PDF(Pubmed)
Abstract：
Limiting harm to organisms caused by genetic sampling is an important consideration for rare species, and a number of non-destructive sampling techniques have been developed to address this issue in freshwater mussels. Two methods, visceral swabbing and tissue biopsies, have proven to be effective for DNA sampling, though it is unclear as to which method is preferable for genotyping-by-sequencing (GBS). Tissue biopsies may cause undue stress and damage to organisms, while visceral swabbing potentially reduces the chance of such harm. Our study compared the efficacy of these two DNA sampling methods for generating GBS data for the unionid freshwater mussel, the Texas pigtoe (Fusconaia askewi). Our results find both methods generate quality sequence data, though some considerations are in order. Tissue biopsies produced significantly higher DNA concentrations and larger numbers of reads when compared with swabs, though there was no significant association between starting DNA concentration and number of reads generated. Swabbing produced greater sequence depth (more reads per sequence), while tissue biopsies revealed greater coverage across the genome (at lower sequence depth). Patterns of genomic variation as characterized in principal component analyses were similar regardless of the sampling method, suggesting that the less invasive swabbing is a viable option for producing quality GBS data in these organisms.
摘要：
限制基因取样对生物造成的危害是稀有物种的重要考虑因素，并且已经开发了许多无损采样技术来解决淡水贻贝的这一问题。两种方法,内脏擦拭和组织活检，已经证明对DNA取样是有效的，尽管尚不清楚哪种方法更适合测序基因分型（GBS）。组织活检可能会对生物体造成过度的压力和损害，而内脏擦拭可能会减少这种伤害的机会。我们的研究比较了这两种DNA采样方法在生成unionid淡水贻贝GBS数据中的功效，德州猪头（Fusconaiaaskewi）。我们的结果发现两种方法都能产生质量序列数据，虽然有些考虑是有序的。与拭子相比，组织活检产生了更高的DNA浓度和更多的读数，尽管起始DNA浓度和产生的读数数量之间没有显着关联。擦拭产生更大的序列深度（每个序列更多的读段），而组织活检显示整个基因组的覆盖率更高（在较低的序列深度）。无论采样方法如何，主成分分析中表征的基因组变异模式都是相似的，这表明侵入性较小的拭子是在这些生物体中产生高质量GBS数据的可行选择。
