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Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

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Armbrecht, L, Hallegraeff, G ORCID: 0000-0001-8464-7343, Bolch, CJS ORCID: 0000-0001-9047-2391, Woodward, C and Cooper, A 2021 , 'Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes' , Scientific Reports, vol. 11 , pp. 1-14 , doi: 10.1038/s41598-021-82578-6.

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Abstract

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Item Type: Article
Authors/Creators:Armbrecht, L and Hallegraeff, G and Bolch, CJS and Woodward, C and Cooper, A
Keywords: hybridisation capture, DNA analysis, marine sedimentary ancient DNA
Journal or Publication Title: Scientific Reports
Publisher: Nature Publishing Group
ISSN: 2045-2322
DOI / ID Number: 10.1038/s41598-021-82578-6
Copyright Information:

Copyright 2021 The Authors. This article is licensed under a Creative Commons Attribution 4.0 International License

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