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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 (up to 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
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)
- Resolve complex and repetitive genomic regions
- Generate high-quality de novo animal genomes and correct reference genomes
- Analyse long-range haplotypes and phasing, even with targeted sequencing approaches
- Annotate animal genomes using full-length transcripts
- Get isoform-level transcriptome characterisation and quantification
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 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
Platform costs and infrastructure requirements can limit global accessibility. Sample batching may also be required for optimal efficiency, potentially delaying results.
Real-time data streaming
- Get immediate access to results for time critical applications such as pathogen identification
- 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.
Typically, lengthy sample preparation requirements and long sequencing run times, reducing workflow efficiency.
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 animal conservation and management.
Get more animal sequencing content, including getting started guides, workflows, and videos, in our Resource centre.
Understanding the genetic differences between humans and chimpanzees
Chimpanzee and human genomes differ by just 1.2% if only single nucleotide variants (SNVs) are considered; however, when also accounting for structural variants (SVs), there is a >5% difference — indicating the importance of SVs in trait divergence. Using long nanopore sequencing reads, along with other genome analysis technologies, researchers at University of California, Davis, USA, have generated ‘the most contiguous chimpanzee assembly to date’.
'We identified 209 chimpanzee-specific deletions and 18 chimpanzee-specific inversions, that were impacting 56 protein encoding genes'Daniela Soto, University of California, Davis, US
Scalable sequencing for animal research
From powerful, portable Flongle and MinION devices to the high-throughput benchtop GridION and PromethION platforms — scale your sequencing to match your specific research requirements.
Our most powerful platform, offering flexible, high-throughput sequencing using up to 48 independent, high-capacity flow cells — complete genomic and transcriptomic characterisation, ideal for large animal genome sequencing projects.View product
From genome assembly to gene expression, run multiple experiments on-demand using 5 independent MinION Flow Cells — perfect for busy labs running multiple projects.View product
Access the benefits of nanopore technology from just $1,000 — suitable for small animal genomes, targeted sequencing, and gene expression studies.View product
Integrated sequencing and analysis in a powerful handheld device — suitable for small animal genomes, targeted sequencing, and gene expression studies.View products
Adapting MinION and GridION for smaller, routine tests and analyses. Low plex targeted sequencing, RNA isoform analysis, and quality control applications.View product
Automated sample extraction and library preparation.View product