MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

Everett, Rosie and Cribdon, Becky (2023) MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale. Frontiers in Ecology and Evolution, 10. p. 888421. ISSN 2296-701X

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The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction.

Item Type: Article
Additional Information: Funding information: RE would like to thank the Natural Environment Research Council (NERC) and the University ofWarwick for the financial support of this research.
Uncontrolled Keywords: sedaDNA, metagenomics, authentication, paleoecology, shotgun sequencing
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
F800 Physical and Terrestrial Geographical and Environmental Sciences
Department: Faculties > Health and Life Sciences > Applied Sciences
Depositing User: John Coen
Date Deposited: 27 Jan 2023 15:04
Last Modified: 27 Jan 2023 15:15

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