National supercomputing and expertise to enable the Australian Fish Genomics Initiative
Fish populations across Australian freshwater and marine ecosystems are struggling to cope with the combined threats of invasive species, pollution, and climate events. A significant proportion of Australia’s 5,000 fish species remains poorly understood, lacking the essential referential biomolecular data that could inform improved population monitoring, environmental assessment, and the sustainable management of fisheries and aquatic ecosystems. This conservation issue is exemplified by the critical gap in genomic data, with only 3% of marine species and 25% of freshwater species even having species-level data.
The Australian Fish Genomics Initiative (AFGI) is responding to this dire situation by characterising 85 species of Australia’s fish species through the generation of high-quality reference genomes.
Queensland groper (Epinephelus lanceolatus). Image credit: Getty images
Minderoo Foundation and Bioplatforms Australia established the Initiative with the aim to collaborate nationally with marine and freshwater research communities to generate essential data for researchers and practitioners to enhance our understanding of species adaptation, population dynamics, and evolutionary relationships.
The AFGI consists of 56 partner projects that will generate genomics, genetics (e.g., population genetics) and transcriptomics data from fish species from all major Australian habitats: freshwater, estuarine and marine environments. Analysing this huge volume of high-quality data presents a challenge that fish biologist and AFGI Bioinformatician, Dr Amy Tims, has been tasked with solving. Amy joined the BioCommons team to facilitate AFGI’s access to national supercomputing resources and specialised bioinformatics expertise. Data is already arriving via the Bioplatforms Australia Data Portal, and Amy is providing hands-on assistance to consortium partners to perform data QC, genome assembly, and data curation.
"We need to look at population connectivity to manage fisheries sustainably, and understand genetic diversity to implement effective conservation breeding programs,” said Dr Tims.
“We also need to know what is happening at the genetic level to determine whether a species can survive extreme weather conditions. In short: we need genomes!"
A dedicated compute allocation at Pawsey Supercomputing Research Centre (Pawsey) has been provided to all AFGI partners via the Australian BioCommons Leadership Share (ABLeS), removing the computational constraint that can be a barrier to entry for researchers. This is complemented by the Australian Tree of Life (AToL) project that is building systems to automate the complex process of genome assembly and publication at scale. This combination of dedicated expertise and national infrastructure is already delivering results, and the first draft genomes have already been assembled.
The high quality data that AFGI is generating will unlock new insights into fish biodiversity, evolution, conservation, aquaculture, and biosecurity, including pest and disease management. It demonstrates that strategic collaboration and the right research infrastructure can support critical research that addresses our biggest challenges, like the sustainable management of Australia’s aquatic ecosystems.
