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Whole genome sequences from non-invasively collected samples
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  • Rebecca Taylor,
  • Micheline Manseau,
  • Bridget Redquest,
  • Paul Wilson
Rebecca Taylor
Trent University Department of Biology

Corresponding Author:[email protected]

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Micheline Manseau
Environment and Climate Change Canada National Wildlife Research Centre
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Bridget Redquest
Trent University Department of Biology
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Paul Wilson
Trent University, Trent University Department of Biology
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Conservation genomics is an important tool to manage threatened species under current biodiversity loss. Recent advances in sequencing technology mean that we can now use whole genomes to investigate demographic history, local adaptation, inbreeding, and more in unprecedented detail. However, for many rare and elusive species only non-invasive samples such as faeces can be obtained, making it difficult to take advantage of whole genome data. We present a method to extract DNA from the mucosal layer of faecal samples to reconstruct high coverage whole genomes using standard laboratory techniques, therefore in a cost-effective and efficient way. We use wild collected faecal pellets collected from wild caribou (Rangifer tarandus), a species undergoing declines in many parts of its range in Canada and subject to comprehensive conservation and population monitoring measures. We compare four faecal genomes to two tissue genomes sequenced in the same run. Quality metrics were similar between faecal and tissue samples with the main difference being the alignment success of raw reads to the reference genome likely due to differences in endogenous DNA content, affecting overall coverage. One of our faecal genomes was only reconstructed at low coverage (1.6X), however the other three obtained between 7 and 15X, compared to 19 and 25X for the tissue samples. We successfully reconstructed high-quality whole genomes from faecal DNA and, to our knowledge, are the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species, representing an important advancement for non-invasive conservation genomics.
10 Apr 2020Submitted to Molecular Ecology Resources
28 Apr 2020Submission Checks Completed
28 Apr 2020Assigned to Editor
01 May 2020Reviewer(s) Assigned
29 May 2020Review(s) Completed, Editorial Evaluation Pending