Capture enrichment of aquatic environmental DNA: a first proof of concept

Environmental DNA (eDNA) sampling – the detection of genetic material in the environment to infer species presence – has rapidly grown as a tool for sampling aquatic animal communities. A potentially powerful feature of environmental sampling is that all taxa within the habitat shed DNA and so may be detectable, creating opportunity for whole-community assessments. However, animal DNA in the environment tends to be comparatively rare, making it necessary to enrich for genetic targets from focal taxa prior to sequencing. Current metabarcoding approaches for enrichment rely on bulk amplification using conserved primer annealing sites, which can result in skewed relative sequence abundance and failure to detect some taxa because of PCR bias. Here we test capture enrichment via hybridization as an alternative strategy for target enrichment using a series of experiments on environmental samples and lab-generated, known-composition DNA mixtures. Capture enrichment resulted in detecting multip...

环境DNA（Environmental DNA，eDNA）采样——即通过检测环境中的遗传物质以推断物种存在情况——近年来已迅速发展成为水生动物群落采样的重要工具。环境采样的一项极具应用潜力的特性在于，生境内的所有分类群均会脱落DNA，因此均可被检测到，这为全群落评估提供了可行路径。然而，环境中的动物DNA通常含量较低，因此在测序前需对目标分类群的遗传靶标进行富集。当前用于富集的宏条形码（metabarcoding）方法依赖于利用保守引物退火位点开展批量扩增，这可能会导致相对序列丰度偏倚，且因聚合酶链式反应（Polymerase Chain Reaction，PCR）偏差无法检测到部分分类群。本研究通过一系列针对环境样本与实验室构建的已知组成DNA混合物的实验，验证了杂交捕获富集法作为靶标富集替代策略的有效性。杂交捕获富集法成功检测到多...