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Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes
Citation
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]
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DOI: doi:10.1038/s41598-021-82578-6
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 Details
Item Type: | Refereed Article |
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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: | 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) |
Deposited By: | Directorate |
Deposited On: | 2021-02-12 |
Last Modified: | 2021-02-15 |
Downloads: | 0 |
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