Whole genome sequences from non-invasively collected caribou faecal samples

Rebecca S. Taylor,Patrick Gagné,Bridget Redquest,Micheline Manseau,Paul J. Wilson,Sonesinh Keobouasone,Christine Martineau

doi:10.1007/s12686-021-01235-2

Rebecca S. Taylor, Patrick Gagné + Show 5 more

Open Access

https://doi.org/10.1007/s12686-021-01235-2

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Abstract

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 re-sequence high coverage whole genomes using standard laboratory techniques. We use wild collected faecal pellets collected from 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 due to differences in low quality and endogenous DNA content, affecting overall coverage. One of our faecal genomes was only re-sequenced at low coverage (1.6 ×), however the other three obtained between 7 and 15 ×, compared to 19 and 25 × for the tissue samples. We successfully re-sequenced high-quality whole genomes from faecal DNA and are one of the first to obtain genome-wide data from wildlife faecal DNA in a non-primate species. Our work represents an important advancement for non-invasive conservation genomics.

Highlights

Human induced global biodiversity loss, for example due to habitat destruction and/or climate change, is accelerating (Harrison et al 2014; McMahon et al 2014; Shafer et al 2015; Brandies et al 2019)
Multiple faecal samples from these locations had been genotyped at microsatellite loci and to select which faecal samples to re-extract for whole genome sequencing, we surveyed the raw genotype files and looked for those with the cleanest, highest peaks, to select those most likely to have the highest amounts of high-quality endogenous DNA
Results from the TapeStation analysis vary between individuals, the faecal samples show increased numbers of smaller fragment sizes (Supplementary Material S4 and S5 for full TapeStation and Fragment analyzer/Bioanalyzer results, respectively)

Summary

Introduction

Human induced global biodiversity loss, for example due to habitat destruction and/or climate change, is accelerating (Harrison et al 2014; McMahon et al 2014; Shafer et al 2015; Brandies et al 2019). For many threatened taxa obtaining high-quality samples can be difficult, advances in non-invasive genetics have been important for conservation initiatives as they allow the study of rare or elusive species without needing to handle, or sometimes even see, the target species (Smith and Wang 2014; Snyder-Mackler et al 2016; Ozga et al 2020). A recent study by Ozga et al (2020) tested different non-invasive samples from chimpanzees using both whole genome and exome capture methods, and found that urine had much higher success than faecal DNA, producing genome-wide data using the same extraction and sequencing methods as with high quality tissue samples (needing no extra methodological considerations). Urine is not always collected for many taxa, and the capture method still does not give unbiased whole genome coverage

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