Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

L. Armbrecht, G. Hallegraeff, C. J.S. Bolch, C. Woodward, A. Cooper

Research output: Contribution to journalArticlepeer-review

34 Citations (Scopus)
24 Downloads (Pure)


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.
Original languageEnglish
Article number3220
Pages (from-to)1-14
Number of pages14
JournalScientific Reports
Early online dateFeb 2021
Publication statusPublished - Dec 2021


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