Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/130079
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Type: | Journal article |
Title: | Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes |
Author: | Armbrecht, L. Hallegraeff, G. Bolch, C.J.S. Woodward, C. Cooper, A. |
Citation: | Scientific Reports, 2021; 11(1):3220-1-3220-14 |
Publisher: | Nature Publishing Group |
Issue Date: | 2021 |
ISSN: | 2045-2322 2045-2322 |
Statement of Responsibility: | L. Armbrecht, G. Hallegraeff, C. J. S. Bolch, C. Woodward and A. Cooper |
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. |
Keywords: | Animals Zooplankton Phytoplankton DNA Damage Nucleic Acid Hybridization Geologic Sediments Metagenome Eukaryota Aquatic Organisms DNA, Ancient |
Rights: | © The Author(s) 2021. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/. |
DOI: | 10.1038/s41598-021-82578-6 |
Grant ID: | http://purl.org/au-research/grants/arc/FL140100260 http://purl.org/au-research/grants/arc/DP170102261 |
Published version: | http://dx.doi.org/10.1038/s41598-021-82578-6 |
Appears in Collections: | Agriculture, Food and Wine publications Aurora harvest 4 |
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hdl_130079.pdf | Published version | 3.33 MB | Adobe PDF | View/Open |
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