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.

保护基因组学是在当前生物多样性丧失的情况下管理受威胁物种的重要工具。测序技术的最新进展意味着我们现在可以使用全基因组以前所未有的细节研究人口历史、当地适应、近亲繁殖等。然而，对于许多稀有和难以捉摸的物种，只能获得粪便等非侵入性样本，因此很难利用全基因组数据。我们提出了一种从粪便样本的粘膜层中提取 DNA 的方法，以使用标准实验室技术对高覆盖度的全基因组进行重新测序。我们使用从驯鹿 ( Rangifer tarandus)，该物种在加拿大分布范围的许多部分都在减少，并受到综合保护和种群监测措施的约束。我们将四个粪便基因组与在同一运行中测序的两个组织基因组进行比较。粪便和组织样本之间的质量指标相似，主要区别在于原始读数与参考基因组的比对成功，因为低质量和内源性 DNA 含量的差异影响了整体覆盖率。我们的粪便基因组之一仅在低覆盖率 (1.6 ×) 下重新测序，但其他三个在 7 至 15 × 之间获得，而组织样本为 19 和 25 ×。我们成功地从粪便 DNA 中重新测序了高质量的全基因组，并且是最早从非灵长类物种的野生动物粪便 DNA 中获得全基因组数据的公司之一。