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Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes


Armbrecht, L and Hallegraeff, G and Bolch, CJS and Woodward, C and Cooper, A, Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes, Scientific Reports, 11 Article 3220. ISSN 2045-2322 (2021) [Refereed Article]


Copyright Statement

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

DOI: doi:10.1038/s41598-021-82578-6


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 Details

Item Type:Refereed Article
Keywords:hybridisation capture, DNA analysis, marine sedimentary ancient DNA
Research Division:Biological Sciences
Research Group:Genetics
Research Field:Genomics
Objective Division:Environmental Management
Objective Group:Marine systems and management
Objective Field:Marine biodiversity
UTAS Author:Armbrecht, L (Dr Linda Armbrecht)
UTAS Author:Hallegraeff, G (Professor Gustaaf Hallegraeff)
UTAS Author:Bolch, CJS (Associate Professor Christopher Bolch)
ID Code:142874
Year Published:2021
Funding Support:Australian Research Council (DP170102261)
Web of Science® Times Cited:9
Deposited By:Directorate
Deposited On:2021-02-12
Last Modified:2021-09-30
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