Please use this identifier to cite or link to this item:
https://hdl.handle.net/2440/126163
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dc.contributor.author | Armbrecht, L. | - |
dc.contributor.author | Herrando-Pérez, S. | - |
dc.contributor.author | Eisenhofer, R. | - |
dc.contributor.author | Hallegraeff, G.M. | - |
dc.contributor.author | Bolch, C.J.S. | - |
dc.contributor.author | Cooper, A. | - |
dc.date.issued | 2020 | - |
dc.identifier.citation | Molecular Ecology Resources, 2020; 20(4):906-919 | - |
dc.identifier.issn | 1755-098X | - |
dc.identifier.issn | 1755-0998 | - |
dc.identifier.uri | http://hdl.handle.net/2440/126163 | - |
dc.description.abstract | Marine sedimentary ancient DNA (sedaDNA) provides a powerful means to reconstruct marine palaeo-communities across the food web. However, currently there are few optimized sedaDNA extraction protocols available to maximize the yield of small DNA fragments typical of ancient DNA (aDNA) across a broad diversity of eukaryotes. We compared seven combinations of sedaDNA extraction treatments and sequencing library preparations using marine sediments collected at a water depth of 104 m off Maria Island, Tasmania, in 2018. These seven methods contrasted frozen versus refrigerated sediment, bead-beating induced cell lysis versus ethylenediaminetetraacetic acid (EDTA) incubation, DNA binding in silica spin columns versus in silica-solution, diluted versus undiluted DNA in shotgun library preparations to test potential inhibition issues during amplification steps, and size-selection of low molecular-weight (LMW) DNA to increase the extraction efficiency of sedaDNA. Maximum efficiency was obtained from frozen sediments subjected to a combination of EDTA incubation and bead-beating, DNA binding in silica-solution, and undiluted DNA in shotgun libraries, across 45 marine eukaryotic taxa. We present an optimized extraction protocol integrating these steps, with an optional post-library LMW size-selection step to retain DNA fragments of ≤500 base pairs. We also describe a stringent bioinformatic filtering approach for metagenomic data and provide a comprehensive list of contaminants as a reference for future sedaDNA studies. The new extraction and data-processing protocol should improve quantitative paleo-monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eukaryote DNA in sediments. | - |
dc.description.statementofresponsibility | Linda Armbrecht, Salvador Herrando-Pérez, Raphael Eisenhofer, Gustaaf M. Hallegraeff, Christopher J. S. Bolch, Alan Cooper | - |
dc.language.iso | en | - |
dc.publisher | Wiley | - |
dc.rights | © 2020 John Wiley & Sons Ltd | - |
dc.source.uri | http://dx.doi.org/10.1111/1755-0998.13162 | - |
dc.subject | ancient DNA | - |
dc.subject | diatoms | - |
dc.subject | dinoflagellates | - |
dc.subject | haptophytes | - |
dc.subject | Maria Island | - |
dc.subject | metagenomics | - |
dc.subject | plankton | - |
dc.subject | seafloor | - |
dc.subject | Tasmania | - |
dc.title | An optimized method for the extraction of ancient eukaryote DNA from marine sediments | - |
dc.type | Journal article | - |
dc.identifier.doi | 10.1111/1755-0998.13162 | - |
dc.relation.grant | http://purl.org/au-research/grants/arc/CE170100015 | - |
dc.relation.grant | http://purl.org/au-research/grants/arc/DP170102261 | - |
dc.relation.grant | http://purl.org/au-research/grants/arc/FL140100260 | - |
pubs.publication-status | Published | - |
dc.identifier.orcid | Armbrecht, L. [0000-0002-1213-1257] | - |
dc.identifier.orcid | Herrando-Pérez, S. [0000-0001-6052-6854] | - |
dc.identifier.orcid | Cooper, A. [0000-0002-7738-7851] | - |
Appears in Collections: | Aurora harvest 8 Australian Centre for Ancient DNA publications |
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