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Animal sequencing

Animal genomics provides valuable insights into many scientific research areas — from the use of model organisms to study human disease, through to animal health, breeding, conservation, and evolution. Long nanopore sequencing reads (>4 Mb), provide novel and cost-effective insights into animal genomes, transcriptomes, and microbiomes, through the accurate resolution of complex genomic regions, haplotypes, and full-length transcripts. Direct sequencing of native DNA or RNA further allows simultaneous identification of base modifications (e.g. methylation) alongside nucleotide sequence.

Assembling the largest animal genome to date — the 43 Gb lungfish genome

Read the paper
To overcome the challenges of sequencing and assembling the even-larger genomes of lungfish, we used long- and ultra-long-read nanopore technology... Meyer, A. et al. Nature 590 (2021)

Oxford Nanopore sequencing

Traditional short-read technologies

Unrestricted read length (>4 Mb achieved) Long-read sequencing

Read length typically 50–300 bp

Short reads do not typically span entire regions of interest, including repeats and structural variants, or full-length RNA transcripts, resulting in fragmented assemblies and ambiguous transcript isoform identification.

Direct, amplification-free protocols Amplification-free sequencing

Amplification required

Amplification can introduce bias — reducing uniformity of coverage with the potential for coverage gaps — and removes base modifications (e.g. methylation), necessitating additional sample prep, sequencing runs, and expense.

Flexible and on-demand Flexible, on-demand sequencing

  • Scale to your throughput needs
  • Sequence in the lab or field with portable Flongle and MinION
  • Tackle large animal genome projects with flexible, high-throughput GridION and PromethION devices
  • No sample batching required

Limited flexibility

Platform costs and infrastructure requirements can limit global accessibility, with no facility for sequencing samples in the field. Sample batching may also be required for optimal efficiency, potentially delaying results.

Real-time data streaming Immediate access to data

  • Get immediate access to results for time critical applications such as pathogen identification
  • Enrich targeted regions based on real-time sequence composition using adaptive sampling
  • Stop sequencing when sufficient data generated — wash and reuse flow cell
  • Use simple EPI2ME workflows for real-time microbiome analysis

Fixed run time with bulk data delivery

Increased time-to-result and inability to identify workflow errors until it’s too late, plus additional complexities of handing large volumes of bulk data.

Streamlined workflows Streamlined sequencing workflows

Laborious workflows

Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.

White paper

New insights into large genomes

From delineating complex genomic regions, such as repeats and structural variants, to simultaneous calling of methylated bases alongside nucleotide sequence, discover how nanopore sequencing is being used to generate enhanced, highly-contiguous animal genome assemblies. Specific case studies reveal how researchers are applying the benefits of long, real-time nanopore sequencing reads to a wide range of research areas, including solving a chromosome conundrum in the creeping vole that had puzzled researchers for over 60 years.

Get more animal sequencing content, including getting started guides, workflows, and videos, in our Resource centre.

Case study

Solving Ohno’s puzzle — resolving an ancient sex chromosome system

The cytogeneticist Susumu Ohno described the novel sex chromosome system of the creeping vole (Microtus oregoni) in the 1960s, in which females had an XO and the males had an XY karyotype; females contributed the X chromosome and males contributed either the Y chromosome or no sex chromosome at all. However, the mechanisms behind this remained a puzzle for almost 60 years. Couger et al. (2021) used the Oxford Nanopore Ultra-Long DNA Sequencing Kit to prepare libraries for sequencing on PromethION Flow Cells, then generated a whole-genome assembly from the ultra-long data the data, which also enabled SNP calling and phasing. With a read length N50 of 91 kb, these long sequencing reads were able to assemble the repeat-rich sex chromosomes and reveal a unique sex chromosome system whereby males have both maternal (XM) and paternal (XP) X chromosomes, with Xist-based silencing of the paternal copy, while females inherit just one X chromosome (XM) from the mother; thus solving a 60-year-old puzzle. 

Case study

Using nanopore ultra-long reads for highly accurate telomere-to-telomere assembly of the tammar wallaby genome

At the NCM2022, Patrick Grady (University of Connecticut, USA) presented his work using nanopore sequencing to create complete and phased telomere-to-telomere genome assemblies and epigenetic profiles for the tammar wallaby, Macropus eugenii. The new assemblies provided a significant improvement to the currently available genome data for this model organism and will provide insights into mammalian evolution.

From animal genome assembly to support disease models, breeding programmes, conservation, and evolutionary analysis, through to the analysis of animal pathogens, gene expression, and base modifications, find comprehensive information on our Investigations pages.

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Scalable sequencing for animal research

From powerful, portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION devices — scale your sequencing to match your specific research requirements.

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Graph demonstrating yield per device.

Recommended for animal genomics

PromethION 24

Combining up to 24 independently addressable, high-capacity flow cells with powerful, integrated compute, PromethION 24 delivers flexible, on-demand access to terabases of sequencing data — ideal for cost-effective, high-throughput sequencing of animal genomes, large animal genome sequencing projects, transcript-based genome annotation, and isoform-level transcriptomics.

PromethION 2 & 2 Solo

Offering two independently addressable PromethION Flow Cells for low-cost access to high-output sequencing — ideal for animal genome sequencing projects with smaller sample numbers. 

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PromethION 48

Our most powerful device, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells. Complete genomic & transcriptomic characterisation, ideal for large genome sequencing projects.

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From genome assembly to gene expression, run multiple experiments on-demand using 5 independent MinION Flow Cells — perfect for busy labs running multiple projects.

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Access the benefits of nanopore technology from just $1,000 — suitable for small animal genomes, targeted sequencing, and gene expression studies.

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Integrated sequencing and analysis in a powerful handheld device — suitable for small animal genomes, targeted sequencing, and gene expression studies.

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Adapting MinION and GridION for smaller, routine tests and analyses. Low plex targeted sequencing, RNA isoform analysis, and quality control applications.

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Automated sample extraction and library preparation.

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