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

Molecular Ecology Resources
Taylor M WilcoxMichael K Schwartz

Abstract

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 laboratory-generated, known-composition DNA mixtures. Capture enrichment resulted in detecting multiple species in both kinds of samples, and postcapture relative sequence abundance accurately reflected initial relative template abundance. However, further optimization is needed to permit reliable species detection at the very low-DNA quanti...Continue Reading

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Citations

Nov 21, 2019·Proceedings. Biological Sciences·Jori B HarrisonSean M Rogers
Jul 28, 2019·Molecular Ecology Resources·Peter Andreas SeeberAlex D Greenwood
Oct 30, 2019·Scientific Reports·Bettina ThalingerJosef Wanzenböck
Jan 30, 2020·Evolutionary Applications·Eva Egelyng SigsgaardPhilip Francis Thomsen
Nov 13, 2020·Molecular Ecology Resources·Mads Reinholdt JensenPhilip Francis Thomsen
Mar 27, 2021·Forensic Science International. Genetics·Erin M GordenCharla Marshall
Sep 29, 2021·Molecular Ecology Resources·Tomasz SuchanLudovic Orlando

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