IMAS Metadata Catalogue
Antarctic marine sedimentary ancient DNA (sedaDNA) sequences: Extraction method comparison for diatom sedaDNA recovery
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.
Simple
Identification info
- Date (Publication)
- 2025-06-19T00:00:00
Identifier
- Title
- Information and documentation - Digital object identifier system
- Citation identifier
- ISO 26324:2012
- Codespace
- doi.org
- Description
- Digital Object Identifier (DOI)
Resource provider
Principal investigator
Institute for Marine and Antarctic Studies - Singh, Prashasti
University of Tasmania
Tasmania
Australia
Principal investigator
Institute for Marine and Antarctic Studies - Armbrecht, Linda
University of Tasmania
Tasmania
Australia
Author
Author
Institute for Marine and Antarctic Studies - Bolch, Christopher
University of Tasmania
Tasmania
Australia
Collaborator
- Credit
- This research was supported by the Australian Research Council Special Research Initiative, Australian Centre for Excellence in Antarctic Science (ACEAS) (Project Number SR200100008).
- Credit
- This research was also 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.
- Status
- Completed
Point of contact
Institute for Marine and Antarctic Studies - Singh, Prashasti
University of Tasmania
Tasmania
Australia
Point of contact
Institute for Marine and Antarctic Studies - Armbrecht, Linda
University of Tasmania
Tasmania
Australia
- Topic category
-
- Geoscientific information
Extent
N
S
E
W
))
N
S
E
W
))
Temporal extent
- Time period
- 2025-02-02 2025-03-07
- Maintenance and update frequency
- Not planned
- Keywords (Theme)
-
- metagenomics
- diatom DNA
- sedimentary ancient DNA
- Keywords (Taxon)
-
- Bacillariophyta
- Global Change Master Directory Earth Science Keywords, Version 8.5
Resource constraints
- Linkage
-
https://licensebuttons.net/l/by/4.0/88x31.png
License Graphic
- Title
- Creative Commons Attribution 4.0 International License
- Alternate title
- CC-BY
- Edition
- 4.0
- Website
-
https://creativecommons.org/licenses/by/4.0/
License Text
- Other constraints
- Cite data 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. https://doi.org/10.25959/AMSEDADNA-2025A
- Language
- English
- Character encoding
- UTF8
- Supplemental Information
- Enhanced sedimentary ancient DNA (sedaDNA) retrieval from Antarctic diatoms
Content Information
- Content type
- Physical measurement
Identifier
- Code
- Read count
- Name
- Count
Identifier
- Code
- Fragment Length
- Name
- base pairs
Distribution Information
- Distribution format
-
- .kxdd and .rma6
- OnLine resource
- DATA ACCESS – browse and download available files
- Distribution format
-
Resource lineage
- 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.
- Hierarchy level
- Dataset
- Hierarchy level
- Dataset
Platform
Identifier
- Code
- Illumina
Instrument
Identifier
- Code
- Illumina NextSeq
Metadata
- Metadata identifier
- urn:uuid/95f1da3a-5aba-4d50-8c66-c84c53ecce75
- Language
- English
- Character encoding
- UTF8
Type of resource
- Resource scope
- Dataset
- Name
- IMAS Dataset level record
- Metadata linkage
-
https://metadata.imas.utas.edu.au/geonetwork/srv/eng/catalog.search#/metadata/95f1da3a-5aba-4d50-8c66-c84c53ecce75
Point of truth URL of this metadata record
- Date info (Creation)
- 2025-06-13T00:00:00
- Date info (Revision)
- 2025-10-09T19:28:39
Metadata standard
- Title
- ISO 19115-3:2018
Overviews
Spatial extent
N
S
E
W
N
S
E
W
Provided by
Associated resources
Not available