Project title
Antarctic paleo-genomics
Collaborators and funding
Institute for Marine and Antarctic Studies (IMAS);
Contact(s)
Project description and aims
Antarctica is key in the context of climate change, as its melting contributes to sea-level rise, alterations in ocean currents and nutrient cycling with impacts on all polar marine life. But the continent is remote and thus difficult to access, and as a result Antarctic and Southern Ocean organisms are genetically much less well characterised than Northern Hemisphere ones. This lack of genetic reference information creates a significant hindrance to accurately reconstructing palaeo-environments and biodiversity monitoring. Without appropriate reference genomes and taxonomic marker sequences, environmental and ancient DNA studies suffer from low taxonomic resolution, biased identifications, and large proportions of unassigned reads (‘genomic dark matter’). At present, there is no alternative to resolving this bottleneck other than the targeted generation of new reference sequences from modern organisms. This project directly addresses this critical gap by creating new reference genomes for Southern Ocean organisms and using them in circum-Antarctic paleo-ecosystem reconstructions. Thus, the aims of this project are:
-
Generate a new, comprehensive database of DNA reference sequences for Southern Ocean marine life using the newest sequencing technologies (“Southern Ocean EcoBase”).
-
Improve sedaDNA derived Plaeo-ecosystem reconstructions by re-analysing existing sedaDNA datasets from around Antarctica against the new SO-EcoBase.
Methodologically, the project will involve database generation, indexing, alignments of metagenomic shotgun data with these databases and the creation of pangenomes. These steps are computationally intensive, so that we are currently unable to proceed efficiently with our analyses using our in-house UTAS High-Performance Computing system.
At present, the project is supported by an Australian Research Council Discovery Project to the proponent Dr Linda Armbrecht (DP250100886). Miss Emily Elisabeth Davis is a PhD student affiliated with this project and undertaking the majority of this bioinformatics research.
This combination of using existing and generating new reference sequences, and integrating this information in sedimentary ancient DNA datasets from around Antarctica, data will provide the most robust paleo-ecosystem reconstruction to date. The latter will provide new insights into how polar ecosystems respond to climate change, which is especially important with ongoing global warming.
How is ABLeS supporting this work?
This work is supported through the Production Bioinformatics scheme provided by ABLeS. The support includes storage and compute allocation.
Expected outputs enabled by participation in ABLeS
Data will be made available via NCBI RAS or the IMAS Research Data Portal.
Publications will be made open access. We anticipate at least 2 high-impact publications, one about the database, one about the use of the database in Antarctic palaeo-reconstructions.
These details have been provided by project members at project initiation. For more information on the project, please consult the contact(s) or project links above.