THE AUSTRALIAN FISH GENOMICS INITIATIVE
Bioplatforms Australia and the Minderoo Foundation are investing in the generation of referential molecular data to advance knowledge of Australia’s fish species and support critical research and management strategies. Fish play a crucial role in Australia’s environmental health and economy. As the largest and most diverse group of vertebrates, with over 34,500 species described globally, Australia hosts approximately 5,000 fish species, including around 400 native freshwater species. A substantial proportion of Australia’s fish are endemic, and many species are still being discovered or described.
Advancements in our understanding of how aquatic organisms adapt to and interact with their environments, coupled with improved population monitoring and environmental assessment, are facilitated by genomics-informed technologies. These technologies address a broad range of needs related to fish evolution and biodiversity, conservation, fisheries, aquaculture, and environmental biosecurity.
AIMS OF THE INITIATIVE
The Australian Fish Genomics Initiative, in collaboration with the marine and freshwater research communities, aims to generate essential data for researchers and practitioners to accelerate the knowledge about Australia’s fishes and to enhance our understanding of evolutionary relationships, adaptive potential, population structure and dynamics, and best conservation management strategies.
The Australian Fish Genomics Initiative will operate across two parallel themes:
- Freshwater Fish Genomics Theme
- Marine Fish Genomics Theme
ACTIVITIES AND PRIORITY SETTING
The initiative will support projects seeking to generate:
- Reference genomes – long read sequencing (PacBio HiFi – ONT), Hi-C, transcriptomics (Illumina)
- Population genomics – whole genome sequencing (Illumina short read sequencing)
Species Prioritisation:
The Initiative will support question-driven projects on Australian marine and freshwater fish species, where data serves immediate and future research needs.
The initiative aims to provide coordination to ensure critical gaps are filled with reduced data duplication. The main priority is to fill the gap for Australian fish families with no genomic referential data for both marine and freshwater habitats. There are 7 freshwater families identified: Retropinnidae, Percichthyidae, Ehiravidae, Geotriidae, Lepidogalaxiidae, Pseudaphritidae, and Tetrarogidae.
In addition, the initiative Advisory Committee will look favourably on projects on species with:
- No existing data for species
- Low-quality or insufficient data
- Existing data, but not from Australian specimens
The initiative will not support work on introduced and invasive species. For these species, please refer to our Invasive Plants and Animals Initiative.
Support provided
Bioplatforms Australia will provide the following resources:
- Genomics data generation through our network of facilities (including AGRF, BRF, Ramaciotti, SAGC and Genomic WA)
- Project management and data management (raw data storage and access, with associated metadata).
- Automated reference genome assembly and data submission to the European Nucleotide Archive (ENA) through the Australian Tree of Life Genome Engine pipeline
- The Australian Fish Genomics Initiative will provide access to the required high-performance computing (Pawsey and NCI) and analytical resources through the Australian BioCommons Leadership Share (ABLeS).
- Collaboration in a national consortium of ichthyology and omics experts.
The budget for this second round RFP is limited, please be conscious of the scale of your demand.
Examples of suitable submission would include:
- A request for reference genome on one or two species (includes Long Read sequencing, HiC and RNASeq)
- A request for reference genome on one species (includes Long Read sequencing, HiC and RNASeq) and 20 specimens for population genomics through Illumina WGS at ~20X coverage
Co-contributions
Project teams will provide co-contribution for the following:
- Project design
- Sample provision, preparation (DNA extraction etc), shipping and supply of metadata within 12 months of the project approved
- Bioinformatics/data analysis (support available)
- End-use application of the data
- Data publication
- Raw and analysed sequence data submission to international repositories
Data and Collaboration Policy
Data generated from the Australian Fish Genomics Initiative will be made accessible to project teams in the Bioplatforms Australia Data Portal as per the Initiative’s Data and Collaboration Policy.
Note: There is a 12-month embargo on the data to allow first access to project teams. During this time, access will only be given to you and your project collaborators. After the 12-month period, the data will be scheduled for public release in the “Open-access” phase, as outlined in Australian Fish Genomics Initiative Data and Collaboration Policy.
Genomic data generated from your project will also be assembled through the Australian Tree of Life Genome Engine, which will include submission of the data to ENA that will be held under the 12- month embargo period. This does not preclude the project team from generating and submitting an updated version of the genome, but rather aims to accelerate the team’s research activity by providing the team with a high-quality draft genome assembly ready for use. Genome note publication authorship remains with the project team. You can read more about this in the Data and Collaboration Policy.
INSTRUCTIONS FOR FILLING IN THIS FORM
- Please ensure you have read all information provided before completing your application, as well as the details of the initiative’s Data Use and Collaboration policy.
- Complete the online form here and submit one document per species or activity (multiple species can be submitted in one form if part of a single research aim). For preparation purposes, you can find a downloadable template here.
- Address all criteria/questions listed.
*Please note that you are able to edit this form after its submission and until the deadline if logged in with a gmail account. Non-gmail account unfortunately cannot access this feature.
Deadline: COB Friday 13 November, 2026
Support through the Australian Fish Genomics Initiative is intended to be catalytic, enabling or enhancing existing research activities rather than serving as the sole source of funding for data acquisition within a project.
It should be noted that this is not a competitive grant opportunity and the Australian Fish Genomics Initiative will endeavour to support projects that aim to enhance Australia’s knowledge and application of fish species. Project assessment will be guided by Bioplatforms Australia facilities and the Australian Fish Genomics Advisory Committees.
Contact information:
Dr Sophie Mazard, Program Manager smazard@bioplatforms.com – 0403 562 230
We welcome collaborations and parties interested in participating in the Australian Fish Genomics Initiative, including this RFP, are welcome to get in contact with the Program Manager (Sophie Mazard).