PDF(Pubmed)
Abstract：
Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.
摘要：
尽管基因组测序和生物信息学取得了进展，保守基因组学仍然经常受到对非侵入性样本的依赖的阻碍。外源DNA的存在以及非侵入性样本中DNA的数量少、质量差一直是测序的障碍,从而限制了濒危物种基因组监测的潜力。最近的分子进展，如宿主DNA富集，有希望促进从非侵入性样品测序。我们使用FecalSeq方法富集了从野生收集的新英格兰棉尾粪便颗粒中提取的DNA，并从3RAD测序中鉴定了SNP。我们从兔颗粒中获得了SNP，包括在恶劣环境条件下收集的颗粒和微卫星表现不佳的样品。测序成功的测量随着更大量的起始DNA而改善,并且32%的样品产生通过质量控制过滤的SNP基因型。基因分型错误率很高，然而,该方法无法始终如一地区分独特的个体或匹配的基因型，虽然适合恢复预期的人口结构。将FecalSeq富集与RADseq配对是一种有前途的低成本方法，用于在环境背景下使用非侵入性样品监测野生种群，但它可能更适合通过人口基因组学为保护提供信息。
