase (HAT) complex.

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Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing

Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome.

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Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences.

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Long-read sequencing improves the detection of structural variations impacting complex non-coding elements of the genome

The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases.

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An integrated sequencing approach for updating the pseudorabies virus transcriptome

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression.

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ANCHOR, a technical approach to monitor single-copy locus localization in planta

Gene expression is governed by several layers of regulation which in addition to genome organization, local chromatin structure, gene accessibility and the presence of transcription factors also includes gene positioning.

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A peek into the plasmidome of global sewage

Plasmids can provide a selective advantage for microorganisms to survive and adapt to new environmental conditions.

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Rapid characterization of complex genomic regions using Cas9 enrichment and Nanopore sequencing

Long-read sequencing approaches have considerably improved the quality and contiguity of genome assemblies. Such platforms bear the potential to resolve even extremely complex regions, such as multigenic families and repetitive stretches of DNA.

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Haplotype-aware variant calling enables high accuracy in nanopore long-reads using deep neural networks

Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read based phasing.

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The genome sequence of the cereal pest Sitophilus oryzae: an unprecedented transposable element content

Background Among beetles, the rice weevil Sitophilus oryzae is one of the most important pests causing extensive damage to cereal in fields and to stored grains. S.

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High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes

By offering extremely long contiguous characterization of individual DNA molecules, rapidly emerging long-read sequencing strategies offer comprehensive insights into the organization of genetic information in genomes and metagenomes.

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Genomic evaluation of Bordetella spp. originating from Australia

Bordetella pertussis is the primary causative agent of pertussis, a highly infectious respiratory disease associated with prolonged coughing episodes. Pertussis infections are typically mild in adults, however in neonates, infections can be fatal.

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Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions

Introduction: SARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics.

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High-quality complete genome resource of plant pathogenic bacterium Dickeya solani strain IPO 2019 isolated from Hyacinthus orientalis

Dickeya solani is an emerging plant pathogenic bacterium, causing disease symptoms in a variety of agriculturally relevant crop species worldwide. To date a number of D.

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Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A.

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Epstein-Barr virus long non-coding RNA RPMS1 full-length spliceome in transformed epithelial tissue

Epstein-Barr virus is associated with two types of epithelial neoplasms, nasopharyngeal carcinoma and gastric adenocarcinoma. The viral long non-coding RNA RPMS1 is the most abundantly expressed poly-adenylated viral RNA in these malignant tissues.

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Wolbachia in the spittlebug Prosapia ignipectus: Variable infection frequencies, but no apparent effect on host reproductive isolation

Animals serve as hosts for complex communities of microorganisms, including endosymbionts that live inside their cells. Wolbachia bacteria are perhaps the most common endosymbionts, manipulating host reproduction to propagate.

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Rapid and detailed characterization of transgene insertion sites in genetically modified plants via Nanopore sequencing

Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization.

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IsoTV: processing and visualizing functional features of translated transcript isoforms

Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure.

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Gene flux and acid-imposed selection are the main drivers of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg

Salmonella enterica serovar Heidelberg (SH) is one of the prolific serovars causing poultry-associated food-borne illness in the world.

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NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millions of long‐read sequences.

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Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis

Background

Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative.

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High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells

Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years.

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Nanopore Flongle sequencing as a rapid, single specimen clinical test for fusion detection

The identification of gene fusions is a cornerstone of diagnosis and treatment decision making for tumors of many forms and primary sites.

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Genomic characterisation of a multidrug-resistant Escherichia coli strain carrying the mcr-1 gene recovered from a paediatric patient in China

Objectives

The global spread of carbapenem-resistant Enterobacterales is a leading public-health threat. Lack of effective treatment has resulted in use of colistin as a last-resort therapeutic option for multidrug-resistant (MDR) bacterial infections.

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Automated strain separation in low-complexity metagenomes using long reads

High-throughput short-read metagenomics has enabled large-scale species-level analysis and functional characterization of microbial communities.

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Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of Bacillus-plant mutualistic interaction

Bacillus velezensis is considered as model species belonging to the so-called B. subtilis complex that typically evolved to dwell in the soil rhizosphere niche and establish intimate association with plant roots.

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A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental genes partitioning in Toxoplasma

Correct 3’end processing of mRNAs is regarded as one of the regulatory cornerstones of gene expression.

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Oxford Nanopore sequencing-based protocol to detect CpG methylation in human mitochondrial DNA

Methylation on CpG residues is one of the most important epigenetic modifications of nuclear DNA, regulating gene expression.

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Molecular characterization of vancomycin-resistant Enterococcus faecium isolates collected from the Dallas, Texas area

Molecular characterization was performed for 46 vancomycin-resistant E. faecium (VREfm) isolates and one vancomycin-sensitive comparator obtained during routine fecal surveillance of high-risk patients from a Dallas, Texas area hospital system.

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Genomic architecture of 5S rDNA cluster and its variations within and between species

Ribosomal genes (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosome. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution.

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Ancient migrations - The first complete genome assembly, annotation and variants of the Zoroastrian-Parsi community of India

With the advent of Next Generation Sequencing, many population specific whole genome sequences published thus far, predominantly represent individuals of European ancestry.

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The genome of the CTG(Ser1) yeast Scheffersomyces stipitis is plastic

Microorganisms need to adapt to environmental changes, and genome plasticity can lead to adaptation by increasing genetic diversity.

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Long-reads are revolutionizing 20 years of insect genome sequencing

The first insect genome (Drosophila melanogaster) was published two decades ago. Today, nuclear genome assemblies are available for a staggering 601 different insects representing 20 orders.

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A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data

The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships.

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A conserved role of the duplicated Masculinizer gene in sex determination of the Mediterranean flour moth, Ephestia kuehniella

Sex determination in the silkworm, Bombyx mori, is based on Feminizer (Fem), a W-linked Fem piRNA that triggers female development in WZ individuals, and the Z-linked Masculinizer (Masc), which initiates male

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Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species

Polyploidization events are observed across the tree of life and occurred in many fungi, plant and animal species. Polyploidy is thought to be an important source of speciation and tumorigenesis.

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Small intestine lactobacilli growth promotion and immunomodulation in weaner pigs fed Cyberlindnera jadinii yeast high inclusion diet and exposed to enterotoxigenic Escherichia coli F4+: O149

Enterotoxigenic Escherichia coli (ETEC) F4+: O149 is a causative agent for the development of post-weaning diarrhoea (PWD) in pigs that contributes to production losses.

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Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptation

A complete characterization of genetic variation is a fundamental goal of human genome research. Long-read sequencing (LRS) improves the sensitivity for structural variant (SV) discovery and facilitates a better understanding of the SV spectrum in human genomes.

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Genome-wide detection of cytosine methylations in plant from Nanopore sequencing data using deep learning

Methylation states of DNA bases can be detected from native Nanopore reads directly. At present, there are many computational methods that can detect 5mCs in CpG contexts accurately by Nanopore sequencing. However, there is currently a lack of methods to detect 5mCs in non-CpG contexts.

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DNA methylation profiling of a cnidarian-algal symbiosis using nanopore sequencing

Symbiosis with protists is common among cnidarians such as corals and sea anemones, and is associated with homeostatic and phenotypic changes in the host that could have epigenetic underpinnings, such as methylation of CpG dinucleotides.

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LoopViz: A uLoop assembly clone verification tool for nanopore sequencing reads

Cloning has been an integral part of most laboratory research questions and continues to be an essential tool in defining the genetic elements determining life.

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Using de novo assembly to identify structural variation of complex immune system gene regions

Driven by the necessity to survive environmental pathogens, the human immune system has evolved exceptional diversity and plasticity, to which several factors contribute including inheritable structural polymorphism of the underlying genes.

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Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development

Chayote (Sechium edule) is an agricultural crop in the Cucurbitaceae family that is rich in bioactive components. To enhance genetic research on chayote, we used Nanopore third-generation sequencing combined with Hi–C data to assemble a draft chayote genome.

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MicroPIPE: An end-to-end solution for high-quality complete bacterial genome construction

Oxford Nanopore Technology (ONT) long-read sequencing has become a popular platform for microbial researchers; however, easy and automated construction of high-quality bacterial genomes remains challenging.

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High-quality genome resource of Clonostachys rosea strain CanS41 by Oxford Nanopore long-read sequencing

Clonostachys rosea is a necrotrophic mycoparasitic fungus with excellent biological control ability against numerous fungal plant pathogens. Here, we performed genomic sequencing of C. rosea strain CanS41 using Oxford Nanopore sequencing technology.

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Rampant prophage movement among transient competitors drives rapid adaptation during infection

Interactions between bacteria, their close competitors, and viral parasites are common in infections but understanding of these eco-evolutionary dynamics is limited. Most examples of adaptations caused by phage lysogeny are through the acquisition of new genes.

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GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Long reads and Hi-C have revolutionized the field of genome assembly as they have made highly continuous assemblies accessible for challenging genomes.

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Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii

In most eukaryotes, subtelomeres are dynamic genomic regions populated by multi-copy sequences of different origins, which can promote segmental duplications and chromosomal rearrangements.

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Draft genome resource of Fusarium oxysporum f. sp. capsici, the infectious agent of pepper Fusarium wilt

Fusarium oxysporum f. sp. capsici is the specific pathogen of pepper Fusarium wilt, and causes a significant reduction in pepper yield. Its narrow host specificity has led to the concept of forma speciales.

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The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis

Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes.

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Genome sequence data of Peronophythora litchii, an oomycete pathogen causing litchi downy blight

Peronophythora litchii is an oomycete pathogen that exclusively infects litchi, with infection stages affecting a broad range of tissues. In this study, we obtained a near chromosome-level genome assembly of P.

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MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host evolution

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolution given the read-length limitations of next-generation sequencing platforms.

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Molecular characterisation of the first New Delhi metallo-β-lactamase 1-producing Acinetobacter baumannii from Tanzania

Background

We aimed to characterise the genetic determinants and context of two meropenem-resistant clinical isolates of Acinetobacter baumannii isolated from children hospitalised with bloodstream infections in Dar es Salaam, Tanzania.

Methods

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A deep learning framework for real-time detection of novel pathogens during sequencing

Motivation Novel pathogens evolve quickly and may emerge rapidly, causing dangerous outbreaks or even global pandemics.

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Genome and transcriptome of a pathogenic yeast, Candida nivariensis

We present a highly contiguous genome and transcriptome of the pathogenic yeast, Candida nivariensis. We sequenced both the DNA and RNA of this species using both the Oxford Nanopore Technologies (ONT) and Illumina platforms.

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Microbial population dynamics and evolutionary outcomes under extreme energy-limitation

As the most abundant and diverse form of life on Earth, microorganisms commonly inhabit energy-limited environments where cellular maintenance and growth is highly constrained.

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Hybrid clustering of long and short-read for improved metagenome assembly

Next-generation sequencing has enabled metagenomics, the study of the genomes of microorganisms sampled directly from the environment without cultivation.

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The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway

Tripterygium wilfordii is a Traditional Chinese Medicine (TCM) from family Celastraceae and celastrol is one of the strongest active ingredients belonging to friedelane-type pentacyclic triterpenoid, which has a large clinical application value of anti-tumor, immunosuppression, and

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Raven: a de novo genome assembler for long reads

We present new methods for the improvement of long-read de novo genome assembly incorporated into a straightforward tool called Raven (https://github.com/lbcb-sci/raven).

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Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii

Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis.

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Application of targeted next-generation sequencing assay on a portable sequencing Platform for culture-free detection of drug-resistant tuberculosis from clinical samples

Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samples for clinical diagnosis of drug-resistant tuberculosis (DR-TB).

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Mutational pressure drives differential genome conservation in two bacterial endosymbionts of sap feeding insects

Compared to free-living bacteria, endosymbionts of sap-feeding insects have tiny and rapidly evolving genomes. Increased genetic drift, high mutation rates, and relaxed selection associated with host control of key cellular functions all likely contribute to genome decay.

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Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells

Facioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle.

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A Transposon Story: from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore

Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies.

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Benchmarking challenging small variants with linked and long reads

Genome in a Bottle (GIAB) benchmarks have been widely used to validate clinical sequencing pipelines and develop new variant calling and sequencing methods.

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Fatal perinatal mitochondrial cardiac failure caused by recurrent de novo duplications in the ATAD3 locus

Background: In about half of all patients with a suspected monogenic disease, genomic investigations fail to identify the diagnosis. A contributing factor is the difficulty with repetitive regions of the genome, such as those generated by segmental duplications.

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Horizontal plasmid transfer among Klebsiella pneumoniae isolates is the key factor for dissemination of extended-spectrum β-lactamases among children in Tanzania

Increased knowledge about the role of horizontal gene transfer is key to improve our understanding of the spread of antimicrobial resistance (AMR) in human populations.

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

True fungi (Fungi) and fungus-like organisms (e.g. MycetozoaOomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species.

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The Salmonella enterica plasmidome as a reservoir of antibiotic resistance

The emergence of multidrug-resistant bacterial strains worldwide has become a serious problem for public health over recent decades.

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HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding

Background Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions.

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Ubiquitous selfish toxin-antidote elements in Caenorhabditis species

Toxin-antidote elements (TAs) are selfish genetic dyads that spread in populations by selectively killing non-carriers. TAs are common in prokaryotes, but few examples are known in animals.

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The genome of a persistent giant algal virus encodes an unprecedented number of genes involved in energy metabolism

Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions—the synthesis of which is energetically demanding.

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Whole genome sequence data of Lactobacillus fermentum HFD1, the producer of antibacterial peptides

Here we report the whole genome sequence of Lactobacillus fermentum HFD1 strain, the producer of antibacterial peptides.

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High-quality carnivore genomes from roadkill samples enable species delimitation in aardwolf and bat-eared fox

In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is becoming essential for conservation. The thousands of yearly mammalian roadkill could potentially provide a useful source material for genomic surveys.

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LIQA: Long-read Isoform Quantification and Analysis

Long-read RNA sequencing (RNA-seq) technologies have made it possible to sequence fulllength transcripts, facilitating the exploration of isoform-specific gene expression over conventional short-read RNA-seq.

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Chromosome-level genome assembly of a benthic associated Syngnathiformes species: the common dragonet, Callionymus lyra

Background The common dragonet, Callionymus lyra, is one of three Callionymus species inhabiting the North Sea. All three species show strong sexual dimorphism.

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Regulation of Wolbachia proliferation by the amplification and deletion of an addictive genomic island

Wolbachia is one of the most prevalent bacterial endosymbionts, infecting approximately 40% of terrestrial arthropod species. Wolbachia is often a reproductive parasite but can also provide fitness benefits to its host, as for example protection against viral path

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Generating single-sex litters: development of CRISPR-Cas9 genetic tools to produce all-male offspring

Animals are extremely useful genetic tools in science and global resources in agriculture. However, a single sex is often required in surplus, and current genetic methods for producing all-female or all-male litters are inefficient.

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The draft genome of Labeo catla

Objective

Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar.

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Accurate spliced alignment of long RNA sequencing reads

Long-read RNA sequencing techniques are quickly establishing themselves as the primary sequencing technique to study the transcriptome landscape. Many such analyses are dependent upon splice alignment of reads to the genome.

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The beginning of the end: a chromosomal assembly of the new world malaria mosquito ends with a novel telomere

Chromosome level assemblies are accumulating in various taxonomic groups including mosquitoes. However, even in the few reference-quality mosquito assemblies, a significant portion of the heterochromatic regions including telomeres remain unresolved.

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Prophylactic application of tailocins prevents infection by Pseudomonas syringae

Tailocins are phage-derived bacteriocins that demonstrate great potential as agricultural antimicrobials given their high killing efficiency and their precise strain-specific targeting ability.

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De novo genome assembly of the land snail Candidula unifasciata (Mollusca: Gastropoda)

Among all molluscs, land snails are an economically and scientifically interesting group comprising edible species, alien species and agricultural pests. Yet, despite its high diversity, the number of whole genomes publicly available is still scarce.

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Genomic analysis of a novel species Halomonas shambharensis isolated from hypersaline lake in Northwest India

Genome analysis of Halomonas shambharensis, a novel species, was performed to understand the osmoprotectant strategies used by the strain to overcome the salinity stress and to explore the prospective industrial uses.

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Improvements in the sequencing and assembly of plant genomes

Background Advances in DNA sequencing have reduced the difficulty of sequencing and assembling plant genomes.

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Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms

Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective target of personalized cancer therapeutics.

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Genome recombination-mediated tRNA up-regulation conducts general antibiotic resistance of bacteria at early stage

Bacterial antibiotic resistance sets a great challenge to human health. It seems that the bacteria can spontaneously evolve resistance against any antibiotic within short time without the horizontal transfer of heterologous genes and before accumulating drug-resistant mutations.

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Limited genetic diversity of blaCMY-2-containing IncI1-pST12 plasmids from Enterobacteriaceae of human and broiler chicken origin in the Netherlands

Distinguishing epidemiologically related and unrelated plasmids is essential to confirm plasmid transmission.

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A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585.

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Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants

Background

Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments.

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Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding

Solanum pimpinellifolium (SP) is the wild progenitor of cultivated tomato. Because of its remarkable stress tolerance and intense flavor, SP has been used as an important germplasm donor in modern breeding of tomato.

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Genetic characterisation of a large antibiotic resistant environmental ST131 E. coli plasmid using a long read hybrid assembly approach

Escherichia coli Strain Type 131 are a globally disseminated environmental E. coli that has been linked to the capture and spread of plasmid mediated blaCTX-M type extended spectrum beta-lactamase (ESBLs).

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The First complete Zoroastrian-Parsi Mitochondria Reference Genome: implications of mitochondrial signatures in an endogamous, non-smoking population

The present-day Zoroastrian-Parsis have roots in ancient pastoralist migrations from circumpolar regions leading to their settlement on the Eurasian Steppes and later, as Indo Iranians in the Fertile Crescent

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Unraveling the features of somatic transposition in the Drosophila intestine

Transposable elements (TEs) play a significant role in evolution by contributing to genetic variation through germline insertional activity. However, how TEs act in somatic cells and tissues is not well understood.

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Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

White Guinea yam (Dioscorea rotundata) is an important staple tuber crop of West Africa. However, its origin remains unclear.

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Template switching mechanism drives the tandem amplification of chromosome 20q11.21 in human pluripotent stem cells

Copy number variants (CNVs) are genomic rearrangements implicated in numerous congenital and acquired diseases, including cancer. In human pluripotent stem cells (PSC), the appearance of culture-acquired CNVs prompted concerns for their use in regenerative medicine applications.

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Genomic network analysis of an environmental and livestock IncF plasmid population

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae.

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Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a potential host for heterologous expression of biosynthetic gene cluster

Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S.

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Characterization of the genomic sequence data around common cutworm resistance genes in soybean (Glycine max) using short- and long-read sequencing methods

The common cutworm (CCW, Spodopteraab litura Fabricius) is one of the pests that most severely infect soybean (Glycine max L. Merr.).

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AsmMix: A pipeline for high quality diploid de novo assembly

In this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps.

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Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

The reconstruction of the evolutionary histories of pathogen populations in space and time often improves our understanding of their epidemiology. However, analyses are usually restricted to the nonrecombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome.

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Whole genome sequencing of Hepatitis A virus using a PCR-free single-molecule nanopore sequencing approach

Hepatitis A virus (HAV) is one of the most common causes of acute viral hepatitis in humans. Although HAV has a relatively small genome, there are several factors limiting whole genome sequencing such as PCR amplification artefacts and ambiguities in de novo assembly.

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Complete genome of Lactobacillus iners KY using Flongle provides insight into the genetic background of optimal adaption to vaginal econiche

Despite the importance of Lactobacillus iners and its unique characteristics for the study of vaginal adaption, its genome and genomic researches for identifying molecular backgrounds of these specific phenotypes are still limited.

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Nanopore sequencing reveals genomic map of CTX-M-type extended-spectrum β-lactamases carried by Escherichia coli strains isolated from blue mussels (Mytilus edulis) in Norway

Background

Environmental surveillance of antibiotic resistance can contribute towards better understanding and management of human and environmental health.

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Complete mitochondrial genome of a gymnosperm, Sitka spruce (Picea sitchensis), indicates a complex physical structure

Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions.

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Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences and chromosomal rearrangements

Neospora caninum primarily infects cattle causing abortions with an estimated impact of a billion dollars on worldwide economy, annually.

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SEQU-INTO: Early detection of impurities, contamination and off-targets (ICOs) in long read/MinION sequencing

The MinION sequencer by Oxford Nanopore Technologies turns DNA and RNA sequencing into a routine task in biology laboratories or in field research. For downstream analysis it is required to have a sufficient amount of target reads.

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Improving the chromosome-level genome assembly of the Siamese fighting fish (Betta splendens) in a university master's course

Ever decreasing costs along with advances in sequencing and library preparation technologies enable even small research groups to generate chromosome-level assemblies today.

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Comparison of third-generation sequencing approaches to identify viral pathogens under public health emergency conditions

The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses timely makes it a powerful tool for public health emergency response. Third-generation sequencing (TGS) offers advantages in speed and length of detection over second-generation sequencing (SGS).

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A giant genome for a giant crayfish (Cherax quadricarinatus) with insights into cox1 pseudogenes in Decapod genomes

Following on from mitogenomic and transcriptomic studies, we present the first draft genome for the red claw crayfish (Cherax quadricarinatus) based on relatively large volumes of short and long genomic reads from Illumina and Oxford Nanopore (ONT) platforms.

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Reorganization of mcr-1-bearing large MDR plasmids resolved by nanopore sequencing

The emergence of plasmid-borne mcr genes among pathogens poses great public concern. Different mcr variants have been identified from various sources and the plasmids encoding mcr genes are diverse and evolve constantly.

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Plastid genomes of the early vascular plant genus Selaginella have unusual direct repeat structures and drastically reduced gene numbers

The early vascular plants in the genus Selaginella, which is the sole genus of the Selaginellaceae family, have an important place in evolutionary history, along with ferns, as such plants are valuable resources for deciphering plant evolution.

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Is oxford nanopore sequencing ready for analyzing complex microbiomes?

This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies.

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Single-molecule nanopore sequencing reveals extreme target copy number heterogeneity in arylomycin-resistant mutants

Tandem gene amplification is a frequent and dynamic source of antibiotic resistance in bacteria. Ongoing expansions and contractions of repeat arrays during population growth are expected to manifest as cell-to-cell differences in copy number (CN).

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Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures

Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries.

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An improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundances of chloroplastic proteins favoring energy production

Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination.

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Real-time culture-independent microbial profiling onboard the International Space Station using Nanopore sequencing

For the past two decades, microbial monitoring of the International Space Station (ISS) has relied on culture-dependent methods that require return to Earth for analysis.

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Rhizobium desertarenae sp. nov., isolated from the Saline Desert Soil from the Rann of Kachchh, India

A novel bacterial strain designated ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78T grows best at 28°C and pH 7.0 and can tolerate up to 2% (w/v) NaCl.

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Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery

Ale brewing yeast are the result of admixture between diverse strains of Saccharomyces cerevisiae, resulting in a heterozygous tetraploid that has since undergone numerous genomic rearrangements.

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Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome

Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution.

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S-IRFindeR: stable and accurate measurement of intron retention

Accurate quantification of intron retention levels is currently the crux for detecting and interpreting the function of retained introns.

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Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

Long-read sequencing techniques, such as the Oxford Nanopore Technology, can generate reads that are tens of kilobases in length and are therefore particularly relevant for microbiome studies.

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Safety assessment of a nham starter culture Lactobacillus plantarum BCC9546 via whole-genome analysis

The safety of microbial cultures utilized for consumption is vital for public health and should be thoroughly assessed. Although general aspects on the safety assessment of microbial cultures have been suggested, no methodological detail nor procedural guideline have been published.

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Draft genome sequence of the pulse crop blackgram [Vigna mungo (L.) Hepper] reveals potential R-genes

Blackgram [Vigna mungo (L.) Hepper] (2n = 2x = 22), an important Asiatic legume crop, is a major source of dietary protein for the predominantly vegetarian population.

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Nanopore-based long-read transcriptome data of Nosema ceranae-infected and un-infected western honeybee workers’ midguts

Apis mellifera ligustica is a subspecies of western honeybee, Apis mellifera. Nosema ceranae is known to cause bee microspodiosis, which seriously affects bee survival and colony productivity.

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Merqury: reference-free quality and phasing assessment for genome assemblies

Recent long-read assemblies often exceed the quality of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.

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Plasmid carrying mcr-9 from an extensively drug-resistant NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae clinical isolate

The extensively drug-resistant NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae M17277 (Kqsq-M17277) was only susceptible to colistin and fosfomycin.

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Constrained non-coding sequence provides insights into regulatory elements and loss of gene expression in maize

DNA sequencing technology has advanced so quickly, identifying key functional regions using evolutionary approaches is required to understand how those genomes work.

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A high-quality de novo genome assembly from a single parasitoid wasp

Sequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines.

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Genomic characterization of MICA gene using multiple next generation sequencing platforms: a validation study

We have developed a protocol regarding the genomic characterization of the MICA gene by next generation sequencing (NGS). The amplicon includes the full length of the gene and is about 13 kb. A total of 156 samples were included in the study.

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AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates

Abstract

Objectives

To investigate the genomic context of a novel resistance island (RI) in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates and global isolates.

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Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes, where genes move intra- and inter-species via horizontal gene transfer

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Comparison of long read sequencing technologies in resolving bacteria and fly genomes

Background The newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has democratized the genome sequencing and assembly process.

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Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes

Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA.
 

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Reference genome for the highly transformable Setaria viridis ME034V

Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S.

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The bacterial and viral complexity of postinfectious hydrocephalus in Uganda

Postinfectious hydrocephalus (PIH), often following neonatal sepsis, is the most common cause of pediatric hydrocephalus world-wide, yet the microbial pathogens remain uncharacterized.

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RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning

Antimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria.

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Complete mitochondrial genomes of five subspecies of the Eurasian magpie Pica pica, obtained with Oxford Nanopore MinION, and their interpretation regarding intraspecific taxonomy

The complete mitochondrial (mt) genomes of five subspecies of the Eurasian (Common) magpie Pica pica were determined for the first time.

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Transcriptome variation in human tissues revealed by long-read sequencing

Regulation of transcript structure generates transcript diversity and plays an important role in human disease. The advent of long-read sequencing technologies offers the opportunity to study the role of genetic variation in transcript structure.

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stLFRsv: a germline SV analysis pipeline using co-barcoded reads

Co-barcoded reads originated from long DNA fragment (mean length larger than 50Kbp) with barcodes, maintain both single base level accuracy and long range genomic information. We propose a pipeline stLFRsv to detect structure variation using co-barcoded reads.

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Highly accurate barcode and UMI error correction using dual nucleotide dimer blocks allows direct single-cell nanopore transcriptome sequencing

Droplet-based single-cell sequencing techniques have provided unprecedented insight into cellular heterogeneities within tissues. However, these approaches only allow for the measurement of the distal parts of a transcript following short-read sequencing.

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A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases.

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Analyzing the dietary diary of bumble bee

Bumble bees are important crop pollinators and provide important pollination services to their respective ecosystems. Their pollen diet and thus food preferences can be characterized through nucleic acid sequence analysis.

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Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

Large-scale chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems.

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Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

Background

The number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas.

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Minimum error correction-based haplotype assembly: considerations for long read data

The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the genome-phenotype association.

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Higher rates of processed pseudogene acquisition in humans and three great apes revealed by long read assemblies

LINE-1 mediated retrotransposition of protein-coding mRNAs is an active process in modern humans for both germline and somatic genomes.

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Role of NGS and SNP genotyping methods in sugarcane improvement programs

Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy.

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The impact of transposable elements on tomato diversity

Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity.

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Antibiotic tolerance, persistence, and resistance of the evolved minimal cell, Mycoplasma mycoides JCVI-Syn3B

Antibiotic persisters are a small subpopulation of bacteria that tolerate antibiotics due to a physiologically dormant state. As a result, this phenomenon (persistence) is considered a major contributor to the evolution of antibiotic-resistant and relapsing infections.

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Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis

Lithospermum erythrorhizon (red gromwell; zicao) is a medicinal and economically valuable plant belonging to the Boraginaceae family. Roots from L.

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The rise and fall of the ancient northern pike master sex determining gene

Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies.

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Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru

Spoligotyping of Mycobacterium tuberculosis provides a subspecies classification of this major human pathogen. Spoligotypes can be predicted from short read genome sequencing data; however, no methods exist for long read sequence data such as from Nanopore or PacBio.

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MINTyper: A method for generating phylogenetic distance matrices with long read sequencing data

In this paper we present a complete pipeline for generating a phylogenetic distance matrix from a set of sequencing reads.

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Verification of CRISPR editing by Xdrop™ Indirect Sequence Capture followed by short- and long- read sequencing

Validation of CRISPR-Cas9 editing typically explore the immediate vicinity of the target site and distal off-target sequences, which have led to the conclusion that CRISPR-Cas9 editing is very specific.

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Two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing

Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long-reads reveals the true complexity of processing, however the relatively high error rates of long-read technologies can reduce the accuracy of intron identification.

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Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads

Background

The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics.

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Characterization of systemic genomic instability in budding yeast

Conventional models of genome evolution are centered around the principle that mutations form independently of each other and build up slowly over time.

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Evolutionary transition to XY sex chromosomes associated with Y-linked duplication of a male hormone gene in a terrestrial isopod

Sex chromosomes are highly variable in some taxonomic groups, but the evolutionary mechanisms underlying this diversity are not well understood.

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Improved reference genome for Cyclotella Cryptica CCMP332, a model for cell wall morphogenesis, salinity adaptation, and lipid production in diatoms (Bacillariophyta)

The diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms.

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The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation

Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes.

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Chromosome scale reference genome of Cluster bean (Cyamopsis tetragonoloba (L.) Taub.)

Clusterbean (Cyamopsis tetragonoloba (L.) Taub.), also known as Guar is a widely cultivated dryland legume of Western India and parts of Africa.

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The structural variation landscape in 492 Atlantic salmon genomes

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species.

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NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data

Summary NanoCLUST is an analysis pipeline for classification of amplicon-based full-length 16S rRNA nanopore reads.

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Hospital outbreak of linezolid-resistant and vancomycin-resistant ST80 Enterococcus faecium harbouring an optrA-encoding conjugative plasmid investigated by whole-genome sequencing

Background: Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr.

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abPOA: an SIMD-based C library for fast partial order alignment using adaptive band

Summary Partial order alignment, which aligns a sequence to a directed acyclic graph, is now frequently used as a key component in long-read error correction and assembly.

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Giant lungfish genome elucidates the conquest of land by vertebrates

Lungfishes belong to lobe-fined fish (Sarcopterygii) that in the Devonian ‘conquered’ land and gave rise to all land vertebrates, including humans.

We determined the largest chromosome-quality animal genome, the Australian lungfish, Neoceratodus forsteri.

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Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

Species-level genetic characterization of complex bacterial communities has important clinical applications. In the present study, we assessed the performance of full-length 16S rRNA gene analysis of human gut microbiota using the nanopore long-read sequencer MinION™.

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Analysis of the mouse Y chromosome by single-molecule sequencing with Y chromosome enrichment

Since human and mouse Y chromosomes contain repeated sequences, it is difficult to determine the precise sequences and analyze the function of individual Y chromosome genes.

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A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume

We have sequenced the genome of grass pea (Lathyrus sativus), a resilient diploid (2n=14) legume closely related to pea (Pisum sativum). We determined the genome size of the sequenced European accession (LS007) as 6.3 Gbp.

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A highly contiguous genome for the golden-fronted woodpecker (Melanerpes aurifrons) via hybrid Oxford Nanopore and short read assembly

Woodpeckers are found in nearly every part of the world and have been important for studies of biogeography, phylogeography, and macroecology. Woodpecker hybrid zones are often studied to understand the dynamics of introgression between bird species.

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The draft mitochondrial genome of Magnolia biondii and mitochondrial phylogenomics of angiosperms

The mitochondrial genomes of flowering plants are well known for their large size, variable coding-gene set and fluid genome structure.

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Long-read Nanopore sequencing validated for human leukocyte antigen class I typing in routine diagnostics

Matching of human leukocyte antigen (HLA) gene polymorphisms by high-resolution DNA sequence analysis is the gold standard for determining compatibility between patient and donor for hematopoietic stem cell transplantation.

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Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium

Objectives

To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France.

Methods

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A general model to explain repeated turnovers of sex determination in the Salicaceae

Dioecy, the presence of separate sexes on distinct individuals, has evolved repeatedly in multiple plant lineages. However, the specific mechanisms through which sex systems evolve and their commonalities among plant species remain poorly understood.

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De novo genome assembly of a Han Chinese male and genome-wide detection of structural variants using Oxford Nanopore sequencing

Advances in third-generation sequencing technologies provide an opportunity to investigate the complex organizational structure of the genome and unravel the genetic mechanisms of disease and physiological traits.

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The effect of recombination on the evolution of a population of Neisseria meningitidis

Neisseria meningitidis (the meningococcus) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa.

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Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America

The cricetine rodent Peromyscus leucopus is an important reservoir for several human zoonoses, including Lyme disease, in North America. Akin to hamsters, the white-footed deermouse has been unevenly characterized in comparison to the murid Mus musculus.

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Large domains of heterochromatin direct the formation of short mitotic chromosome loops

During mitosis chromosomes reorganise into highly compact, rod-shaped forms, thought to consist of consecutive chromatin loops around a central protein scaffold.

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Nanopore long-read transcriptome data of fungal pathogen of chalkbrood disease, Ascosphaera apisemporal landscape

Ascosphaera apis is a fungal pathogen that exclusively infects honeybee larvae, leading to chalkbrood disease, which damages the number of adult honeybees and colony productivity. In this article, A.

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Long-read transcriptome data of bee fungal parasite, Nosema ceranae

Nosema ceranae, a widespread fungal parasite that infects honeybee and many other bee species, can seriously affect bee health and colony productivity. In this article, N.

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Genomic signals of admixture and reinforcement between two closely related species of European sepsid flies

Interspecific gene flow by hybridization may weaken species barriers and adaptive divergence, but also initiate reinforcement of reproductive isolation trough natural and sexual selection. The extent and consequences of interspecific gene flow in natural systems remain poorly understood.

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Genome assembly and annotation of Macadamia tetraphylla

Macadamia is a kind of evergreen nut trees which belong to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. Catherine et al. reported M.

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Massive rhizobial genomic variations associated with partner quality in Lotus–Mesorhizobium symbiosis

In diverse mutualistic relationships, genetic variations in impact on the growth of interacting partners—variations in partner quality—are common, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variations.

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Rhizomicrobiomics of Caesalpinia bonducella, a wonder plant for PCOS treatment

Plant and rhizobacterial interactions contribute partly to a plant’s medicinal properties and are well studied through metagenomics.

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Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Current knowledge about the microbial communities inhabiting the stormwater quality improvement devices (SQIDs) for road runoff is scarce.

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Genome sequencing of fiber flax cultivar Atlant Using Oxford Nanopore and Illumina Platforms

In this study, the genome of fiber flax cultivar Atlant was sequenced for the first time, using both Oxford Nanopore and Illumina platforms. For successful Nanopore sequencing, a protocol for extraction of pure high-molecular-weight DNA from the leaves of a single flax plant was developed.

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Single-cell RNA-seq analysis reveals penaeid shrimp hemocyte subpopulations and cell differentiation process

Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. An immune priming system of shrimp is crucial for a sustainable supply, as shrimp do not have an adaptive immune system; however, little is known about their immunity.

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Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing

Sparassis latifolia is a valuable edible mushroom cultivated in China. In 2018, our research group reported an incomplete and low quality genome of S. latifolia was obtained by Illumina HiSeq 2500 sequencing.

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West Nile virus detection in horses in three Brazilian states

We report genetic evidence of WNV circulation from southern and northeastern Brazilian states isolated from equine red blood cells. In the northeastern state the tenth human case was also detected, presenting neuroinvasive disease compatible with WNV infection.

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Maribellus comscasis sp. nov., isolated from the deep-sea cold seep

A facultatively anaerobic, Gram-stain-negative, non-motile, curved rod-shaped bacterium, designated WC007T, was isolated from the deep-sea cold seep, P. R. China.

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Cultivation and characterization of a novel clade of deep-sea Chloroflexi: providing a glimpse of the phylum Chloroflexi involved in sulfur cycling

Chloroflexi bacteria are abundant and globally distributed in various unexplored biospheres on Earth. However, only few Chloroflexi members have been cultivated, hampering further understanding of this important group.

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Benchmarking Oxford Nanopore read assemblers for high-quality molluscan genomes

Choosing the optimum assembly approach is essential to achieving a high-quality genome assembly suitable for comparative and evolutionary genomic investigations.

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Large palindromes on the primate X chromosome are preserved by natural selection

Mammalian sex chromosomes carry large palindromes that harbor protein-coding gene families with testis-biased expression. However, there are few known examples of sex-chromosome palindromes conserved between species.

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Chromosome-scale genome assembly provides insights into speciation of allotetraploid and massive biomass accumulation of elephant grass (<i>Pennisetum purpureum</i> Schum.)

Elephant grass (Pennisetum purpureum Schum., A’A’BB, 2n=4x=28), which is characterized as robust growth and high biomass, and widely distributed in tropical and subtropical areas globally, is an important forage, biofuels and industrial plant.

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yacrd and fpa: upstream tools for long-read genome assembly

Motivation Genome assembly is increasingly performed on long, uncorrected reads. Assembly quality may be degraded due to unfiltered chimeric reads; also, the storage of all read overlaps can take up to terabytes of disk space.

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Emergence of optrA-mediated linezolid resistance in multiple lineages and plasmids of Enterococcus faecalis revealed by long read sequencing

Objectives To characterise the genetic environment of optrA in linezolid-resistant Enterococcus faecalis isolates from Scotland.

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Short and long-read sequencing survey of the dynamic transcriptomes of African swine fever virus and its host

African swine fever virus (ASFV) is an important animal pathogen causing substantial economic losses in the swine industry globally. At present, little is known about the molecular biology of ASFV, including its transcriptome organization.

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New tools for diet analysis: nanopore sequencing of metagenomic DNA from rat stomach contents to quantify diet

Background Using metagenomics to determine animal diet offers a new and promising alternative to current methods.

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A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor

Gut colonization by the pathogen Klebsiella pneumoniae (Kp) is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. However, colonizing strains likely vary in their potential to cause infection.

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A spontaneous complex structural variant in rcan-1 increases exploratory behavior and laboratory fitness of Caenorhabditis elegans

Over long evolutionary timescales, major changes to the copy number, function, and genomic organization of genes occur, however, our understanding of the individual mutational events responsible for these changes is lacking.

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Laboratory evolution experiments help identify a predominant region of constitutive stable DNA replication initiation

The bacterium E. coli can initiate replication in the absence of the replication initiator protein DnaA and / or the canonical origin of replication oriC in a ΔrnhA background.

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Comparative genome analysis of Scutellaria baicalensis and Scutellaria barbata reveals the evolution of active flavonoid biosynthesis

Scutellaria baicalensis and Scutellaria barbata, common medicinal plants of the Lamiaceae family, produce specific flavonoid compounds with antioxidant and antitumor activities, including baicalein, scutellarein, norwogonin, wogonin, and their glycosides.

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Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens

Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. Information on the parasite’s underpinning mechanisms to support its life strategy is recently being investigated.

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First draft genome of the trypanosomatid Herpetomonas muscarum ingenoplastis through MinION Oxford Nanopore Technology and Illumina Sequencing

Here, we present first draft genome sequence of the trypanosomatid Herpetomonas muscarum ingenoplastis. This parasite was isolated repeatedly in the black blowfly, Phormia regina, and it forms a phylogenetically distinct clade in the Trypanosomatidae family.

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Yersinia canariae sp. nov., isolated from a human yersiniosis case

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom.

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Whole-genome sequencing and analysis of the Chinese herbal plant Gelsemium elegans

Background

Gelsemium elegans (G. elegans) (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family.

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The human Origin Recognition Complex is essential for pre-RC assembly, mitosis and maintenance of nuclear structure

The Origin Recognition Complex (ORC) cooperates with CDC6, MCM2-7, and CDT1 to form pre- RC complexes at origins of DNA replication. Here we report tiling-sgRNA CRISPR screens that show that each subunit of ORC and CDC6 are essential in human cells.

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Single-cell individual complete mtDNA sequencing uncovers hidden mitochondrial heterogeneity in human and mouse oocytes

The ontogeny and dynamics of mtDNA heteroplasmy remain unclear due to limitations of current mtDNA sequencing methods.

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Development of an NGS-based workflow for improved monitoring of circulating plasmids in support of risk assessment of antimicrobial resistance gene dissemination

Antimicrobial resistance (AMR) is one of the most prominent public health threats. AMR genes localized on plasmids can be easily transferred between bacterial isolates by horizontal gene transfer, thereby contributing to the spread of AMR.

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NanoReviser: an error-correction tool for Nanopore sequencing based on a deep learning algorithm

Nanopore sequencing is regarded as one of the most promising third-generation sequencing (TGS) technologies. Since 2014, Oxford Nanopore Technologies (ONT) has developed a series of devices based on nanopore sequencing to produce very long reads, with an expected impact on genomics.

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Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression

Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood.

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Genomic background of the Klebsiella pneumoniae NDM-1 outbreak in Poland, 2012-18

Objectives

To characterize genomes of Klebsiella pneumoniae ST11 NDM-1 responsible for a countrywide outbreak in Poland and compare them phylogenetically with other Polish and international ST11 strains.

Methods

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P-elements strengthen reproductive isolation within the Drosophila simulans species complex

Determining mechanisms that underlie reproductive isolation is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes.

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Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection

Background

Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially.

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Complete genome sequence of the fire blight pathogen Erwinia amylovora strain Ea1189

Erwinia amylovora causes fire blight, the most devastating bacterial disease of apples and pears in the United States and worldwide. The model strain E.

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HASLR: Fast Hybrid Assembly of Long Reads

Third-generation sequencing technologies from companies such as Oxford Nanopore and Pacific Biosciences have paved the way for building more contiguous and potentially gap-free assemblies.

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First genomic characterization of blaVIM-1 and mcr-9-coharbouring Enterobacter hormaechei isolated from food of animal origin

We describe here the complete genome sequence of an Enterobacter hormaechei ST279 coharbouring blaVIM-1 and mcr-9 recovered from uncooked beef patty in June 2017, Egypt.

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Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection

Background Tenacibaculum maritimum is a worldwide-distributed fish pathogen known for causing dramatic damages on a broad range of wild and farmed marine fish populations. Recently sequenced genome of T.

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High-quality genome assembly of Fusarium oxysporum f. sp. Lini

In the present work, a highly pathogenic isolate of Fusarium oxysporum f. sp. lini, which is the most harmful pathogen affecting flax (Linum usitatissimum L.), was sequenced for the first time.

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A novel canis lupus familiaris reference genome improves variant resolution for use in breed-specific GWAS

Reference genome fidelity is critically important for genome wide association studies, yet most vary widely from the study population. A typical whole genome sequencing approach implies short-read technologies resulting in fragmented assemblies with regions of ambiguity.

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A computational strategy for rapid on-site 16S metabarcoding with Oxford Nanopore sequencing

The investigation of microbial communities through nucleotide sequencing has become an essential asset in environmental science, not only for research oriented activities but also for on-site monitoring; one technology, in particular, holds great promises for its application directly in the field

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Unearthing the genes of plant-beneficial marine yeast - Wickerhamomyces anomalus strain MSD1

The de novo genome of unique marine yeast, Wickerhamomyces anomalus isolated from seaweed along Indian coast is presented.

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In vivo genetic screen identifies a SLC5A3-dependent myo-inositol auxotrophy in acute myeloid leukemia

An enhanced requirement for extracellular nutrients is a hallmark property of cancer cells.

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Herpes Simplex Virus type 1 co-Infection leads to the formation of rolling circle amplification-like adeno-associated virus DNA replication products

Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1).

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Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates

Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections.

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Novel multicellular prokaryote discovered next to an underground stream

The emergence of multicellularity is a key event in the evolution of life and is an attractive challenge among researchers, including those investigating the artificial design of cellular behavior.

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A benchmark of structural variation detection by long reads through a realistic simulated model

Despite the rapid evolution of new sequencing technologies, structural variation detection remains poorly ascertained. The high discrepancy between the results of structural variant analysis programs makes it difficult to assess their performance on real datasets.

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Chromosome-level genome assembly of a regenerable maize inbred line A188

The highly embryogenic and transformable maize inbred line A188 is an attractive model for analyzing maize gene function. Here we constructed a chromosome-level genome assembly of A188 using long reads and optical maps.

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Amyloid-β1–43 cerebrospinal fluid levels and the interpretation of APP, PSEN1 and PSEN2 mutations

Background

Alzheimer’s disease (AD) mutations in amyloid precursor protein (APP) and presenilins (PSENs) could potentially lead to the production of longer amyloidogenic Aβ peptides.

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Sequencing and analysis of Arabidopsis thaliana NOR2 reveal its distinct organization and tissue-specific expression of rRNA ribosomal variants

Despite vast differences between organisms, some characteristics of their genomes are conserved, such as the nucleolus organizing region (NOR).

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Genome structure and content of the rice root‐knot nematode (Meloidogyne graminicola)

Discovered in the 1960s, Meloidogyne graminicola is a root‐knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood.

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Tripartite holobiont system in a vent snail broadens the concept of chemosymbiosis

Many animals inhabiting deep-sea vents are energetically dependent on chemosynthetic endosymbionts, but how such symbiont community interacts with host, and whether other nutritional sources are available to such animals remain unclear.

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First genome of Labyrinthula, an opportunistic seagrass pathogen, reveals novel insight into marine protist phylogeny, ecology and CAZyme cell-wall degradation

Labyrinthula spp. are saprobic, marine protists that also act as opportunistic pathogens and are the causative agents of seagrass wasting disease (SWD).

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The genome of the American groundhog, Marmota monax

We sequenced the genome of the North American groundhog, Marmota monax, also known as the woodchuck. Our sequencing strategy included a combination of short, high-quality Illumina reads plus long reads generated by both Pacific Biosciences and Oxford Nanopore instruments.

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Engaging the next generation of plant geneticists through sustained research: an overview of a post-16 project

Student career aspirations are directly linked to the careers that they are exposed to and the esteem that they are given in society. Where schools are located in areas with low visibility of scientific careers this will have an impact on student aspirations.

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Deletion in the Bardet–Biedl syndrome gene TTC8 results in a syndromic retinal degeneration in dog

In golden retriever dogs, a 1 bp deletion in the canine TTC8 gene has been shown to cause progressive retinal atrophy (PRA), the canine equivalent of retinitis pigmentosa. In humans, TTC8 is also implicated in Bardet–Biedl syndrome (BBS).

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Consistent ultra-long DNA sequencing with automated slow pipetting

Background Oxford Nanopore Technologies’ instruments can sequence reads of great length. Long reads improve sequence assemblies by unambiguously spanning repetitive elements of the genome.

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Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient with e14a3 BCR‐ABL1 transcript using Nanopore sequencing

Background

The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations.

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Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome

Animals endemic to deep-sea hydrothermal vents often form obligatory relationships with bacterial symbionts, maintained by intricate host-symbiont interactions.

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Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

The direct use of medical zinc oxide (ZnO) in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders.

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Extraintestinal pathogenic (ExPEC) lineages explain prolonged faecal carriage of travel-acquired extended-spectrum β-lactamase-producing Escherichia coli

International travel contributes significantly to the spread of extended-spectrum β-lactamase (ESBL) gene positive Escherichia coli (ESBL-Ec).

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Genomic region associated with pod color variation in pea (Pisum sativum)

Pea (Pisum sativum) was chosen as the research material by Gregor Mendel to discover the laws of inheritance. Out of seven traits studied by Mendel, genes controlling three traits including pod shape, pod color, and flower position have not been identified to date.

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Decoding the architecture of the varicella-zoster virus transcriptome

Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain.

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Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses.

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A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa

Alfalfa (Medicago sativa L.) is one of the most important and widely cultivated forage crops. It is commonly used as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value.

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Prophage-dependent recombination drives genome structural variation and phenotypic heterogeneity in Escherichia coli O157:H7

The human zoonotic pathogen Escherichia coli O157 is defined by its extensive prophage repertoire including those that encode Shiga toxin, the factor responsible for inducing life-threatening pathology in humans.

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Rapid selection response to ethanol in S. eubayanus emulates the domestication process under brewing conditions

Although the typical genomic and phenotypic changes that characterize the evolution of organisms under the human domestication syndrome represent textbook examples of rapid evolution, the molecular processes that underpin such changes are still poorly understood.

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Genomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains

Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis.

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Pseudodesulfovibrio cashew sp. nov., a novel deep-sea sulfate-reducing bacterium, linking heavy metal resistance and sulfur cycle

Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments.

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A highly contiguous genome assembly of Brassica nigra (BB) and revised nomenclature for the pseudochromosomes

Background

Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B.

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TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes

Background The quality of gene annotation determines the interpretation of results obtained in transcriptomic studies.

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Chromosome‐level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi‐C technology

Aphidius gifuensis is a parasitoid wasp that has been commercially bred and released in large scale as a biocontrol agent for the management of aphid pests. As a highly efficient endoparasitoid, it is also an important model for exploring mechanisms of parasitism.

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Highly contiguous assemblies of 101 drosophilid genomes

Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution.

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Hapo-G, Haplotype-Aware Polishing Of Genome assemblies

Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and co

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Phospho-RNA sequencing with CircAID-p-seq

Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fate in living cells.

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Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear.

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Nanopore RNA sequencing revealed long non-coding and LTR retrotransposon-related RNAs expressed at early stages of triticale seed development

The intergenic space of plant genomes encodes many functionally important yet unexplored RNAs. The genomic loci encoding these RNAs are often considered “junk”, DNA as they are frequently associated with repeat-rich regions of the genome.

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blaOXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands

Carbapenem-hydrolyzing enzymes belonging to the OXA-48-like group are encoded by blaOXA-48-like alleles and are abundant among Enterobacterales in the Netherlands.

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Genome evolution in bacteria isolated from million-year-old subseafloor sediments

Deep below the seafloor, microbial life subsists in isolation from the surface world under perpetual energy limitation. The extent to which subsurface microbes evolve and adapt to their subseafloor habitat is unclear, given their ultra-slow metabolic rates.

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Truncated denitrifiers dominate the denitrification pathway in tundra soil metagenomes

In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in these soils remain largely uncharacterized.

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Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology

Malaria parasite genomes have been generated predominantly using short read sequencing technology which can be slow, requires advanced laboratory training and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants.

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Long-read assemblies reveal structural diversity in genomes of organelles - an example with Acacia pycnantha

Although organelle genomes are typically represented as single, static, circular molecules, there is evidence that the chloroplast genome exists in two structural haplotypes and that the mitochondrial genome can display multiple circular, linear or branching forms.

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Characterization of fecal microbiota with clinical specimen using long-read and short-read sequencing platform

Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications.

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Gross chromosomal rearrangements in Kluyveromyces marxianus revealed by Illumina and Oxford Nanopore Sequencing

Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome.

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Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, co-infection of multiple pathogens.

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Streamlining quantitative analysis of long RNA sequencing reads

Transcriptome analyses allow for linking RNA expression profiles to cellular pathways and phenotypes. Despite improvements in sequencing methodology, whole transcriptome analyses are still tedious, especially for methodologies producing long reads.

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Comprehensive comparative genomics reveals over 50 phyla of free-living and pathogenic bacteria are associated with diverse members of the Amoebozoa

The association of bacteria with microbial eukaryotes has been extensively studied. Among these the supergroup Amoebozoa containing predominantly amoeboid unicellular protists has been shown to play an important ecological role in controlling environmental bacteria.

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Transposon-insertion sequencing in a clinical isolate of Legionella pneumophila identifies essential genes and determinants of natural transformation

Legionella pneumophila is a Gram-negative bacterium ubiquitous in freshwater environments which, if inhaled, can cause a severe pneumonia in humans. The emergence of L.

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Genomic analysis of Caldalkalibacillus thermarum TA2.A1 reveals aerobic alkaliphilic metabolism and evolutionary hallmarks linking alkaliphilic bacteria and plant life

The aerobic thermoalkaliphile Caldalkalibacillus thermarum strain TA2.A1 is a member of a separate order of alkaliphilic bacteria closely related to the Bacillales order.

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Complete genome of a methicillin-resistant Staphylococcus vitulinus from Danish grounded beef meat carrying a mecA2 resistance gene and a novel ccr allotype

Objectives

To report the complete genome sequence of a methicillin-resistant Staphylococcus vitulinus from ground beef to allow comparison with other available S.

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Sensitive alignment using paralogous sequence variants improves long-read mapping and variant calling in segmental duplications

The ability to characterize repetitive regions of the human genome is limited by the read lengths of short-read sequencing technologies.

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Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively).

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Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection

SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics.

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CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

A substantial fraction of the human genome is difficult to interrogate with short-read DNA sequencing technologies due to paralogy, complex haplotype structures, or tandem repeats.

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Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota (Fungi) and a potential to switch between hosts

Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores.

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Genome diversity and quorum sensing variations in laboratory strains of Pseudomonas aeruginosa PAO1

The Pseudomonas aeruginosa strain PAO1 has routinely been used as a laboratory model for quorum sensing (QS) studies due to its extensively coordinated regulatory circuits. However, the microevolution of P.

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Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

Alternative splicing is a post-transcriptional regulatory mechanism producing multiple distinct mRNA molecules from a single pre-mRNA.

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Soil disturbance affects plant growth via soil microbial community shifts

Recent advances in climate research have discovered that permafrost is particularly vulnerable to the changes occurring in the atmosphere and climate, especially in Alaska where 85% of the land is underlain by mostly discontinuous permafrost.

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DNA methylation is required to maintain DNA replication timing precision and 3D genome integrity

DNA replication timing and three-dimensional (3D) genome organisation occur across large domains associated with distinct epigenome patterns to functionally compartmentalise genome regulation.

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Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance

Background Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan.

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Evaluation of assembly methods combining long-reads and short-reads to obtain Paenibacillus sp. R4 high-quality complete genome

We sequenced the Paenibacillus sp. R4 using Oxford Nanopore Technology (ONT), single molecule real-time (SMRT) technology from Pacific Biosciences (PacBio), and Illumina technologies to investigate the application of nanopore reads in de novo sequencing of bacterial genomes.

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A chromosome‐scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

Brassica juncea (AABB), commonly referred to as mustard, is a natural allopolyploid of two diploid species—B. rapa (AA) and B. nigra (BB).

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Isoform-level transcriptome Atlas of Macrophage Activation

RNA-seq is routinely used to measure gene expression changes in response to cell perturbation. Genes that are up or down-regulated following perturbation in RNA-seq studies are designated as target genes for follow-up.

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High-resolution phylogenetic and population genetic analysis of microbial communities with RoC-ITS

Microbial communities are inter-connected systems of incredible complexity and dynamism that play crucial roles in health, energy, and the environment.

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Sequencing of E. coli strain UTI89 on multiple sequencing platforms

Objectives

The availability of matched sequencing data for the same sample across different sequencing platforms is a necessity for validation and effective comparison of sequencing platfor

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The genomic and transcriptomic foundations of viviparous seed development in mangroves

Vivipary in plants refers to a specific seed development and reproductive strategy where seeds minimize the dormancy stage and germinate while still attached to their maternal plants.

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Slaying the last unicorn - discovery of histones in the microalga Nanochlorum eucaryotum

Histones are the principal constituents of eukaryotic chromatin. The four core histones (H2A, H2B, H3, and H4) are conserved across sequenced eukaryotic genomes and therefore thought to be universal to eukaryotes.

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Single molecule, near full-length genome sequencing of dengue virus

Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome.

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Limited and strain-specific transcriptional and growth responses to acquisition of a multidrug resistance plasmid in genetically diverse Escherichia coli lineages

Multi-drug resistant (MDR) Escherichia coli are a major global threat to human health, wherein multi-drug resistance is primarily spread by MDR plasmid acquisition. MDR plasmids are not widely distributed across the entire E.

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Free-living psychrophilic bacteria of the genus Psychrobacter are descendants of pathobionts

Host-adapted microbiota are generally thought to have evolved from free-living ancestors. This process is in principle reversible, but examples are few.

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Combining protein-based transcriptome assembly, and efficient MinION long read sequencing for targeted transcript sequencing in orphan species

Orphan species that are evolutionarily distant from their closest sequenced/assembled neighbour provide a significant challenge in terms of gene or transcript assembly for functional analysis.

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Characterization of IncC Plasmids in Enterobacterales of food-producing animals originating from China

Incompatibility group C (IncC) plasmids have received attention due to their broad host range and because they harbor key antibiotic resistance genes.

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The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the “library hypothesis”

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms.

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VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers.

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Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis

Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC). Currently, only three complete C.

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An exploration of assembly strategies and quality metrics on the accuracy of the Knightia excelsa (rewarewa) genome.

Background We used long read sequencing data generated from Knightia excelsaI R.Br, a nectar producing Proteaceae tree endemic to Aotearoa New Zealand, to explore how sequencing data type, volume and workflows can impact final assembly accuracy an

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Evolution and adaptation of Pseudomonas aeruginosa in the paranasal sinuses of people with cystic fibrosis

People with the genetic disorder cystic fibrosis (CF) harbor lifelong respiratory infections, with morbidity and mortality frequently linked to chronic lung infections dominated by the opportunistically pathogenic bacterium Pseudomonas aeruginosa.

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Transcriptional response to host chemical cues underpins expansion of host range in a fungal plant pathogen lineage

The host range of parasites is an important factor in assessing the dynamics of disease epidemics. The evolution of pathogens to accommodate new hosts may lead to host range expansion, a process the molecular bases of which are largely enigmatic.

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A Python-based optimization framework for high-performance genomics

Exponentially-growing next-generation sequencing data requires high-performance tools and algorithms.

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Addition of daptomycin to levofloxacin increased the efficacy of levofloxacin monotherapy against a methicillin-susceptible Staphylococcus aureus strain in experimental meningitis and prevented development of resistance

Daptomycin and levofloxacin were tested as monotherapies and in combination against the antibiotic-susceptible S. aureus strain MSSA 1112 in a rabbit meningitis model and the effect of the combination on induction of resistance was determined in vitro.

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Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella

Infections caused by Klebsiella pneumoniae are a major public health threat. Extensively drug-resistant and even pan-resistant strains have been reported. Understanding K.

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Genetic diversity of blaKPC-gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae

Background Limited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequen

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Genome ARTIST_v2 software – a support for annotation of class II natural transposons in new sequenced genomes

Transposon annotation is a very dynamic field of genomics and various tools assigned to support this bioinformatics endeavor were reported. Genome ARTIST (GA) software was initially developed for mapping artificial transposons mobilized during insertional mutagenesis projects.

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Choice of library preparation and its effects on sequence quality, assembly, and precise in silico prediction of virulence genes in shiga toxin producing E.coli

Whole genome sequencing (WGS) provides essential public health information and is used worldwide for pathogen surveillance, epidemiology, and source tracking. The sequencing of foodborne pathogens is commonly performed with Illumina sequencing chemistry to obtain data with high accuracy.

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Human genomics of the humoral immune response against polyomaviruses

Human polyomaviruses are widespread in human populations and are able to cause severe disease in immunocompromised individuals. There remains an incomplete understanding of the potential impact of human genetic variation on inter-individual responses to polyomaviruses.

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Genomic and morphologic characterization of a planktonic Thiovulum (Campylobacterota) dominating the surface waters of the sulfidic Movile Cave, Romania

Life in Movile Cave (Romania) relies entirely on primary carbon fixation by bacteria oxidizing sulfide, methane and ammonia with oxygen, nitrate, sulfate, and ferric iron.

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Genome skimming and NMR chemical fingerprinting provide quality assurance biotechnology to validate Sarsaparilla identity and purity

Sarsaparilla is a popular natural health product (NHP) that has been reported to be one of the most adulterated botanicals in the marketplace.

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Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries

Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera.

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Chromosome integrity is required for the initiation of meiotic sex chromosome inactivation in Caenorhabditis elegans

During meiosis of heterogametic cells, such as XY meiocytes, sex chromosomes of many species undergo transcriptional silencing known as meiotic sex chromosome inactivation (MSCI). Silencing also occurs in aberrantly unsynapsed autosomal chromatin.

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Analysis of genomes of bacterial isolates from lameness outbreaks in broilers

We investigated lameness outbreaks at commercial broiler farms in Arkansas. From Bacterial Chondronecrosis with Osteomyelitis (BCO) lesions, we isolated several distinct bacterial species. The results show that BCO-lameness pathogens on particular farms can differ significantly.

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Human Chr18: “Stakhanovite” genes, missing and uPE1 proteins in liver tissue and HepG2 cells

Missing (MP) and functionally uncharacterized proteins (uPE1) comprise less than 5% of the total number of human Chr18 genes.

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Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing

Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem.

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Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly

Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections.

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DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples

Background High resolution HLA genotyping of donors and recipients is a crucially important prerequisite for haematopoetic stem-cell transplantation and relies heavily on the quality and completeness of immuno-genetic reference sequence databases

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Characterization and engineering of Streptomyces griseofuscus DSM 40191 as a Potential Host for heterologous expression of biosynthetic gene clusters

Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S.

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High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing

Background

Implementation of Third-Generation Sequencing approaches for Whole Genome Sequencing (WGS) all-in-one diagnostics in human and veterinary medicine, requires the rapid and accurate generation of consensus genomes.

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Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

Background Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo.

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Nucleotide-resolution bacterial pan-genomics with reference graphs

Bacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core) - the alignable fraction of two genomes from a single species might be only 50%.

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A phased Vanilla planifolia genome enables genetic improvement of flavour and production

The global supply of vanilla extract is primarily sourced from the cured beans of the tropical orchid species Vanilla planifolia. Vanilla plants were collected from Mesoamerica, clonally propagated and globally distributed as part of the early spice trade.

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High-resolution transcriptome atlas and improved genome assembly of common buckwheat, Fagopyrum esculentum

Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce.

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Metagenomic characterization of a harmful algal bloom using nanopore sequencing

Water bodies around the world are increasingly threatened by harmful algal blooms (HABs) under current trends of rising water temperature and nutrient load.

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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level.

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Desert Dingo (Canis lupus dingo) genome provides insights into their role in the Australian ecosystem.

The dingo is Australia’s iconic top-order predator and arrived on the continent between 5,000-8,000 years ago.

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Rapid evolution and horizontal gene transfer in the genome of a male-killing Wolbachia

Wolbachia are widespread bacterial endosymbionts that infect a large proportion of insect species. While some strains of this bacteria do not cause observable host phenotypes, many strains of Wolbachia have some striking effects on their hosts.

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Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA

Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat receptor (NLR) genes are found in plant genomes and are required for disease resistance.

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Draft genome assemblies and annotations of Agrypnia vestita walker, and Hesperophylax magnus banks reveal substantial repetitive element expansion in tube case-making caddisflies (Insecta: Trichoptera)

Trichoptera (caddisflies) play an essential role in freshwater ecosystems; for instance, larvae process organic material from the water and are food for a variety of predators.

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Third-generation sequencing: any future opportunities for PGT?

Purpose

To investigate use of the third-generation sequencing (TGS) Oxford Nanopore system as a new approach for preimplantation genetic testing (PGT).

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Classification of changes in the fecal microbiota associated with colonic adenomatous polyps using a long-read sequencing platform

The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological impacts on the organism it inhabits.

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Control of mitochondrial superoxide production includes programmed mtDNA deletion and restoration

Age-related diseases are intimately linked to mitochondrial impairment. Whether oxidative stress is a major driver of this impairment is still a contentious issue.

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Metabolic differentiation of co-occurring Accumulibacter clades revealed through genome-resolved metatranscriptomics

Microbial communities in their natural habitats consist of closely related populations that may exhibit phenotypic differences and inhabit distinct niches.

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The female (XX) and male (YY) genomes provide insights into the sex determination mechanism in spinach

Sexual reproduction is the primary means of reproduction for the vast majority of macroscopic organisms, including almost all animals and plants. Sex chromosomes are predicted to play a central role in sexual dimorphism. Sex determination in spinach is controlled by a pair of sex chromosomes.

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Heterochiasmy facilitated the establishment of gsdf as a novel sex determining gene in Atlantic halibut

Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known.

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Use of Oxford Nanopore MinION to generate full-length sequences of the Blastocystis small subunit (SSU) rRNA gene

Background

Blastocystis sp. is one of the most common enteric parasites of humans and animals worldwide.

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Benchmarking metagenomic classification tools for long-read sequencing data

In recent years, both long-read sequencing and metagenomic analysis have been significantly advanced. Although long-read sequencing technologies have been primarily used for de novo genome assembly, they are rapidly maturing for widespread use in other applications.

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Chromosome-level de novo assembly of Coprinopsis cinerea A43mut B43mut pab1-1 #326 and genetic variant identification of mutants using Nanopore MinION sequencing

The homokaryotic Coprinopsis cinerea strain A43mut B43mut pab1-1 #326 is a widely used experimental model for developmental studies in mushroom-forming fungi. It can grow on defined artificial media and complete the whole lifecycle within two weeks.

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Identification of a novel tetracycline resistance gene, tet(63), located on a multiresistance plasmid from Staphylococcus aureus

Objectives

To identify and characterize a novel tetracycline resistance gene on a multiresistance plasmid from Staphylococcus aureus SA01 of chicken origin.

Methods

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Evaluation of single-molecule sequencing technologies for structural variant detection in two Swedish Human Genomes

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution.

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A long-read sequencing approach for direct haplotype phasing in clinical settings

The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings.

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The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

Background The “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe.

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Antibiotic sensitivity screening of Klebsiella spp. and Raoultella spp. isolated from Marine Bivalve Molluscs reveal presence of CTX-M-Producing K. pneumoniae

Klebsiella spp. are a major cause of both nosocomial and community acquired infections, with K. pneumoniae being responsible for most human infections. Although Klebsiella spp.

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Prevalence of hypervirulence-associated pathogenicity loci among Klebsiella pneumoniae bloodstream isolates at a United States Hospital

Klebsiella pneumoniae is a major threat to human health worldwide. “Classical” K. pneumoniae (cKp) strains commonly cause multidrug-resistant (MDR) infections in debilitated patients residing in hospitals and long-term care facilities.

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FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

The broad application of large-scale single-cell RNA profiling in plants has been restricted by the prerequisite of protoplasting. We recently found that the Arabidopsis nucleus contains abundant polyadenylated mRNAs, many of which are incompletely spliced.

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Characterization of structural variation in Tibetans reveals new evidence of high-altitude adaptation and introgression

Structural variation (SV) acts as an essential mutational force shaping the evolution and function of the human genome.

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EcDNA hubs drive cooperative intermolecular oncogene expression

Extrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation. Gene expression typically involves distal enhancer DNA elements that contact and activate genes on the same chromosome.

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Identification of high confidence human poly(A) RNA isoform scaffolds using nanopore sequencing

Nanopore sequencing devices read individual RNA strands directly. This facilitates identification of exon linkages and nucleotide modifications; however, using conventional methods the 5' and 3' ends of poly(A) RNA cannot be identified unambiguously.

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Takeaways from Mobile DNA Barcoding with BentoLab and MinION

Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space.

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lra: the Long Read Aligner for Sequences and Contigs

It is computationally challenging to detect variation by aligning long reads from single-molecule sequencing (SMS) instruments, or megabase-scale contigs from SMS assemblies.

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A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis

Garlic, an economically important vegetable, spice, and medicinal crop, produces highly enlarged bulbs and unique organosulfur compounds.

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In Vivo Validation of Alternative FDXR Transcripts in Human Blood in Response to Ionizing Radiation

Following cell stress such as ionising radiation (IR) exposure, multiple cellular pathways are activated. We recently demonstrated that ferredoxin reductase (FDXR) has a remarkable IR-induced transcriptional responsiveness in blood.

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A long read mapping method for highly repetitive reference sequences

About 5-10% of the human genome remains inaccessible for functional analysis due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays.

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Characterization of a COPD-Associated NPNT Functional Splicing Genetic Variant in Human Lung Tissue via Long-Read Sequencing

Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide. Genome-wide association studies (GWAS) have identified over 80 loci that are associated with COPD and emphysema, however for most of these loci the causal variant and gene are unknown.

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Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data

Clinical decision making is increasingly guided by accurate and recurrent determination of presence and frequency of (somatic) variants and their haplotype through panel sequencing of disease-relevant genomic regions.

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Selection on old variants drives adaptive radiation of Metrosideros across the Hawaiian Islands

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology.

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Assessing Nanopore sequencing for clinical diagnostics: A comparison of NGS methods for Mycobacterium tuberculosis

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories.

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Unearthing the boreal soil resistome associated with permafrost thaw

Understanding the distribution and mobility of antibiotic resistance genes (ARGs) in soil bacteria from diverse ecological niches is critical in assessing their impacts on the global spread of antibiotic resistance.

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Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION

Plastic debris in the ocean form a new ecosystem, termed ‘plastisphere’, which hosts a variety of marine organisms. Recent studies implemented DNA metabarcoding to characterize the taxonomic composition of the plastisphere in different areas of the world.

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Chromosomal translocation disrupting the SMAD4 gene resulting in the combined phenotype of Juvenile polyposis syndrome and Hereditary Hemorrhagic Telangiectasia

Background

Patients with germline variants in SMAD4 can present symptoms of both juvenile polyposis syndrome (JPS) and Hereditary Hemorrhagic Telangiectasia (HHT): JP‐HHT syndrome.

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Complete and haplotype-specific sequence assembly of segmental duplication-mediated genome rearrangements using targeted CRISPR-targeted ultra-long read sequencing (CTLR-Seq)

We have developed a generally applicable method based on CRISPR/Cas9-targeted ultra-long read sequencing (CTLR-Seq) to completely and haplotype-specifically resolve, at base-pair resolution, large, complex, and highly repetitive genomic regions that had been previously impenetrable to ne

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Single cell transcriptome sequencing on the Nanopore platform with ScNapBar

The current ecosystem of single cell RNA-seq platforms is rapidly expanding, but robust solutions for single cell and single molecule full- length RNA sequencing are virtually absent.

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BugSeq: a highly accurate cloud platform for long-read metagenomic analyses

As the use of nanopore sequencing for metagenomic analysis increases, tools capable of performing long-read taxonomic classification in a fast and accurate manner are needed. Existing tools were either designed for short-read data (eg.

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Transposable element expression at unique loci in single cells with CELLO-seq

The role of Transposable Elements (TEs) in regulating diverse biological processes, from early development to cancer, is becoming increasing appreciated.

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Main Routes of Entry and Genomic Diversity of SARS-CoV-2, Uganda

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease (COVID-19), has been spreading globally since it was first reported in Wuhan, China, on December 30, 2019, infecting >10 million persons and causing massive disruption of daily lives and su

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Chromosome-level genome of Poropuntius huangchuchieni provides a diploid progenitor-like reference genome for the allotetraploid Cyprinus carpio

The diploid Poropuntius huangchuchieni in the cyprinid family, which is distributed in the Mekong and Red River basins, is one of the most closely related diploid progenitor-like species of allotetraploid common carp. Therefore, the P.

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Unraveling molecular mechanisms of immunity and cancer-resistance using the genomes of the Neotropical bats Artibeus jamaicensis and Pteronotus mesoamericanus

Bats are exceptional among mammals for harbouring diverse pathogens and for their robust immune systems. In addition, bats are unusually long-lived and show low rates of cancer.

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Minimal detection and low biological fluctuation of mitochondrial CpG methylation at the single-molecule level

Cytosine DNA methylation in the CpG context (5mCpG) is associated with the transcriptional status of nuclear DNA. Due to technical limitations, it has been less clear if mitochondrial DNA (mtDNA) is methylated and whether 5mCpG has a regulatory role in this context.

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The structure, function, and evolution of a complete human chromosome 8

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembly of a human autosome, chromosome 8.

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Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34+

Our previous study demonstrated that whole genome sequencing (WGS) data generated by Oxford Nanopore Technologies (ONT) can be used for rapid and accurate prediction of Salmnonella serotypes.

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CRISPR-Cas9 enrichment and long read sequencing for fine mapping in plants

Background

Genomic methods for identifying causative variants for trait loci applicable to a wide range of germplasm are required for plant biologists and breeders to understand the genetic control of trait variation.

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Applications of Oxford Nanopore sequencing in Schizosaccharomyces pombe

Recent years have seen great progresses in third-generation sequencing.

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Metagenomics Strain Resolution on Assembly Graphs

We introduce a novel bioinformatics pipeline, STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, when multiple metagenome samples from the same community are available.

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A telomere to telomere assembly of Oscheius tipulae and the evolution of rhabditid nematode chromosomes

Eukaryotic chromosomes have phylogenetic persistence. In many taxa, the number of chromosomes is related to the number of centromeres. However, in some groups, such as rhabditid nematodes, centromeric function is distributed across multiple sites on each chromosome.

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A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

Alternative RNA splicing varies across brain regions, but the single-cell resolution of such regional variation is unknown.

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A DNA nanoscope that identifies and precisely localizes over a hundred unique molecular features with nanometer accuracy

Techniques that can both spatially map out molecular features and discriminate many targets would be highly valued for their utility in studying fundamental nanoscale processes.

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Long-read sequencing resolves structural variants in SERPINC1 causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods

The identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs.

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De novo genome assembly of the Tobacco Hornworm moth (Manduca sexta)

The Tobacco hornworm, Manduca sexta, is a lepidopteran insect that is used extensively as a model system for studying insect biology, development, neuroscience and immunity.

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Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing

Sweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus.

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Landscape and function of multiple mutations within individual oncogenes

Sporadic reports have described cancer cases in which multiple driver mutations (MMs) occur in the same oncogene. However, the overall landscape and relevance of MMs remain elusive.

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Robust Benchmark Structural Variant Calls of An Asian Using the State-of-Art Long Fragment Sequencing Technologies

The importance of structural variants (SVs) on phenotypes and human diseases is now recognized.

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Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing

Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level.

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Long-read sequencing to understand genome biology and cell function

Determining the sequence of DNA and RNA molecules has a huge impact on the understanding of cell biology and function.

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Nanopore sequencing reveals full-length Tropomyosin 1 isoforms and their regulation by RNA binding proteins during rat heart development

Alternative splicing (AS) increases the variety of the proteome by producing multiple isoforms from a single gene.

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Nanopore direct RNA sequencing detects differential expression between human cell populations

Accurately quantifying gene and isoform expression changes is essential to understanding cell functions, differentiation and disease. Therefore, a crucial requirement of RNA sequencing is identifying differential expression.

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The isolate Caproiciproducens sp. 7D4C2 produces n-caproate at mildly acidic conditions from hexoses: genome and rBOX comparison with related strains and chain-elongating bacteria

Background Bulk production of medium-chain carboxylates (MCCs) with 6-12 carbon atoms is of great interest to biotechnology. Open cultures (e.g., reactor microbiomes) have been utilized to generate MCCs in bioreactors.

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Genetic Variation, Comparative Genomics, and the Diagnosis of Disease

The discovery of mutations associated with human genetic disease is an exercise in comparative genomics (see Glossary).

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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized.

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Nanopore sequencing and its clinical applications

Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore).

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nPhase: An accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes, i.e. deducing haplotypes from genomic data, remains a challenge.

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Precise characterization of somatic structural variations and mobile element insertions from paired long-read sequencing data with nanomonsv

We introduce our novel software, nanomonsv, for detecting somatic structural variations (SVs) using tumor and matched control long-read sequencing data with a single-base resolution.

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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing

Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide.

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Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of Transcription Start Sites (TSSs) in several species.

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Inflammation drives alternative first exon usage to regulate immune genes including a novel iron regulated isoform of Aim2

Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease.

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Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

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The long and the short of it: unlocking nanopore long-read RNA sequencing data with short-read tools

Application of Oxford Nanopore Technologies’ long-read sequencing platform to transcriptomic analysis is increasing in popularity.

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Major impacts of widespread structural variation on gene expression and crop improvement in tomato

Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging.

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Long-read human genome sequencing and its applications

Over the past decade, long-read, single-molecule DNA sequencing technologies have emerged as powerful players in genomics.

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Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible.

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Oxford Nanopore Sequencing: New opportunities for plant genomics?

DNA sequencing was dominated by Sanger’s chain-termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time.

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CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes

Background
Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.

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Towards complete and error-free genome assemblies of all vertebrate species

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are only available for a few non-microbial species.

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Short- and long-read metagenomics of South African gut microbiomes reveal a transitional composition and novel taxa

To date, human gut microbiome research in adults has focused on western populations, with an additional minority of studies examining nonwestern populations including agriculturalist or hunter-gatherer societies.

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Rapid, highly accurate and cost‐effective open‐source simultaneous complete HLA typing & phasing of Class I & II alleles using nanopore sequencing

Introduction
Accurate rapid genotyping of the genes within the HLA region presents many difficulties due to the complexity of this region.

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GALA: gap-free chromosome-scale assembly with long reads

High-quality genome assembly has wide applications in genetics and medical studies. However, it is still very challenging to achieve gap-free chromosome-scale assemblies using current workflows of long-read platforms.

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Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing

Microorganisms are critical to water recycling, pollution removal and resource recovery processes in the wastewater industry.

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A long road/read to rapid high-resolution HLA typing: The nanopore perspective

Next-generation sequencing (NGS) has been widely adopted for clinical HLA typing and advanced immunogenetics researches.

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Nanopore sequencing reveals novel targets for the diagnosis and surveillance of human and avian influenza A virus

Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance.

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The coronavirus proofreading exoribonuclease mediates extensive viral recombination

Coronaviruses (CoVs) emerge as zoonoses and cause severe disease in humans, demonstrated by the SARS-CoV-2 (COVID-19) pandemic.

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Characterisation of the poll allele in Brahman cattle using long read Oxford Nanopore sequencing

Brahman cattle (Bos indicus) are well adapted to thrive in tropical environments. Since their introduction to Australia in 1933, Brahman’s ability to grow and reproduce on marginal lands has proven their value in the tropical beef industry.

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The Scaly-foot Snail genome and implications for the origins of biomineralised armour

The Scaly-foot Snail, Chrysomallon squamiferum, presents a combination of biomineralised features, reminiscent of enigmatic early fossil taxa with complex shells and sclerites such as sachtids, but in a recently-diverged living species which

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Reorganization of 3D genome structure in the Drosophila melanogaster species group

Topologically associating domains, or TADs, are functional units that organize chromosomes into 3D structures of interacting chromatin.

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Complete and validated genomes from a metagenome

The assembly and binning of metagenomically-assembled genomes (MAGs) using Illumina sequencing has improved the genomic characterization of unculturable communities.

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MinION-in-ARMS: Nanopore sequencing to expedite barcoding of specimen-rich macrofaunal samples from Autonomous Reef Monitoring Structures

Autonomous Reef Monitoring Structure (ARMS) are standardised devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices greatly expand our ability to document marine biodiversity.

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Generating high quality assemblies for genomic analysis of transposable elements

The advent of long-read sequencing holds great promise for research on transposable elements (TEs).

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Short and long-read genome sequencing methodologies for somatic variant detection; genomic analysis of a patient with diffuse large B-cell lymphoma

Recent advances in throughput and accuracy mean that the Oxford Nanopore Technologies (ONT) PromethION platform is a now a viable solution for genome sequencing.

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Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not yet available.

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A reference genome sequence for giant sequoia

The giant sequoia (Sequoiadendron giganteum) of California are massive, long-lived trees that grow along the U.S. Sierra Nevada mountains.

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Benchmarking the MinION: Evaluating long reads for microbial profiling

Nanopore based DNA-sequencing delivers long reads, thereby simplifying the decipherment of bacterial communities.

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The architecture of SARS-CoV-2 transcriptome

SARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown.

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Direct RNA sequencing approach to compare non-model mitochondrial transcriptomes: an application to a cephalopod host and its mesozoan parasite

To identify non-protein coding as well as truncated or premature RNA sequences expressed and obtain more complete transcriptome information, we combined the MinION direct RNA-sequencing of a conventional poly(A) RNA purification method with poly(A)-tagging of the non-coding RNA (ncRNA) fraction.

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Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

Adherent-invasive Escherichia coli (AIEC) are a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn’s disease, and colorectal cancer. AIEC have no known molecular or genomic markers, but instead are defined by in vitro functional attributes.

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Amplicon-based detection and sequencing of SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19 and identification of deletions in the viral genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19).

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Identification of structural variation in chimpanzees using optical mapping and nanopore sequencing

Recent efforts to comprehensively characterize great ape genetic diversity using short-read sequencing and single-nucleotide variants have led to important discoveries related to selection within species, demographic history, and lineage-specific traits.

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Whole-genome sequencing of rare disease patients in a national healthcare system

Most patients with rare diseases do not receive a molecular diagnosis and the aetiological variants and mediating genes for more than half such disorders remain to be discovered.

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Long-read cDNA sequencing enables a ‘gene-like’ transcript annotation of Arabidopsis transposable elements

High-quality transcript-based annotations of genes facilitates both genome-wide analyses and detailed single locus research. In contrast, transposable element (TE) annotations are rudimentary, consisting of only information on location and type of TE.

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DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

Identification of bacteria causing tissue infections can be comprehensive and, in the cases of non- or slow-growing bacteria, near impossible with conventional methods.

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A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes

There is a growing awareness of the importance of indoor microbiomes for human health. Given their complexity, these microbiomes can only be adequately surveyed using high throughput sequencing techniques.

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Evaluation of real-time nanopore sequencing for Salmonella serotype prediction

The use of whole genome sequencing (WGS) data generated by short-read sequencing technologies such as the Illumina sequencing platforms has been shown to provide reliable results for Salmonella serotype prediction.

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Direct nanopore sequencing of mRNA reveals landscape of transcript isoforms in apicomplexan parasites

Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites.

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nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples

Multilocus sequence typing (MLST) is one of the most commonly used methods for studying microbial lineage worldwide. However, the traditional MLST process using Sanger sequencing is time-consuming and expensive.

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Nanopore sequencing in blood diseases: a wide range of opportunities

The molecular pathogenesis of hematological diseases is often driven by genetic and epigenetic alterations. Next-generation sequencing has considerably increased our genomic knowledge of these disorders becoming ever more widespread in clinical practice.

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Analysis of the transgene insertion pattern in a transgenic mouse strain using long-read sequencing

Transgene insertion patterns are critical for the analysis of transgenic animals because the influence of transgenes may change depending on the insertion pattern (such as copy numbers and orientations of concatenations) and the insertion position in the genome.

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The genome sequence of the Jean-Talon strain, an archeological tetraploid beer yeast from Québec

The genome sequences of archeological yeast isolates can reveal insights about the history of human baking, brewing and winemaking activities and migration around the globe.

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The hornwort genome and early land plant evolution

Hornworts, liverworts and mosses are three early diverging clades of land plants, and together comprise the bryophytes.

Here, we report the draft genome sequence of the hornwort Anthoceros angustus.

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Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development

Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5′ or 3′ splice site or polyadenylation site, and RNA modification.

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Long-read individual-molecule sequencing reveals CRISPR-induced genetic heterogeneity in human ESCs

Accurately quantifying the genetic heterogeneity of a cell population is essential to understanding of biological systems.

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Complete, closed bacterial genomes from microbiomes using nanopore sequencing

Microbial genomes can be assembled from short-read sequencing data, but the assembly contiguity of these metagenome-assembled genomes is constrained by repeat elements.

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Amplification-free long read sequencing reveals unforeseen CRISPR-Cas9 off-target activity

A much-debated concern about CRISPR-Cas9 genome editing is that unspecific guide RNA (gRNA) binding may induce off-target mutations. However, accurate prediction of CRISPR-Cas9 off-target sites and activity is challenging.

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Metagenomics workflow for hybrid assembly, differential coverage binning, transcriptomics and pathway analysis (MUFFIN)

Metagenomics has redefined many areas of microbiology. However, metagenome-assembled genomes (MAGs) are often fragmented, primarily when sequencing was performed with short reads. Recent long-read sequencing technologies promise to improve genome reconstruction.

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Opportunities and challenges in long-read sequencing data analysis

Long-read technologies are overcoming early limitations in accuracy and throughput, broadening their application domains in genomics.

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High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing

The rise of antimicrobial resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission.

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The sudden emergence of a Neisseria gonorrhoeae strain with reduced susceptibility to extended-spectrum cephalosporins, Norway

The Neisseria gonorrhoeae multilocus sequence type (ST) 7827 emerged in dramatic fashion in Norway in the period 2016-2018. Here, we aim to determine what enabled it to establish and spread so quickly.

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Duplications drive diversity in Bordetella pertussis on an underestimated scale

Bacterial genetic diversity is often described using solely base pair changes despite a wide variety of other mutation types likely being major contributors.

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Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Understanding genome organization and gene regulation requires insight into RNA transcription, processing and modification.

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Rapid and real-time identification of fungi up to the species level with long amplicon nanopore sequencing from clinical samples

The availability of long-read technologies, like Oxford Nanopore Technologies, provides the opportunity to sequence longer fragments of the fungal ribosomal operon, up to 6 Kb (18S-ITS1-5.8S-ITS2-28S) and to improve the taxonomy assignment of the communities up to species level

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Location of balanced chromosome-translocation breakpoints by long-read sequencing on the Oxford Nanopore platform

Genomic structural variants, including translocations, inversions, insertions, deletions, and duplications, are challenging to be reliably detected by traditional genomic technologies.

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High-quality genome assembly of Eriocheir japonica sinensis reveals its unique genome evolution

As an important freshwater aquaculture species in China, the Chinese mitten crab (Eriocheir japonica sinensis) has high economic and nutritional value. However, limited genomic information is currently available for studying its basic development and genetic diversity.

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The parasite Schistocephalus solidus secretes proteins with putative host manipulation functions

Manipulative parasites are predicted to liberate molecules in their external environment acting as manipulation factors with biological functions implicated in their host's physiological and behavioural alterations.

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High contiguity long read assembly of Brassica nigra allows localization of active centromeres and provides insights into the ancestral Brassica genome

High-quality nanopore genome assemblies were generated for two Brassica nigra genotypes (Ni100 and CN115125); a member of the agronomically important Brassica species.

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Profiling of human gut virome with Oxford Nanopore technology

The human gut virome plays critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology.

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Immunoglobulin switch-like recombination regions implicated in the formation of extrachromosomal circular 45S rDNA involved in the maternal-specific translation system of zebrafish

Cellular translation is essential to all life on earth and in recent years we have reported on the discovery of a unique dual translation system in zebrafish.

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High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

The yam species Dioscorea dumetorum is one example of an orphan crop, not traded internationally. Post-harvest hardening starts within 24 hours after harvesting and renders the tubers inedible.

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Species boundaries and molecular markers for classification among 16SrI phytoplasmas informed by genome analysis

Phytoplasmas are diverse plant-pathogenic bacteria that greatly impact agriculture worldwide. The current classification system for these uncultivated bacteria is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes.

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High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

Genotyping methods and genome sequencing are indispensable for revealing the genomic structure of bacterial species displaying high levels of genome plasticity.

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Flow sorting enrichment and nanopore sequencing of chromosome 1 from a Chinese individual

Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome.

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Long-read sequencing reveals widespread intragenic structural variants in a recent allopolyploid crop plant

Genome structural variation (SV) contributes strongly to trait variation in eukaryotic species and may have an even higher functional significance than single nucleotide polymorphism (SNP).

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Long-read assays shed new light on the transcriptome complexity of a viral pathogen

Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps.

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Characterization of mating type genes in heterothallic Neonectria species with emphasis on N. coccinea, N. ditissima, and N. faginata

Neonectria ditissima and N. faginata are canker pathogens involved in an insect-fungus disease complex of American beech (Fagus grandifolia) commonly known as beech bark disease (BBD). In Europe, both N. ditissima and N.

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Plasmid diversity among genetically related Klebsiella pneumoniae blaKPC-2 and blaKPC-3 isolates collected in the Dutch national surveillance

Carbapenemase-producing Klebsiella pneumoniae emerged over the past decades as an important pathogen causing morbidity and mortality in hospitalized patients.

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An educational guide for nanopore sequencing in the classroom

The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods of data storage and analysis.

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Low ribosomal RNA genes copy number provoke genomic instability and chromosomal segment duplication events that modify global gene expression and plant-pathogen response

Among the hundreds of ribosomal RNA (rRNA) gene copies organized as tandem repeats in the nucleolus organizer regions (NORs), only a portion is usually actively expressed in the nucleolus and participate in the ribosome biogenesis process.

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Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producing Enterobacter hormaechei

Carbapenem-resistant Enterobacteriaceae (CRE) represent an urgent threat to human health.

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The Arabidopsis "retrovirome" and its regulation by epigenetically activated small RNA

In Arabidopsis, LTR-retrotransposons are activated by mutations in the chromatin remodeler DECREASE in DNA METHYLATION 1 (DDM1), giving rise to 21-22nt epigenetically activated siRNAs (easiRNAs).

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Genomic dynamics of species and mobile genetic elements in a prolonged blaIMP-4-associated carbapenemase outbreak in an Australian hospital

Background
Hospital outbreaks of carbapenemase-producing organisms, such as blaIMP-4-containing organisms, are an increasing threat to patient safety.

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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds.

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Three genomes of Osteoglossidae shed light on ancient teleost evolution

Osteoglossiformes is a basal clade of teleost, originating from the late Jurassic period, which has experienced the process of continental drift. The genomic differences between Osteoglossiformes species should reflect the unique evolutionary history of that time.

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Gapless assembly of maize chromosomes using long read technologies

Creating gapless telomere-to-telomere assemblies of complex genomes is one of the ultimate challenges in genomics.

We used long read technologies and an optical map based approach to produce a maize genome assembly composed of only 63 contigs.

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The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom.

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Comparative genomics of three clinical Ureaplasma species: analysis of their core genomes and multiple banded antigen locus

Aim
To compare the genome sequences among clinical and American Type Culture Collection Ureaplasma strains and to reveal the potential molecular mechanisms of multiple banded antigen (MBA) variation. 

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A strategy for complete telomere-to-telomere assembly of ciliate macronuclear genome using ultra-high coverage Nanopore data

Ciliates contain two kinds of nuclei: the germline micronucleus (MIC) and the somatic macronucleus (MAC) in a single cell. The MAC usually have fragmented chromosomes.

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Genetic underpinnings of host manipulation by Ophiocordyceps as revealed by comparative transcriptomics

The ant-infecting Ophiocordyceps fungi are globally distributed, host manipulating, specialist parasites that drive aberrant behaviors in infected ants, at a lethal cost to the host.

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Enhancer hijacking determines intra- and extrachromosomal circular MYCN amplicon architecture in neuroblastoma

MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA.

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Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

Tandem repeats are highly mutable and contribute to the development of human disease by a variety of mechanisms. However, it is difficult to predict which tandem repeats may cause a disease.

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Nanopore-based native RNA sequencing provides insights into prokaryotic transcription, operon structures, rRNA maturation and modifications

The prokaryotic transcriptome is shaped by transcriptional and posttranscriptional events that define the characteristics of an RNA, including transcript boundaries, the base modification status, and processing pathways to yield mature RNAs.

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HyPo: Super fast and accurate polisher for long read genome assemblies

Efforts towards making population-scale long read genome assemblies (especially human genomes) viable have intensified recently with the emergence of many fast assemblers. The reliance of these fast assemblers on polishing for the accuracy of assemblies makes it crucial.

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Nanopore sequencing of native adeno-associated virus single-stranded DNA using a transposase-based rapid protocol

Monitoring DNA integrity and DNA contaminants in adeno-associated virus (AAV) gene therapy vectors is of major interest, because of clinical applications with increasing therapeutic doses.

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Genomic analysis of carbapenemase-producing Enterobacteriaceae in Queensland reveals widespread transmission of bla IMP-4 on an IncHI2 plasmid

Carbapenemase-producing Enterobacteriaceae (CPE) are an increasingly common cause of healthcare-associated infections and may occasionally be identified in patients without extensive healthcare exposure.

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A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants

Background
Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes.

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De novo assembly of the Brugia malayi genome using long reads from a single MinION Flow Cell

Filarial nematode infections cause a substantial global disease burden. Genomic studies of filarial worms can improve our understanding of their biology and epidemiology. However, genomic information from field isolates is limited and available reference genomes are often discontinuous.

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Non-destructive enzymatic deamination enables single molecule long read sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single base resolution

The predominant methodology for DNA methylation analysis relies on the chemical deamination by sodium bisulfite of unmodified cytosine to uracil to permit the differential readout of methylated cytosines.

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MinION sequencing of Streptococcus suis allows for functional characterization of bacteria by multilocus sequence typing and antimicrobial resistance profiling

In recent years, high-throughput sequencing has revolutionized disease diagnosis by its powerful ability to provide high resolution genomic information.

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Genomic adaptations to aquatic and aerial life in mayflies and the origin of wings in insects

The first winged insects underwent profound morphological and functional transformations leading to the most successful animal radiations in the history of earth. Despite this, we still have a very incomplete picture of the changes in their genomes that underlay this radiation.

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Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system

Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure‐function relationships in complex environments.

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Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing

Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. The HPV infection-related cervical microbiome could be an inducing factor of cervical cancer.

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A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer

The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches and the ability to identify a broad diversity of fungal taxa.

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Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota.

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Characterization of a novel conjugative plasmid in Edwardsiella piscicida strain MS-18-199

Edwardsiella piscicida is a pathogenic bacterium responsible for significant losses in important wild and cultured fish species. E.

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Randomly primed, strand-switching MinION-based sequencing for the detection and characterization of cultured RNA viruses

RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false negative detection results.

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Novel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts

Adenovirus is a common human pathogen that relies on host cell processes for production and processing of viral RNA.

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Generation of a transcriptional radiation exposure signature in human blood using long-read nanopore sequencing

In the event of a large-scale event leading to acute ionizing radiation exposure, high-throughput methods would be required to assess individual dose estimates for triage purposes.

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Nanopore targeted sequencing for rapid gene mutations detection in acute myeloid leukemia

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold targeted therapy.

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Comparative genomic analysis of Cristatella mucedo provides insights into Bryozoan evolution and nervous system function

The modular body organization is an enigmatic feature of different animal phyla scattered throughout the phylogenetic tree.

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Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations.

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Determining antimicrobial resistance profiles and identifying novel mutations of Neisseria gonorrhoeae genomes obtained by multiplexed MinION sequencing

Gonorrhea is one of the most common sexually transmitted diseases worldwide. To cure infection and prevent transmission, timely and appropriate antimicrobial therapy is necessary.

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Critical assessment of bioinformatics methods for the characterization of pathological repeat expansions with single-molecule sequencing data

A number of studies have reported the successful application of single-molecule sequencing technologies to the determination of the size and sequence of pathological expanded microsatellite repeats over the last 5 years.

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Genomic investigation of the strawberry pathogen Phytophthora fragariae indicates pathogenicity is determined by transcriptional variation in three key races

The oomycete Phytophthora fragariae is a highly destructive pathogen of cultivated strawberry (Fragaria × ananassa), causing the root rotting disease, ‘red core’.

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Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment.

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Annotated draft genomes of two caddisfly species Plectrocnemia conspersa CURTIS and Hydropsyche tenuis NAVAS (Insecta: Trichoptera)

Members of the speciose insect order Trichoptera (caddisflies) provide important ecosystem services, e.g. nutrient cycling through breaking down of organic matter. They are also of industrial interest due to their larval silk secretions.

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Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes.

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Approaches to whole mitochondrial genome sequencing on the Oxford Nanopore MinION

Traditional approaches for interrogating the mitochondrial genome often involve laborious extraction and enrichment protocols followed by Sanger sequencing.

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Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs.

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The genome sequence of the octocoral Paramuricea clavata – a key resource to study the impact of climate change in the Mediterranean

The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P.

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A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea.

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Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression.

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Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in human diseases and other traits

Long-read sequencing (LRS) promises to improve characterization of structural variants (SVs), a major source of genetic diversity.

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Chromosome-level assembly of Drosophila bifasciata reveals important karyotypic transition of the X chromosome

The Drosophila obscura species group is one of the most studied clades of Drosophila and harbors multiple distinct karyotypes.

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Long-reads reveal that the chloroplast genome exists in two distinct versions in most plants

The chloroplast genome usually has a quadripartite structure consisting of a large single copy region and a small single copy region separated by two long inverted repeats.

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Application of long-read sequencing for robust identification of correct alleles in genome edited animals

Recent developments in CRISPR/Cas9 genome editing tools have facilitated the introduction of more complex alleles, often spanning genetic intervals of several kilobases, directly into the embryo.

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Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India

River confluences are a hub of biodiversity with limited information with respect to the structure and the functions of the microbial communities. The River Ganges is the national river of India, having manifold significance such as social, mythological, historic, geographic and agro-economic.

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First report of Burkholderia pseudomallei ST412 and ST734 clones harbouring blaOXA-57 but susceptible to imipenem in India

Melioidosis caused by Burkholderia pseudomallei has become an important clinical threat, especially in Northern Australia and Southeast Asia. However, the genome information on this pathogen is limited. 

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Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring

Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies.

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Full-coverage native RNA sequencing of HIV-1 viruses

Objective: To evaluate native RNA sequencing for sequencing HIV-1 viral genomes.

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Whole genome sequencing and assembly of the Asian honey bee Apis dorsata

The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin A. mellifera by a few key characteristics. Most prominently, A. dorsata nest in the open by forming a colony clustered around the honeycomb, while A.

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High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

Tandem repeats (TRs) are highly prone to variation in copy numbers due to their repetitive and unstable nature, which makes them a major source of genomic variation between individuals.

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Complete genome sequence of Oryctes rhinoceros nudivirus isolated from coconut rhinoceros beetle in Solomon Islands

Oryctes nudivirus (species OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations.

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Complete hybrid genome assembly of clinical multidrug-resistant Bacteroides fragilis isolates enables comprehensive identification of antimicrobial-resistance genes and plasmids

Bacteroides fragilis constitutes a significant part of the normal human gut microbiota and can also act as an opportunistic pathogen.

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Retention of CD19 intron 2 contributes to CART-19 resistance in leukemias with subclonal frameshift mutations in CD19

Every successful cancer therapy story has Exhibit B, comprised of patients who either did not respond to the initial treatment or acquired resistance after a seemingly curative intervention.

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High throughput, error corrected Nanopore single cell transcriptome sequencing

Droplet-based high throughput single cell isolation techniques tremendously boosted the throughput of single cell transcriptome profiling experiments. However, those approaches only allow analysis of one extremity of the transcript after short read sequencing.

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Complete microbial genomes for public health in Australia and Southwest Pacific

Complete genomes of microbial pathogens are essential for the phylogenomic analyses that increasingly underpin core public health lab activities. Here, we present complete genomes of pathogen strains of regional importance to the Southwest Pacific and Australia.

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Genetic structure at national and regional scale in a long-distance dispersing pest organism, the bird cherry-oat aphid Rhopalosiphum padi

Genetic diversity is determinant for pest species' success and vector competence. Understanding the ecological and evolutionary processes that determine the genetic diversity is fundamental to help identify the spatial scale at which pest populations are best managed.

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Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify.

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Long reads, short time: feasibility of prenatal sample karyotyping by nanopore genome sequencing

Chromosomal abnormalities causing genomic imbalance are a major cause of congenital developmental defects and intellectual disability, constituting the leading cause of stillbirth and birth with malformations.

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Persistent chromatin states, pervasive transcription, and shared cis-regulatory sequences have shaped the C. elegans genome

Despite highly conserved chromatin states and cis-regulatory elements, studies of metazoan genomes reveal that gene organization and the strategies to control mRNA expression can vary widely among animal species. C.

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A chromosome-scale genome assembly of European Hazel (Corylus avellana L.) reveals targets for crop improvement

European hazelnut (Corylus avellana L.) is a tree crop of economic importance worldwide, but especially to northern Turkey, where the majority of production takes place.

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Lost in Translation: population genomics of porcini mushrooms (Boletus edulis) challenges use of ITS for DNA barcoding in Fungi

The internal transcribed spacers (ITS) of the rDNA cistron are the most commonly used DNA barcoding region in Fungi.

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Third generation sequencing in the clinical laboratory: Exploring the advantages and challenges of nanopore sequencing

Metagenomic sequencing for infectious disease diagnostics is an important tool that holds promise for use in the clinical laboratory. Challenges for implementation so far include high cost, length of time to results, and need for technical and bioinformatics expertise.

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Best foot forward: Nanopore long reads, hybrid meta-assembly, and haplotig purging optimizes the first genome assembly for the Southern Hemisphere Blacklip abalone (Haliotis rubra)

Marine molluscs of the family Haliotidae, commonly referred to as abalone, are a group of benthic reef species targeted by commercial fisheries in 11 countries, forming an important global industry worth approximately US $180 million.

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Multiple long-read sequencing survey of Herpes Simplex virus dynamic transcriptome

Long-read sequencing (LRS) has become increasingly important in RNA research due to its strength in resolving complex transcriptomic architectures.

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Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

Whole-genome sequencing using sequencing technologies such as Illumina enables the accurate detection of small-scale variants but provides limited information about haplotypes and variants in repetitive regions of the human genome.

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Spectral Jaccard Similarity: a new approach to estimating pairwise sequence alignments

A key step in many genomic analysis pipelines is the identification of regions of similarity between pairs of DNA sequencing reads.

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LAMBDR: Long-range amplification and Nanopore sequencing of Mycobacterium bovis direct-repeat region. A novel method for in-silico spoligotyping of M. bovis directly from badger faeces.

The environment is an overlooked source of Mycobacterium bovis, the causative agent of bovine TB. Long read, end to end sequencing of variable repeat regions across the M.

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High molecular weight DNA isolation method from diverse plant species for use with Oxford Nanopore sequencing

The ability to generate long reads on the Oxford Nanopore Technologies sequencing platform is dependent on the isolation of high molecular weight DNA free of impurities.

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Long-read sequencing in deciphering human genetics to a greater depth

Through four decades’ development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical approaches developed independently by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT

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Draft genome of a porcupinefish, Diodon Holocanthus

The long-spine porcupinefish, Diodon holocanthus (Diodontidae, Tetraodontiformes, Actinopterygii), also known as the freckled porcupinefish, attracts great interest of ecology and economy.

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Genome sequence of the cluster root forming white lupin

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch).

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Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

Centromeres are chromosomal regions that serve as platforms for kinetochore assembly and spindle attachments, ensuring accurate chromosome segregation during cell division.

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Identifying transposon insertions in bacterial genomes through nanopore sequencing

Transposon mutagenesis is a widely used tool for carrying out forward genetic screens across systems, but in some cases it can be difficult to identify transposon insertion points after successful phenotypic screens.

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The diagnostic chronic lymphocytic leukaemia genome by nanopore sequencing

Chronic lymphocytic leukaemia (CLL) is characterised by considerable clinical and biological heterogeneity, with specific recurrent genomic alterations, including TP53 mutations, deletions of chromosome 17p, and IgHV mutational status, impacting on response to chemo-immunotherapy and tar

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Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing

Detection of chromosomal translocation is a key component in diagnosis and management of acute myeloid leukemia (AML).

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Telomere-to-telomere assembly of a complete human X chromosome

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of unresolved gaps persist.

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Mapping of transgenic alleles in soybean using a nanopore-based sequencing strategy

Transgenic technology was developed to introduce transgenes into various organisms to validate gene function and add genetic variations >40 years ago. However, the identification of the transgene insertion position is still challenging in organisms with complex genomes.

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De novo genome assembly of the meadow brown butterfly, Maniola jurtina

Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology.

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LARP1 facilitates translational recovery after amino acid refeeding by preserving long poly(A)-tailed TOP mRNAs

Occasionally, cells must adapt to an inimical growth conditions like amino acid starvation (AAS) by downregulating protein synthesis.

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Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture.

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Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

De novo assembly of a human genome using nanopore long-read sequences has been reported, but it used more than 150,000 CPU hours and weeks of wall-clock time.

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SMURF-seq: efficient copy number profiling on long-read sequencers

We present SMURF-seq, a protocol to efficiently sequence short DNA molecules on a long-read sequencer by randomly ligating them to form long molecules.

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Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.)

Despite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment.

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Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats

Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble.

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Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications.

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De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing

Background
The Indian peafowl (Pavo cristanus) is native to South Asia and is the national bird of India. Here we present a draft genome sequence of the male blue peacock using Illumina and Oxford Nanopore technology (ONT).

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Nanopore sequencing: review of potential applications in functional genomics

Molecular biology has been led by various measurement technologies, and increased throughput has developed omics analysis. The development of massively parallel sequencing technology has enabled access to fundamental molecular data and revealed genomic and transcriptomic signatures.

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Characterization of the Candida orthopsilosis agglutinin-like sequence (ALS) genes

Agglutinin like sequence (Als) cell-wall proteins play a key role in adhesion and virulence of Candida species.

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Severe haemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

Background
No F8 genetic abnormality is detected in about 2% of severe haemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting genomic rearrangement could be causal.

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Assembly-free single-molecule nanopore sequencing recovers complete virus genomes from natural microbial communities

Viruses are the most abundant biological entities on Earth and play key roles in host ecology, evolution, and horizontal gene transfer.

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Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

The large genome of the migratory locust (Locusta migratoria) accumulates a massive amount of transposable elements (TEs), which show intrinsic transcriptional activities.

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Two reads to rule them all: Nanopore long read-guided assembly of the iconic Christmas Island red crab, Gecarcoidea natalis (Pocock, 1888), mitochondrial genome and the challenges of AT-rich mitogenomes

Despite recent advances in sequencing technology, a complete mitogenome assembly is still unavailable for the gecarcinid land crabs that include the iconic Christmas Island red crab (Gecarcoidea natalis) which is known for its high population density, annual mass breeding migration and e

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Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

Eukaryotic genes often generate a variety of RNA isoforms that can lead to functionally distinct protein variants. The synthesis and stability of RNA isoforms is however poorly characterized.

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Nanopore sequencing reads improve assembly and gene annotation of the Parochlus steinenii genome

Parochlus steinenii is a winged midge from King George Island. It is cold-tolerant and endures the harsh Antarctic winter.

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The shufflon of IncI1 plasmids is rearranged constantly during different growth conditions

Nanopore long-read sequencing was used to measure recombination of the IncI1 shufflon at different bacterial growth stages and in different host cells.

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Nanopore sequencing for fast determination of plasmids, phages, virulence markers, and antimicrobial resistance genes in Shiga toxin-producing Escherichia coli

Whole genome sequencing can provide essential public health information. However, it is now known that widely used short-read methods have the potential to miss some randomly-distributed segments of genomes.

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications

CYP2D6 is one of the most important and widely studied genes in pharmacogenetics but it is highly polymorphic, can be affected by different forms of structural variation, and has a nearby pseudogene with highly similar sequence; therefore, its accurate genotyping and structural r

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Nanopore sequencing of full-length circRNAs in human and mouse brains reveals circRNA-specific exon usage and intron retention

Circular RNA (circRNA) is a poorly understood class of non-coding RNAs, some of which have been shown to be functionally important for cell proliferation and development.

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Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads

Retroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion sites, but the proviruses within remain unobserved.

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Long-read sequencing identifies GGC repeat expansions in NOTCH2NLC associated with neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease that is characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells.

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Depletion of hemoglobin transcripts and long-read sequencing improves the transcriptome annotation of the polar bear (Ursus maritimus)

Transcriptome studies evaluating whole blood and tissues are often confounded by overrepresentation of highly abundant transcripts. These abundant transcripts are problematic as they compete with and prevent the detection of rare RNA transcripts, obscuring their biological importance.

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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

Illumina sequencing allows rapid, cheap and accurate whole genome bacterial analyses, but short reads (<300 bp) do not usually enable complete genome assembly.

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De novo genome assembly of the olive fruit fly (Bactrocera oleae) developed through a combination of linked-reads and long-read technologies

Long-read sequencing has greatly contributed to the generation of high quality assemblies, albeit at a high cost. It is also not always clear how to combine sequencing platforms.

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Resolving the complex Bordetella pertussis genome using barcoded nanopore sequencing

The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B.

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Nanopore sequencing significantly improves genome assembly of the protozoan parasite Trypanosoma cruzi

Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a two-year-old girl called Berenice. Many T.

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Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

Sequence analyses of RNA virus genomes remain challenging owing to the exceptional genetic plasticity of these viruses.

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Rapid sequencing of multiple RNA viruses in their native form

A direct RNA sequencing protocol on the MinION was established for real-time, simultaneous detection and characterisation of multiple RNA viruses. The protocol described has the potential to be used for rapid genome/subgenome sequencing of other RNA viruses.

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Transcriptome landscape of the developing olive fruit fly embryo delineated by Oxford Nanopore long-read RNA-Seq

The olive fruit fly or olive fly (Bactrocera oleae) is the most important pest of cultivated olive trees. Like all insects the olive fly undergoes complete metamorphosis.

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Improving recovery of member genomes from enrichment reactor microbial communities using MinION-based long read metagenomics

New long read sequencing technologies offer huge potential for effective recovery of complete, closed genomes. While much progress has been made on cultured isolates, the ability of these methods to recover genomes of member taxa in complex microbial communities is less clear.

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Long-read viral metagenomics enables capture of abundant and microdiverse viral populations and their niche-defining genomic islands

Marine viruses impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a universal gene to facilitate community surveys.

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Nanopore native RNA sequencing of a human poly(A) transcriptome

High-throughput complementary DNA sequencing technologies have advanced our understanding of transcriptome complexity and regulation.

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Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

Characterization of microbiomes has been enabled by high-throughput metagenomic sequencing. However, existing methods are not designed to combine reads from short- and long-read technologies.

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Genetic repertoires of anaerobic microbiomes driving generation of biogas

Biogas production is an attractive technology for a sustainable generation of renewable energy. Although the microbial community is fundamental for such production, the process control is still limited to technological and chemical parameters.

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De novo assembly of middle-sized genome using MinION and Illumina sequencers

The plastid acquisition by secondary endosymbiosis is a driving force for the algal evolution, and the comparative genomics was required to examine the genomic change of symbiont.

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Forensic STR profiling using Oxford Nanopore Technologies' MinION

Forensic STR profiling using massively parallel sequencing (MPS) has gained much attention as an alternative for the traditional capillary electrophoresis (CE) methods.

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NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION

Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease.

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Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

We sequenced the genome of the Yoruban reference individual NA19240 on the long read sequencing platform Oxford Nanopore PromethION for evaluation and benchmarking of recently published aligners and germline structural variant calling tools, and a comparison with the performance of structural var

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Genome-wide measurement of local nucleosome array regularity and spacing by nanopore sequencing

The nature of chromatin as regular succession of nucleosomes has gained iconic status.

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High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors.

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Reshuffling yeast chromosomes with CRISPR/Cas9

Untangling the phenotypic impact of chromosomal rearrangements from the contribution of the genetic background requires versatile procedures to generate structural variations. We developed a CRISPR/Cas9-based method to efficiently reshuffle the yeast genome in a scarless and markerless manner.

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MinION nanopore sequencing identifies the position and structure of bacterial antibiotic resistance determinants in a multidrug-resistant strain of enteroaggregative Escherichia coli

The aim of this study was to use single-molecule nanopore sequencing to explore the genomic environment of the resistance determinants in a multidrug-resistant (MDR) strain of enteroaggregative Escherichia coli serotype O51 : H30, sequence type (ST) 38.

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Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies

Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation.

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Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus

Third-generation sequencing is an emerging technology that is capable of solving several problems that earlier approaches were not able to, including the identification of transcripts isoforms and overlapping transcripts.

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An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging.

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Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; ‘tsRNA’) or cis-backsplicing (circular RNA; ‘circRNA’).

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Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO

In order to strengthen the current genetically modified organism (GMO) detection system for unauthorized GMO, we have recently developed a new workflow based on DNA walking to amplify unknown sequences surrounding a known DNA region.

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Genomic insights into Candidatus Amarolinea aalborgensis gen. nov., sp. nov., associated with settleability problems in wastewater treatment plants

Settleability of particles in activated sludge systems can be impaired by an overgrowth of filamentous bacteria, a problem known as bulking. These filaments are often members of the phylum Chloroflexi, sometimes reaching abundances in excess of 30% of the biovolume.

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Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems

Urban sewer systems consist of wastewater and stormwater sewers, of which only wastewater is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting in untreated wastewater entering natural water bodies via the stormwater system.

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Long-Read Sequencing Revealed an Extensive Transcript Complexity in Herpesviruses

Long-read sequencing (LRS) techniques are very recent advancements, but they have already been used for transcriptome research in all of the three subfamilies of herpesviruses. These techniques have multiplied the number of known transcripts in each of the examined viruses.

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Xdrop: targeted sequencing of long DNA molecules from low input samples using droplet sorting

Long-read sequencing can resolve regions of the genome that are inaccessible to short reads, and therefore such technologies are ideal for genome-gap closure, solving structural rearrangements and sequencing through repetitive elements.

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Human-Specific Abnormal Alternative Splicing of Wild-Type PKD1 Induces Premature Termination of Polycystin-1

Background The major form of autosomal dominant polycystic kidney disease is caused by heterozygous mutations in PKD1, the gene that encodes polycystin-1 (PC1).

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Single-cell isoform RNA sequencing (ScISOr-Seq) across thousands of cells reveals isoforms of cerebellar cell types.

Full-length RNA sequencing (RNA-Seq) has been applied to bulk tissue, cell lines and sorted cells to characterize transcriptomes, but applying this technology to single cells has proven to be difficult, with less than ten single-cell transcriptomes having been analyzed thus far.

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Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

While splicing changes caused by somatic mutations in SF3B1 are known, identifying full-length isoform changes may better elucidate the functional consequences of these mutations.

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MinION rapid sequencing: Review of potential applications in neurosurgery

Background: Gene sequencing has played an integral role in the advancement and understanding of disease pathology and treatment.

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Lineage calling can identify antibiotic resistant clones within minutes

Surveillance of circulating drug resistant bacteria is essential for healthcare providers to deliver effective empiric antibiotic therapy. However, the results of surveillance may not be available on a timescale that is optimal for guiding patient treatment.

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Utilization of Hybrid Assembly Approach to Determine the Genome of an Opportunistic Pathogenic Fungus, Candida albicans TIMM 1768

Candida albicans TIMM1768 is a highly virulent strain utilized as a model organism for the study of gastrointestinal and oral candidiasis.

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Exploring the fate of mRNA in aging seeds: protection, destruction, or slow decay?

Seeds exist in the vulnerable state of being unable to repair the chemical degradation all organisms suffer, which slowly ages seeds and eventually results in death.

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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird

Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research.

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Structural, Physiological and Regulatory Analysis of Maltose Transporter Genes in Saccharomyces eubayanus CBS 12357T

Saccharomyces pastorianus lager brewing yeasts are domesticated hybrids of Saccharomyces cerevisiae and cold-tolerant Saccharomyces eubayanus.

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Rapid whole-genome based typing and surveillance of avipoxviruses using nanopore sequencing

Avian pox is an infectious disease caused by avipoxviruses (APV), resulting in cutaneous and/or tracheal lesions. Poxviruses share large genome sizes (from 130 to 360 kb), featuring repetitions, deletions or insertions as a result of a long-term recombination history.

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Rapid and sensitive virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease viruses (NDV), the causative agent of ND.

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Completing bacterial genome assemblies with multiplex MinION sequencing

Illumina sequencing platforms have enabled widespread bacterial whole genome sequencing. While Illumina data is appropriate for many analyses, its short read length limits its ability to resolve genomic structure.

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Streptomyces spp. From Ethiopia Producing Antimicrobial Compounds: Characterization via Bioassays, Genome Analyses, and Mass Spectrometry

A total of 416 actinomycete cultures were isolated from various unique environments in Ethiopia and tested for bioactivity. Six isolates with pronounced antimicrobial activity were chosen for taxonomic identification and further investigation.

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New tools for diet analyses: nanopore sequencing of metagenomic DNA from stomach contents to quantify diet in an invasive population of rats

Introduced species of mammals in New Zealand have had catastrophic effects on populations of diverse native species.

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Long-read metagenomics reveals cryptic and abundant marine viruses

Marine bacteriophages impact global biogeochemical cycles via their influence on host community structure and function, yet our understanding of viral ecology is constrained by limitations in culturing of important hosts and the lack of a 'universal' gene to facilitate community surveys.

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Selective single molecule sequencing and assembly of a human Y chromosome of African origin

Mammalian Y chromosomes are often neglected from genomic analysis. Due to their inherent assembly difficulties, high repeat content, and large ampliconic regions, only a handful of species have their Y chromosome properly characterized.

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Real time portable genome sequencing for global food security

The United Nations has listed Zero Hunger as one of the 17 global sustainable development goals to end extreme poverty by 2030. Plant viruses are a major constraint to crop production globally causing an estimated $30 billion in damage leaving millions of people food insecure.

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Recent Asian origin of chytrid fungi causing global amphibian declines

Globalized infectious diseases are causing species declines worldwide, but their source often remains elusive.

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Paternally inherited cis-regulatory structural variants are associated with autism

The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD.

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Genomic and epidemiological monitoring of yellow fever virus transmission potential

The yellow fever virus (YFV) epidemic that began in Dec 2016 in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes sp. vectors highlights the urgent need to monitor the risk of re-establishment of domestic YFV transmission in the Americas.

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Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A.

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Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy

Epilepsy is a common neurological disorder, and mutations in genes encoding ion channels or neurotransmitter receptors are frequent causes of monogenic forms of epilepsy.

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Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

Generating a complete, de novo genome assembly for prokaryotes is often considered a solved problem. However, we here show that Pseudomonas koreensis P19E3 harbors multiple, near identical repeat pairs up to 70 kilobase pairs in length.

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Direct RNA sequencing of the coding complete Influenza A virus genome

For the first time, a complete genome of an RNA virus has been sequenced in its original form. Previously, RNA was sequenced by the chemical degradation of radiolabelled RNA, a difficult method that produced only short sequences.

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A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra)

The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence.

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Selection of Potential Therapeutic Bacteriophages that Lyse a CTX-M-15 Extended Spectrum β-Lactamase Producing Salmonella enterica Serovar Typhi Strain from the Democratic Republic of the Congo

Recently, a Salmonella Typhi isolate producing CTX-M-15 extended spectrum β-lactamase (ESBL) and with decreased ciprofloxacin susceptibility was isolated in the Democratic Republic of the Congo.

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Harnessing the MinION: An example of how to establish long‐read sequencing in a laboratory using challenging plant tissue from Eucalyptus pauciflora

Long‐read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high‐quality, high‐molecular‐weight (HMW) DNA from the organisms of interest.

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Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies

Pseudomonas baetica strain a390T is the type strain of this recently described species and here we present its high-contiguity draft genome. To celebrate the 16th International Conference on Pseudomonas, the genome of P.

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Enhancer hubs and loop collisions identified from single-allele topologies

Chromatin folding contributes to the regulation of genomic processes such as gene activity.

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Rapid preimplantation genetic screening (PGS) using a handheld, nanopore-based, DNA sequencer

Objective: To determine if a handheld, nanopore-based DNA sequencer can be used for rapid preimplantation genetic screening (PGS).

Design: Retrospective study. Setting: Academic medical center.

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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools.

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Rapid low-cost assembly of the Drosophila melanogaster reference genome using low-coverage, long-read sequencing

Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes.

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A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions

A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required.

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Nanopore sequencing and assembly of a human genome with ultra-long reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced.

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A MinION™‐based pipeline for fast and cost‐effective DNA barcoding

DNA barcodes are useful for species discovery and species identification, but obtaining barcodes currently requires a well‐equipped molecular laboratory and is time‐consuming, and/or expensive.

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Highly parallel direct RNA sequencing on an array of nanopores

Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms.

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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected

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Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer.

OBJECTIVE: Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak.

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Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

Poxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci.

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Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris

Background: Candida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C.

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Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for personalized monitoring of residual disease in chronic myeloid leukemia patients

For monitoring minimal residual disease (MRD) in chronic myeloid leukemia (CML) the most recommended method is quantitative RT-PCR (RT-qPCR) for measuring BCR-ABL1 transcripts.

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NanoPack: visualizing and processing long read sequencing data

Summary
Here we describe NanoPack, a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.

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Barcoding analysis of HIV drug resistance mutations using Oxford Nanopore MinION (ONT) sequencing

Determination of HIV drug resistance (HIVDR) is becoming an integral baseline HIV evaluation for newly infected subjects, as the level of pre-treatment resistance is increasing worldwide.

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Mitochondrial heteroplasmy is responsible for Atovaquone drug resistance in Plasmodium falciparum

Malaria is the most significant parasitic disease affecting humans, with 212 million cases and 429,000 deaths in 20151, and resistance to existing drugs endangers the global malaria elimination campaign. Atovaquone (ATO) is a safe and potent antimalarial drug that acts on cytochrome b (cyt.

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First de novo draft genome sequence of Oryza coarctata, the only halophytic species in the genus Oryza

Oryza coarctata plants, collected from Sundarban delta of West Bengal, India, have been used in the present study to generate draft genome sequences, employing the hybrid genome assembly with Illumina reads and third generation Oxford Nanopore sequencing technology.

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Oxford Nanopore sequencing in a research-based undergraduate course

Background: Nanopore sequencing is a third generation genomic sequencing method that offers real time sequencing of DNA samples.

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Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer*

Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak.

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Picky comprehensively detects high-resolution structural variants in nanopore long reads

Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data.

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Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates

Recent advances in nanopore sequencing technology have led to a substantial increase in throughput and sequence quality. Together, these improvements may permit real-time benchtop genomic sequencing and antimicrobial resistance gene detection in clinical isolates.
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Nanopore Long-Read Guided Complete Genome Assembly of Hydrogenophaga intermedia,

... and Genomic Insights into 4-Aminobenzenesulfonate, p-Aminobenzoic Acid and Hydrogen Metabolism in the Genus Hydrogenophaga.

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First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans)

Here we describe the sequencing and assembly of the pathogenic fungus Lomentospora prolificans using a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads.

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Profiling bacterial communities by MinION sequencing of ribosomal operons

Note: the chemistry used in this paper has since been superseded.

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A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer

Background

A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination.

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Real-time DNA barcoding in a remote rainforest using nanopore sequencing

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet.

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The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides

Bacteroides spp. are dominant components of the phylum Bacteroidetes in the gut microbiota and prosper in glycan enriched environments.

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npInv: accurate detection and genotyping of inversions using long read sub-alignment

Background
Detection of genomic inversions remains challenging. Many existing methods primarily target inversions with a non repetitive breakpoint, leaving inverted repeat (IR) mediated non-allelic homologous recombination (NAHR) inversions largely unexplored.

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Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability.

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Nanopore sequencing enables near-complete de novo assembly of Saccharomyces cerevisiae reference strain CEN.PK113-7D

The haploid Saccharomyces cerevisiae strain CEN.PK113-7D is a popular model system for metabolic engineering and systems biology research. Current genome assemblies are based on short-read sequencing data scaffolded based on homology to strain S288C.

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Linear assembly of a human centromere on the Y chromosome

The human genome reference sequence remains incomplete owing to the challenge of assembling long tracts of near-identical tandem repeats in centromeres.

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Comparative analysis of targeted long read sequencing approaches for characterization of a plant’s immune receptor repertoire

Background

The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments.

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Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology

Note: this publication uses R7 chemistry, which has since been superseded with R9 series.

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Efficient data structures for mobile de novo genome assembly by third-generation sequencing

Mobile/portable (third-generation) sequencing technologies, including Oxford Nanopore’s MinION and SmidgION, are revolutionizing once again –after the advent of high-throughput sequencing– biomedical sciences.

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Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

Dissemination of carbapenem resistance among pathogenic Gram-negative bacteria is a looming medical emergency. Efficient spread of resistance within and between bacterial species is facilitated by mobile genetic elements.

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Mutational analysis in BCR-ABL1 positive leukemia by deep sequencing based on nanopore MinION technology

We report a third-generation sequencing assay on nanopore technology (MinION) for detecting BCR-ABL1 KD mutations and compare the results to a Sanger sequencing(SS)-based test in 24 Philadelphia-positive (Ph +) leukemia cases.

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De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long sequencing reads with average fragment lengths of over 10,000 base-pairs and maximum lengths reaching 100,000 base- pairs.

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Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

Subtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC content. Sequencing these repetitive regions is challenging, even with recent improvements in sequencing technologies.

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Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing

Molecular classification of cancer has entered clinical routine to inform diagnosis, prognosis, and treatment decisions. At the same time, new tumor entities have been identified that cannot be defined histologically.

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Serotyping dengue virus with isothermal amplification and a portable sequencer

The recent development of a nanopore-type portable DNA sequencer has changed the way we think about DNA sequencing. We can perform sequencing directly in the field, where we collect the samples.

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High-quality de novo genome assembly of the Dekkera bruxellensis yeast using Nanopore MinION sequencing

Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship.

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Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

Background: The miniaturised and portable DNA sequencer MinIONTM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, human genome variability, and microbial diversity

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Resolving plasmid structures in Enterobacteriaceae using the MinION nanopore sequencer: assessment of MinION and MinION/Illumina hybrid data assembly approaches

This study aimed to assess the feasibility of using the Oxford Nanopore Technologies (ONT) MinION long-read sequencer in reconstructing fully closed plasmid sequences from eight Enterobacteriaceae isolates of six different species with plasmid populations of varying complexity.

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De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing

Background: The introduction of the MinIONTM sequencing device by Oxford Nanopore Technologies may greatly accelerate whole genome sequencing.

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Nanopore sequencing and assembly of a human genome with ultra-long sequence reads

We report the sequencing and assembly of a reference genome for the human GM12878 Utah/Ceph cell line using the MinION (Oxford Nanopore Technologies) nanopore sequencer. 91.2 Gb of sequence data, representing ∼30× theoretical coverage, were produced.

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Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single cell level.

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Fast and sensitive mapping of nanopore sequencing reads using GraphMap

Realizing the democratic promise of nanopore sequencing requires the development of new bioinformatics approaches to deal with its specific error characteristics.

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Detecting DNA cytosine methylation using nanopore sequencing

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer.

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Cas9-Assisted Targeting of CHromosome segments (CATCH) for targeted nanopore sequencing and optical genome mapping

Variations in the genetic code, from single point mutations to large structural or copy number alterations, influence susceptibility, onset, and progression of genetic diseases and tumor transformation.

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The use of Oxford Nanopore native barcoding for complete genome assembly

The Oxford Nanopore Technologies MinIONTM is a mobile DNA sequencer that can produce long read sequences with a short turn-around time.

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Rapid de novo assembly of the European eel genome from nanopore sequencing reads

We have sequenced the genome of the endangered European eel using the MinION by Oxford Nanopore, and assembled these data using a novel algorithm specifically designed for large eukaryotic genomes. For this 860 Mbp genome, the entire computational process takes two days on a single CPU.

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A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly.

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Annotated mitochondrial genome with Nanopore R9 signal for Nippostrongylus brasiliensis

Nippostrongylus brasiliensis, a nematode parasite of rodents, has a parasitic life cycle that is an extremely useful model for the study of human hookworm infection, particularly in regards to the induced immune response.

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Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization

In this manuscript we evaluate the potential for microbiome characterization by sequencing of near-full length 16S rRNA gene region fragments using the Oxford Nanopore MinION (hereafter Nanopore) sequencing platform. We analyzed pure-culture E. coli and P.

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MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome

Advances in long-read single molecule sequencing have opened new possibilities for ‘benchtop’ whole-genome sequencing. The Oxford Nanopore Technologies MinION is a portable device that uses nanopore technology that can directly sequence DNA molecules.

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NA12878 Human Reference on Oxford Nanopore MinION

We have sequenced the CEPH1463 (NA12878/GM12878, Ceph/Utah pedigree) human genome reference standard on the Oxford Nanopore MinION using 1D ligation kits (450 bp/s) using R9.4 chemistry (FLO-MIN106).

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Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

Routine full characterization of Mycobacterium tuberculosis (TB) is culture-based, taking many weeks.

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Sequencing the gigabase plant genome of the wild tomato species Solanum pennellii using Oxford Nanopore single molecule sequencing

Recent updates in Oxford Nanopore technology (R9.4) have made it possible to obtain GBases of sequence data from a single flowcell.

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The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community

Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens.

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Hybrid assembly pipeline released (using Canu, racon and Pilon)

The long sequencing reads produced by Oxford Nanopore’s platforms enable the assembly of genomes with superior contiguity compared to those produced by second generation technologies.

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The megabase-sized fungal genome of Rhizoctonia solani assembled from nanopore reads only.

The ability to quickly obtain accurate genome sequences of eukaryotic pathogens at low costs provides a tremendous opportunity to identify novel targets for therapeutics, develop pesticides with increased target specificity and breed for resistance in food crops.

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Using MinION nanopore sequencing to generate a de novo eukaryotic draft genome: preliminary physiological and genomic description of the extremophilic red alga Galdieria sulphuraria strain SAG 107.79

Reported here is the de novo assembly of a eukaryotic genome using only MinION nanopore DNA sequence data by examining a novel Galdieria sulphuraria genome: strain SAG 107.79.

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In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third Golden Age.

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Enrichment by hybridisation of long DNA fragments for Nanopore sequencing

Enrichment of DNA by hybridisation is an important tool which enables users to gather target-focused next-generation sequence data in an economical fashion.

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Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches.

Background

Improved DNA sequencing methods have transformed the field of genomics over the last decade.

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Rapid resistome mapping using nanopore sequencing

The emergence of antibiotic resistance in human pathogens has become a major threat to modern medicine and in particular hospitalized patients.

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Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry.

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BWA and LAST have been tuned to work with nanopore reads

Burrow-Wheeler Aligner (BWA) for pairwise alignment between DNA sequences. BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM.

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NanoOk – Flexible, multi-reference software for pre- and post-alignment analysis of nanopore sequencing data, quality and error profiles

The recent launch of the Oxford Nanopore Technologies MinION Access Program (MAP) resulted in the rapid development of a number of open source tools aimed at extracting reads and yield information from the HDF5 format files produced by the platform.

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Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

To assess the performance of the Oxford Nanopore Technologies MinION sequencing platform, cDNAs from the External RNA Controls Consortium (ERCC) RNA Spike-In mix were sequenced. This mix mimics mammalian mRNA species and consists of 92 polyadenylated transcripts with known concentration.

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Sequencing ultra-long DNA molecules with the Oxford Nanopore MinION

Oxford Nanopore Technologies’ nanopore sequencing device, the MinION, holds the promise of sequencing ultra-long DNA fragments >100kb. An obstacle to realizing this promise is delivering ultra-long DNA molecules to the nanopores.

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A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes.

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What’s in my pot? Real-time species identification on the MinION

Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows.

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nanopolish – nanopore sequence analysis and genome assembly software

Jared Simpson, University of Toronto

Release Date: 04-Sept-2015

A nanopore consensus algorithm using a signal-level hidden Markov model.

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Real-time selective sequencing on the MinION

The MinION replaces the conventional model of "sequence followed by analysis to final result" with instant access to data before the completion of a sequencing run. This instant access extends to the analysis of sequence "squiggle" data even before a read has finished traversing the nanopore.

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Progress at UC Santa Cruz: Long DNA fragments, tRNA and Modified Bases

Nanopore strand sequencing is uniquely suited to analysis of long DNA fragments and base modifications. In this presentation, we will discuss recent experiments that demonstrate 99% consensus accuracy for 150kb+ DNA fragments in single MinION runs.

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MinION sequencing of malaria parasites

The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate.

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Nanopore sequencing for metagenomic diagnosis of infectious diseases

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times.

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Real-time nanopore sequencing and analysis of plant genomes in a tent in Snowdonia National Park

Joe Parker from Royal Botanic Gardens, Kew gives a talk at London Calling 2016 on how he used the MinION to analyse plant genomes in a tent in the middle of Snowdonia National Park.

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Genome sequencing a comprehensive communicable diseases solution in the making

Derrick Crook from University of Oxford gives a talk at London Calling 2016.

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A novel approach to elucidate the genomic structure of plants and pathogens

Alexander Wittenberg from KeyGene gives a talk at London Calling 2016.

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The Mystery of the Pink Lake

London Calling talk: The eXtreme Microbiome Project (XMP) Presents: The Mystery of the Pink Lake | Ken McGrath, Australian Genome Research Facility.

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Determining Exon Connectivity by Nanopore Sequencing

Short-read high-throughput DNA sequencing, though powerful, is limited in its ability to directly measure exon connectivity in mRNAs that contain multiple alternative exons located farther apart than the maximum read length.

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Fast and Sensitive Mapping of Nanopore Sequencing Reads with GraphMap

A presentation to the MinION Community by Professor Niranjan Nagarajan, Associate Director and Group Leader, Genome Institute of Singapore, and Adjunct Associate Professor in the Department of Computer Science, National University of Singapore.

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Oxford Nanopore MinION Applications: Kits and Tools, Genetics and Metagenomics

The Applications team at Oxford Nanopore has two overarching responsibilities: creation and development of sample and library preparation protocols for a wide variety of sample types, and undertaking biological projects which highlight the various strengths of Oxford Nanopore’s technology.

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Applications of Long-read Sequencing in Infectious Disease Genomics

Next generation sequencing technology has revolutionised the study of microbial genomics, but most large-scale studies have focused on short-read sequencing. This use of short-read sequencing has limitations however.

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Alignment, error correction and assembly of a eukaryote genome

Here we present our experiences working with MinION device. We discuss the performance, tools and algorithms available for downstream analysis; including alignment methods and parameters. Our interest in the MinION device is its ability to generate long reads for complex genome assembly.

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Sequence capture on the MinION

A presentation at London Calling 2015 by Daniel Fordham.

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Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores.

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De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging.

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Scaffolding and Completing Genome Assemblies in Real-time with Nanopore Sequencing

Genome assemblies obtained from short read sequencing technologies are often fragmented into many contigs because of the abundance of repetitive sequences.

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Clonal expansion of Escherichia coli ST38 carrying chromosomally-integrated OXA-48 carbapenemase gene

Many isolates of Escherichia coli carrying blaOXA-48 referred to Public Health England’s national reference laboratory during 2014 and 2015 shared similar pulsed-field gel electrophoresis (PFGE) profiles, despite coming from patients in multiple hospitals and regions.

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HPG pore: an efficient and scalable framework for nanopore sequencing data

The use of nanopore technologies is expected to spread in the future because they are portable and can sequence long fragments of DNA molecules without prior amplification.

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Nanopore sequencing detects structural variants in cancer

Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect due to the short read length (<300bp) of 2nd generation sequencing.

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Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions.

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Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance.

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Snake venom gland cDNA sequencing using the Oxford Nanopore MinION portable DNA sequencer

Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field.

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Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads

Motivation
Recent emergence of nanopore sequencing technology set a challenge for established assembly methods. In this work, we assessed how existing hybrid and non-hybrid de novo assembly methods perform on long and error prone nanopore reads.

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MinION Analysis and Reference Consortium: Phase 1 data release and analysis

The advent of a miniaturised DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools.

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Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades.

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MinION™ allied with 3D printed iChip – a workflow designed to let anyone discover new bacterial species in days

In this study, we adapt a protocol for the growth of previously uncultured environmental bacterial isolates, to make it compatible with whole genome sequencing.

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Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment

Noninvasive prenatal testing (NIPT) by maternal plasma DNA sequencing is now clinically available for screening fetal chromosomal aneuploidies; these tests have close to 99% sensitivity..

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LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

Owing to the complexity of the assembly problem, we do not yet have complete genome sequences.

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Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

Genome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce the delay between pathogen sampling and data generation is single molecule sequencing.

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A complete bacterial genome assembled de novo using only nanopore sequencing data

We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data.

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Nanopore sequencing for detection of pharmacogenomic variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information.

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An epidemiological river metagenome based on MinION

River waters worldwide are impacted by disease-causing agents including bacteria, protists, flatworms, viruses, and harmful algae that derive from domestic sewage and farm runoff, and/or are emergent due to nutrient pollution and climate change.

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Genome assembly using Nanopore-guided long and error-free DNA reads

Long-read sequencing technologies were launched a few years ago, and in contrast with short-read sequencing technologies, they offered a promise of solving assembly problems for large and complex genomes. Moreover by providing long-range information, it could also solve haplotype phasing.

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Successful test launch for nanopore sequencing

Nanopore sequencing gets a boost with accurate error modelling and variant-calling tools for Oxford Nanopore Technology’s highly anticipated MinION platform.

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Assessing the performance of the Oxford Nanopore Technologies MinION

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it.

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Improved data analysis for the MinION nanopore sequencer

Speed, single-base sensitivity and long read lengths make nanopores a promising technology for high-throughput sequencing.

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Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short sequence reads that are often unable to resolve haplotype information.

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nanoCORR – error correction tool for nanopore sequence data

Sara Goodwin and James Gurtowski at Cold Spring Harbor Laboratory have created error correction software for Oxford Nanopore data

Release Date: 24-Aug-2015

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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes.

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Think Small: Nanopores for Sensing and Synthesis

It is now possible to manipulate individual molecules using a nanopore to read DNA and proteins, or write DNA by inserting mini-genes into cells.

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Poretools: a toolkit for analyzing nanopore sequence data

Motivation: Nanopore sequencing may be the next disruptive technology in genomics, due to its ability to detect single DNA molecules without prior amplification, lack of reliance on expensive optical components, and the ability to sequence very long fragments.

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