Data

Antarctic marine sedimentary ancient DNA (sedaDNA) sequences: Extraction method comparison for diatom sedaDNA recovery

Australian Ocean Data Network
Singh, Prashasti ; Armbrecht, Linda ; Teixeira, Joao ; Bolch, Christopher ; Weber, Michael E
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/95f1da3a-5aba-4d50-8c66-c84c53ecce75&rft.title=Antarctic marine sedimentary ancient DNA (sedaDNA) sequences: Extraction method comparison for diatom sedaDNA recovery&rft.identifier=https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/95f1da3a-5aba-4d50-8c66-c84c53ecce75&rft.description=This dataset is derived from a comparative study evaluating six DNA extraction methods for their efficiency in recovering diatom sedimentary ancient DNA (sedaDNA) from Antarctic marine sediments. Sediment samples were collected from two sites: U1536C (Scotia Sea, West Antarctica) and KC02 (Sabrina Coast, Totten Glacier Region, East Antarctica). Each of the six extraction methods was applied to the same set of samples. Following shotgun metagenomic sequencing, the methods were assessed based on metrics such as diatom DNA recovery, average fragment length, and taxonomic diversity. The purpose of the study was to identify the optimal extraction approach for maximizing the yield and quality of diatom sedaDNA, thereby improving its utility for paleoenvironmental reconstruction.Maintenance and Update Frequency: notPlannedStatement: Sediment samples were collected from two Antarctic marine sites: KC02 (Kasten Core, Sabrina Coast, East Antarctica) and U1536C (Piston Core, Scotia Sea, West Antarctica), during RV Investigator voyage IN2017_V01 and IODP Expedition 382, respectively. Subsampling was conducted on board under sterile conditions using gamma-irradiated or bleach/ethanol-treated tools and 15 mL centrifuge tubes. Samples were flash-frozen in liquid nitrogen and later stored at −20°C / −80°C. In a dedicated ancient DNA clean lab, core intervals (20–21.5, 70–71.5, and 120–121.5 cmbsf) were sub-sampled using sterile spatulas. Each sample (~0.25 g) underwent six different DNA extraction protocols to compare sedaDNA recovery. DNA libraries were constructed following ancient DNA protocols and sequenced using Illumina shotgun metagenomics. The resulting reads were quality-filtered and aligned against multiple reference databases to assess diatom DNA recovery, fragment length, and taxonomic composition.&rft.creator=Singh, Prashasti &rft.creator=Armbrecht, Linda &rft.creator=Teixeira, Joao &rft.creator=Bolch, Christopher &rft.creator=Weber, Michael E &rft.date=2025&rft.coverage=westlimit=-41.20; southlimit=-59.60; eastlimit=-40.90; northlimit=-59.30&rft.coverage=westlimit=-41.20; southlimit=-59.60; eastlimit=-40.90; northlimit=-59.30&rft.coverage=westlimit=115.50; southlimit=-64.60; eastlimit=115.70; northlimit=-64.40&rft.coverage=westlimit=115.50; southlimit=-64.60; eastlimit=115.70; northlimit=-64.40&rft.coverage=uplimit=; downlimit=0&rft.coverage=uplimit=; downlimit=0&rft_rights=This dataset is hosted by the University of Tasmania and the Australian Centre for Excellence in Antarctic Science. This research was supported by the Australian Research Council Special Research Initiative, Australian Centre for Excellence in Antarctic Science (Project Number SR200100008).&rft_rights=Creative Commons Attribution 4.0 International License https://creativecommons.org/licenses/by/4.0/&rft_rights=Cite as: Singh, P., Teixeira, J., Weber, M. E., Bolch, C., & Armbrecht, L. (2025). Antarctic marine sedimentary ancient DNA (sedaDNA) sequences: Extraction method comparison for diatom sedaDNA recovery [Data set]. Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS). https://doi.org/10.25959/AMSEDADNA-2025A&rft_subject=geoscientificInformation&rft_subject=metagenomics&rft_subject=diatom DNA&rft_subject=sedimentary ancient DNA&rft_subject=Bacillariophyta&rft_subject=MICROFAUNA&rft_subject=EARTH SCIENCE&rft_subject=AGRICULTURE&rft_subject=SOILS&rft_subject=Illumina&rft_subject=Read count&rft_subject=Fragment Length&rft_subject=Illumina NextSeq&rft_subject=Agilent TapeStation&rft_subject=Global / Oceans | Global / Oceans | Southern Ocean&rft_subject=Named Locations (Antarctica) | Named Locations (Antarctica) | Totten Glacier&rft_subject=Named Locations (Antarctica) | Named Locations (Antarctica) | Antarctic Peninsula&rft.type=dataset&rft.language=English Access the data
Cite Saved to MyRDA Save to MyRDA

Licence & Rights:

Open Licence view details
CC-BY

Creative Commons Attribution 4.0 International License
https://creativecommons.org/licenses/by/4.0/

This dataset is hosted by the University of Tasmania and the Australian Centre for Excellence in Antarctic Science. This research was supported by the Australian Research Council Special Research Initiative, Australian Centre for Excellence in Antarctic Science (Project Number SR200100008).

Cite as: Singh, P., Teixeira, J., Weber, M. E., Bolch, C., & Armbrecht, L. (2025). Antarctic marine sedimentary ancient DNA (sedaDNA) sequences: Extraction method comparison for diatom sedaDNA recovery [Data set]. Institute for Marine and Antarctic Studies (IMAS), University of Tasmania (UTAS). https://doi.org/10.25959/AMSEDADNA-2025A

Access:

Other

Brief description

This dataset is derived from a comparative study evaluating six DNA extraction methods for their efficiency in recovering diatom sedimentary ancient DNA (sedaDNA) from Antarctic marine sediments. Sediment samples were collected from two sites: U1536C (Scotia Sea, West Antarctica) and KC02 (Sabrina Coast, Totten Glacier Region, East Antarctica). Each of the six extraction methods was applied to the same set of samples. Following shotgun metagenomic sequencing, the methods were assessed based on metrics such as diatom DNA recovery, average fragment length, and taxonomic diversity. The purpose of the study was to identify the optimal extraction approach for maximizing the yield and quality of diatom sedaDNA, thereby improving its utility for paleoenvironmental reconstruction.

Lineage

Maintenance and Update Frequency: notPlanned
Statement: Sediment samples were collected from two Antarctic marine sites: KC02 (Kasten Core, Sabrina Coast, East Antarctica) and U1536C (Piston Core, Scotia Sea, West Antarctica), during RV Investigator voyage IN2017_V01 and IODP Expedition 382, respectively. Subsampling was conducted on board under sterile conditions using gamma-irradiated or bleach/ethanol-treated tools and 15 mL centrifuge tubes. Samples were flash-frozen in liquid nitrogen and later stored at −20°C / −80°C. In a dedicated ancient DNA clean lab, core intervals (20–21.5, 70–71.5, and 120–121.5 cmbsf) were sub-sampled using sterile spatulas. Each sample (~0.25 g) underwent six different DNA extraction protocols to compare sedaDNA recovery. DNA libraries were constructed following ancient DNA protocols and sequenced using Illumina shotgun metagenomics. The resulting reads were quality-filtered and aligned against multiple reference databases to assess diatom DNA recovery, fragment length, and taxonomic composition.

Notes

Credit
Australian Centre for Excellence in Antarctic Science
Credit
This research was supported by a grant of sea time on RV Investigator from the CSIRO Marine National Facility (https://ror.org/01mae9353), and by the Australia and New Zealand International Ocean Discovery Program Consortium (ANZIC) for LA’s participation in International Ocean Discovery Program (IODP) Expedition 382. Sample analysis was supported by an Australian Research Council (ARC) Discovery Early Career Researcher (DECRA) Fellowship (DE210100929) to LA. JCT also acknowledges the ARC for funding support through a DECRA Fellowship (DE210101235). PS is supported by the Tasmanian Graduate Research Scholarship of the University of Tasmania, an Antarctic Science Foundation Traversing the COVID Gap Grant, and by the Institute for Marine and Antarctic Studies Student Research Support Scheme.

Issued: 19 06 2025

Data time period: 2025-02-02 to 2025-03-07

This dataset is part of a larger collection

Click to explore relationships graph
Help

Related Organisations

Related People

-40.9,-59.3 -40.9,-59.6 -41.2,-59.6 -41.2,-59.3 -40.9,-59.3

-41.05,-59.45

115.7,-64.4 115.7,-64.6 115.5,-64.6 115.5,-64.4 115.7,-64.4

115.6,-64.5

text: westlimit=-41.20; southlimit=-59.60; eastlimit=-40.90; northlimit=-59.30

text: westlimit=115.50; southlimit=-64.60; eastlimit=115.70; northlimit=-64.40

text: uplimit=; downlimit=0

Subjects
AGRICULTURE | Agilent TapeStation | Bacillariophyta | EARTH SCIENCE | Fragment Length | Global / Oceans | Global / Oceans | Southern Ocean | Illumina | Illumina NextSeq | MICROFAUNA | Named Locations (Antarctica) | Named Locations (Antarctica) | Antarctic Peninsula | Named Locations (Antarctica) | Named Locations (Antarctica) | Totten Glacier | Read count | SOILS | diatom DNA | geoscientificInformation | metagenomics | sedimentary ancient DNA |

User Contributed Tags    

Login to tag this record with meaningful keywords to make it easier to discover

Identifiers
  • global : 95f1da3a-5aba-4d50-8c66-c84c53ecce75