– ABOUT
Australian Fish Genomics Initiative
In 2024, Bioplatforms Australia and the Minderoo Foundation launched the Australian Fish Genomics Initiative to enhance understanding of Australia’s diverse fish species through referential biomolecular data. This initiative aims to support critical research and enable sustainable management strategies for Australia’s aquatic ecosystems.
Australia is home to around 5,000 fish species, including 400 native freshwater species, many of which are endemic. Despite their importance to the environment and economy, a significant proportion of these species remain poorly understood due to challenges in identification and access. Genomics-informed technologies are unlocking new insights into fish biodiversity, evolution, conservation, aquaculture, and biosecurity, including pest and disease management.
A recent audit highlighted major gaps in available genomic data for Australian fish. While 56.6% of freshwater and estuarine fish genera had some referential genomic data, only 26% had species-level information. For saltwater fish, the numbers were even lower, with 20% of genera and just 3% of species represented in genomic databases.
The Australian Fish Genomics Initiative seeks to address these critical deficiencies by generating high-quality genomic data. This work provide a foundation for improved population monitoring, environmental assessment, and the sustainable management of fisheries and aquatic ecosystems.
OBJECTIVES
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 characterisation of Australia’s fish species, enhancing our understanding of species adaptation, population dynamics, and evolutionary relationships.
Data types will include genomics, genetics (e.g., population genetics), transcriptomics, proteomics and metabolomics where required and include fish species from all major Australian habitats: freshwater, estuarine and marine environments. The Initiative will be progressing as two parallel themes:
- The Australian Freshwater Fish Genomics Program
- The Australian Marine Fish Genomics Program
Estuarine species will be included in the program that best suits the main dwelling environment of the species.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Species name | Initiative theme | Project Summary | Data strategy | Project Lead | Partners |
|---|---|---|---|---|---|
| Silver Bream or Pikey bream (Acanthopagrus pacificus) Longfin eel (Anguilla reinhardtii) Mud cod (Giuris margaritaceus) Tully grunter or Black bream (Hephaestus tulliensis) Jew fish Eel tail or Wet tropics tandan (Tandanus tropicanus) | Freshwater | North Queensland is a freshwater fish biodiversity hotspot with high endemism, and fish are of great cultural importance to not only the Traditional custodians but other groups as well. Despite this, fish habitat is under threat from declines is water quality, habitat modification, introduced species and climate change. Previous efforts to use molecular surveillance for fish populations have been stymied by a lack of genomic resources, making precise taxonomic identifications impossible. Complete genome sequences would improve the databases for barcoding work, enable studies to employ CSIRO’s highly accurate, PCR free TRACE techniques, and enable further study of the biodiversity, evolution, and environmental adaptations of these fish. | Reference genome (PacBio HiFi, transcriptome), Population genomics (Illumina) | Sharon Hook, CSIRO Environment | CSIRO, Mamu Aboriginal Corporation RNTBC |
| Eastern Redfish (Centroberyx affinis) | Marine | As waters in southeastern Australia warm, the outputs of many fisheries have been declining. For instance, the abundance of Eastern Redfish has declined dramatically in the past 25 years, despite a release from fishing pressure, for unknown reasons. We hypothesise that climate pressures or continued fishing pressure may be a contributor to the declines, but without genomics, have not way of verifying these hypotheses. Comparing the genetic diversity inside and outside of fished areas can tell us if fishing has been a bottle neck, and variation in potentially adaptive loci along a latitudinal gradient can support the climate hypothesis. | Population genomics (Illumina) | Sharon Hook, CSIRO Environment | CSIRO |
| Jackass Morwong (Nemadactylus macropterus) | Marine | This commercially important fisheries species is declining in abundance for unknown reasons, though climate change is hypothesised to be an important driver. To better manage this fishery, we need to better understand whether a lack of phenotypic plasticity under climate pressures could be contributing. Epigenomes - which regulate gene expression - are an untapped vehicle for understanding functional biodiversity and evolutionary processes. By examining the utility of assessing the epigenome to understand the adaptation to the environment, we will not only have better tools to manage Morwong but also a better understanding of how functional assessments can determined using epigenomics. | Reference genome (HiFi, HiC, transcriptome) | Sharon Hook, CSIRO Environment | CSIRO |
| Red handfish (Thymichthys politus) | Marine | Under the current national recovery plan for handfish, a captive breeding program has been established for the red handfish. Genetic data is needed to assess founder relatedness within the program and assist with translocation decision-making. Due to the size of the fish and its current threat status, fin clipping is not an option so we will use WGR of deceased individuals from different clutches to undertake a genomic assessment of this species, including ROH analyses. Using the annotated reference genome, we will determine what gene families are impacted by any long ROH, assess current Ne, and also calculate the more conventional population genetic analyses. | Reference genome (HiFi, HiC, transcriptome) | Carolyn Hogg, The University of Sydney | Utas |
| Common jollytail (Galaxias maculatus) Climbing galaxias (Galaxias brevipinnis) | Freshwater | Galaxias maculatus and G. brevipinnis are dominant temperate Australian freshwater fishes that typically complete their larval phase at sea. Despite expected genetic homogenization from marine dispersal, we have identified candidate cryptic taxa potentially meriting conservation concern (Jense et al. 2024). Their ability to adapt to landlocked systems - completing lifecycles in freshwater - may underpin their cryptic diversity. Research in other taxa suggests structural chromosomal variation contributes to such rapid life history shifts. We will test this by categorising and comparing structural variants within the two galaxiids. The genomic resources developed for these species also have broader relevance for their conservation. | Reference genome (HiC), Population genomics (Illumina) | Chris Burridge, University of Tasmania | Uni Otago, Plant and Food NZ |
| Barramundi (Lates calcarifer) | Freshwater, Marine [marine] | Barramundi is an iconic fish in northern Australia that supports a burgeoning aquaculture, wild and recreational fishery, and is of indigenous importance; however, there are no comprehensive genome level resources (ie an Australian reference genome, pangenomes or complete transcriptome) available. Access to comprehensive genomic resources will assist the Australian aquaculture industry with future genomic-informed selective breeding programs, conservationists with understanding levels of natural and adaptive genetic variation among genetic stocks (where 4 major stocks in Aust/PNG and 21 genetic subpopulations are recognised) and evolutionists in comparing Australian L. calcarifer with those found in Asia and India where it also occurs. | Reference genome (HiC), Population genomics (Illumina) | Dean Jerry, James Cook University/ARC Research Hub for Supercharging Tropical Aquaculture through Genetic Solutions | AGRF, UQ, JCU |
| Giant grouper or Queensland groper (Epinephelus lanceolatus) | Marine | The giant grouper, a prized market species, is a key target for aquaculture in Australia and Asia and faces threats from overfishing and hybridization. In Queensland, it is farmed in recirculating systems and ponds to diversify and enhance aquaculture. A chromosome-level reference genome with high-quality gene models will support wild conservation and enhance aquaculture potential. The results will inform breeding programs to optimize growth traits and immune function. Additionally, these genomic resources will aid in managing wild populations, assessing hybridization rates, and improving fisheries management across Australia and Asia. | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Dean Jerry, James Cook University | AGRF, The company One, JCU |
| Obbe's catfish (Porochilus obbesi) | Freshwater | We have recently karyotyped this species and discovered that it has multiple sex chromosomes (X1X1X2X2/X1X2Y). The female karyotype consists of 2n=46 (42 autosomes + 2X1 + 2X2) while males present 2n=45 (42 autosomes + 1X1 + 1X2 + Y). Therefore, generating, high quality, phased, chromosome level and anchored genome assemblies from male and female will provide unique opportunity to develop two phased assemblies from a species with multiple sex chromosomes, which has not been attempted before. In addition, this type of assembly will also help us to better understand evolution of multiple sex chromosomes in fishes as well as in other vertebrates. | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Tariq Ezaz, University of Canberra | Ucan, Uni Sao Carlos, Sao Paulo State Uni (Brazil) |
| Nursery fish (Kurtus gulliveri) | Freshwater | The Australian Nursery Fish Kurtus gulliveri is only known teleost species where males carry eggs on a hook at their head during embryonic development. Evolution of this unique reproductive strategy has been an enigma. Generating phased and chromosome anchored genome assemblies will fill in a significant knowledge gap by providing much anticipated genomic data to unravel the evolution of various reproductive strategies across the tree of life. In addition, this resource will also allow us to characterise the candidate sex determining region(s) including data for comparative genomic analysis across teleosts. Lead coordinator Ezaz karyotyped this species, which contains 44 tiny chromosomes (Ezaz et al. 2006, Chromosome Science 2006). | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Tariq Ezaz, University of Canberra | Ucan, Uni Sao Carlos, Sao Paulo State Uni (Brazil) |
| Dusky flathead (Platycephalus fuscus) | Marine | Dusky flathead is an iconic recreational fishing species and important for the commercial sector, and there are concerns about the sustainability of this population. NSW Department of Primary Industries (NSW DPI) has initiated a large-scale stocking program. However, fish released under this program should not affect the structure of the native populations. Using a few thousand SNPs, the collaborative research between the University of the Sunshine Coast (USC) and NSW DPI revealed a broad genetic structure among populations. This dataset is not enough to infer the fine-scale structure. Since genome data provides millions of SNPs, it is ideal to study the fine-scale population structure and evolutionary relationship among the populations. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Sankar Subramanian, University of the Sunshine Coast | NSW DPI |
| Mulloway (Argyrosomus japonicus) | Marine | In NSW, mulloway is important to both recreational and commercial fisheries, but there have been long-term concerns about the sustainability of this population. The NSW Department of Primary Industries (NSW DPI) has therefore initiated a large-scale stocking program. However, it is important that stocked fish should not affect the genetic structure of native populations. There is currently an ongoing collaboration between NSW DPI and the University of the Sunshine Coast (USC) to study the genetic structure of estuarine populations through resequencing and mapping reads on a mulloway genome from China. Developing a reference genome of Australian mulloway will, therefore, be crucial in this work to accurately infer genotypes. | Reference genome (PacBio HiFi, HiC, transcriptome) | Sankar Subramanian, University of the Sunshine Coast | NSW DPI |
| Sleepy Cod (Oxyeleotris lineolata) Smallhead Grunter (Scortum parviceps) Flyspecked Hardyhead (Craterocephalus stercusmuscarum) Mouth Almighty (Glossamia aprion) | Freshwater | This project aims to investigate the unique evolutionary history of marine-derived freshwater fishes in Australia, where low preexisting diversity and open niches facilitated adaptive radiations via colonisation of novel habitats. The region is home to ~500 species across 28 families, including at least seven adaptive radiations. We will generate reference genomes, many from endemic species, to establish a genomic foundation across these families. We will apply long-read sequencing, differential expression analysis in species with varying salinity tolerances, and novel approaches to detect shifts in DNA substitution rates, gene expansions, and positive selection to explore how ecological opportunity and competition shape adaptive radiations. | Reference genome (HiFi, HiC, transcriptome) | Aaron Davis, James Cook University | Uni California, Uni Oklahoma, JCU |
| River Blackfish (Gadopsis marmoratus) | Freshwater | As threatened and endangered taxa, there is a great need to use genome enabled approaches to enhance conservation and recovery. Captive propagation occurs and is planned in various parts of Australia with different candidate taxa. These fish have traditional use value and are a recreational angling species. Increasing the number of stable populations for all these purposes will at some time rely on direct human intervention, and genome enabled approaches can increase the effectiveness of hatchery propagation, translocations and ensure proper genetic management. We propose to create a reference genome and a genome-wide population genomics data set to further test the relationships and taxonomic status of candidate species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Matthew "Mac" Campbell, The University of Sydney | Usyd, DEECA, Ucan, NSW DPI, DAF, Nature Gleneg Trust |
| Barramundi (Lates calcarifer) | Freshwater, Marine [marine] | Barramundi are iconic and of cultural and economic importance. Wild stock fisheries and aquaculture production provide economic opportunity for many Australians. Although many aspects of barramundi biology are well understood, genomics knowledge greatly lags other economically important fishes in advanced economies (e.g., Pacific salmons and Atlantic salmon). Investments in genomics of salmonids and other fishes have linked key life history traits associated with fishery productivity, such as migration propensity, to genomic and genetic variation. We propose to test for the functional genomic basis of migration propensity in barramundi. The findings have important applications for conservation, sustainable fisheries and aquaculture. | Population genomics (Illumina) | Matthew "Mac" Campbell, The University of Sydney | Usyd, JCU,WA DPIRD, QLD DPI, NT DPIF |
| Bony Herring (Nematalosa erebi) | Freshwater | Bony Herring are crucial in food webs as a forage fish and exhibit highly cyclical population dynamics, often forming the majority of individuals and biomass in mass mortality events in the Murray-Darling Basin (MDB). They form a model system for understanding the genomic effects of mass mortality events on fish populations. Evidence from DArTseq indicates a system of chromosomal inversions in the MDB, that may relate to how adaptive potential is preserved despite otherwise low genetic diversity across their genomes. DArTseq data also indicates that the widespread N. erebi may be five separate species, and the status and origins of the chromosomal inversions remain to be clarified across the five candidate taxa of Nematalosa in Australia. | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Matthew "Mac" Campbell, The University of Sydney | Usyd, Ucan |
| Sparsely-spotted Stingaree (Urolophus paucimaculatus) | Marine | Most species of the family Urolophidae are endemic to Australia and have restricted ranges that overlap with commercial fisheries, where they are substantial bycatch. Their 12-month gestation period and small litter sizes makes these species vulnerable to anthropogenic threats. Taxonomic uncertainties, related to colour pattern variation and low mtDNA divergence, raise questions regarding the appropriate management units for some urolophids. Genomics can resolve these concerns by comparing nuclear DNA difference among species, and asses the basis behind morphological and biological differences. Genomic analyses of historical tissue samples will assess the fisheries and climate change impacts on genetic diversity over the past four decades. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Floriaan Devloo-Delva, CSIRO Australian National Fish Collection. Hobart, Tasmania | CSIRO |
| Carp Gudgeons (Hypseleotris gymnocephala, Hypseleotris bucephala, Hypseleotris acropinna) | Freshwater | Together, carp gudgeons are the most common freshwater fish in eastern Australia, spanning river basins from QLD to SA and a key inhabitant of the Murray-Darling river system. However, the group is extremely difficult to identify in the field because in addition to sexually reproducing species, unisexual lineages (hemiclones) also occur in sympatry. This reproductive mode is very rare and this is the only example reported in the southern hemisphere. Good quality genome sequences for the sexual species will provide the baseline data to try and understand how the reproductive strategy operates in these fish. One of the sexual species is also critically endangered (IUCN red list). | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Terry Bertozzi, South Australian Museum | SAM, Ucan, UniAdel |
| Bluespotted emperor (Lethrinus punctulatus) Rankin cod (Epinephelus rankini) | Marine | The bluespotted emperor and rankin cod are endemic to north-western Australia and are an important component of commercial and recreational catch. The population structure of these species has not been estimated despite being a fundamental premise of fishery assessments. The applicants have collected ~900 tissue samples across each species complete distribution providing an excellent dataset to understand genetic connectivity and environmental adaptation in these species. Interspecific population genomic comparisons will also facilitate a better understanding of how life-history traits influence population structure. This information will be useful for managing diverse multi species fisheries such as those in north-western Australia. | Population genomics (Illumina) | Sam Payet, Department of Primary Industries and Regional Development (DPIRD), Government of Western Australia | WA DPIRD |
| Golden perch (Macquaria ambigua) | Freshwater | To support recreational angling, golden perch are bred in state government and private hatcheries and stocked in rivers in large numbers. However, whole genome data to inform stocking are limited. Proposed population genetics (via whole genome resequencing; WGS) will be used to explore genome-wide signatures of adaptive genetic diversity in wild golden perch. Our project will extend existing research programs based on reduced representation sequencing methods (Dartseq) by providing greater resolution of adaptive processes across the whole genome. Characterization of adaptive genomic diversity will inform hatchery and stocking practices that promote the evolutionary resilience of wild golden perch. | Population genomics (Illumina) | Katherine Harrisson, La Trobe University | Flinders Uni, NSW DPIRD |
| Bloomfield Cod (Guyu wujalwujulensis) | Freshwater | Guyu wujulwujulensis is one of Australia's rarest freshwater fish. It is only known to occur in a single small population in a short (~10km) reach of the Bloomfield River between two waterfalls and is thus highly vulnerable to recent threats caused by introduced fish species (e.g. sooty grunter) and extreme events (e.g. Cyclone Jasper). A new project funded through the NESP Resilient Landscapes Hub will soon commence to fill critical knowledge gaps for this species, including a conservation genetic assessment (genetic Essential Biodiversity Variables including diversity, differentiation, inbreeding and effective population size) to inform conservation actions such as establishment of insurance populations via wild-to-wild translocations. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Dan Bock, Australian Rivers Institute, Griffith University | Monash, Griffith, Ucan |
| Australian Longnose Skate (Dentiraja confusa) | Marine | The Longnose Skate (D. confusa) has threatened status in Australia (EPBC Act), but this is currently being evaluated, with a nomination for a change to match the IUCN Critically Endangered assessment. The IUCN listing is based on an estimated >80% decline in population size over three generations due to fishing impacts. A high-quality genome sequence would have many conservation applications. The genome would be used in a current CSIRO project on population structure using RAD sequencing of skates from SE Australia (Tas-NSW; see co-investment below). The genome would be useful for future applications in close-kin mark–recapture methods to estimate population size, historical demography, epigenetic aging and adaptation genomics. | Reference genome (PacBio HiFi, HiC, transcriptome) | Bruce Deagle, CSIRO | CSIRO |
| Atherton Tablelands Rainbowfishes (Melanotaenia spp., Melanotaenia eachamensis, Melanotaenia splendida splendida, Melanotaenia utcheensis, Malanda rainbowfish (Melanotaenia sp. nov. malanda)) | Freshwater | In a recent WoS Highly-Cited paper of Atherton Tablelands rainbowfishes (Brauer et al. 2023), we described a hybrid zone between several threatened cool-adapted upland species and one widespread warm-adapted lowland species. Using ddRAD SNPs and niche modelling, we found that hybrids had less vulnerability to climate change than pure upland endemics. The two reference genomes and WGS dataset requested here will be used to characterise, for the first time, the genomic landscape of introgression in the hybrid zone and its interaction with the environment. Overlaps between introgressed and adaptive genomic regions (including structural variations, SVs) will be used to identify signal of adaptive introgression and climatic resilience. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Luciano Beheregaray, Flinders University | MAG NT, Ucan, Flinders Uni |
| Murray cod (Maccullochella peelii) | Freshwater | Murray cod is Australia's largest freshwater fish, with significant ecological, cultural, and economic value, however populations are in decline across the Murray-Darling Basin (MDB). Whole genome resequencing will improve insights into demographic history, population structure, impacts of stocking, and adaptive genetic variation. Expected outcomes have potential for real-world impact by guiding ongoing strategic conservation efforts and tackling critical knowledge gaps in our understanding of adaptive evolution. This will enable evidence-based management, including direct applications for selecting hatchery brood stock to build drought resilience into stocked populations, and ensure the long-term sustainability of Murray cod. | Population genomics (Illumina) | Chris Brauer, Flinders University | LaTrobe, NSW DPIRD, Flinders |
| Black jewfish (Protonibea diacanthus) | Marine | Black jewfish is a key commercial species in the Northern Territory, with the region one of the last strongholds worldwide. Golden snapper is heavily fished recreationally, and assessed as “depleting”. As common for coastal species in tropical waters otolith increments are unclear hence traditional ageing is difficult/inaccurate. Age structure is a crucial input for stock assessment hence epigenetic ageing may assist accuracy. Stock assessments assume population is a closed system where there is limited/no movement. Genome sequencing would help identify SNPs, structural variations, and genetic markers crucial for understanding structure. Lastly, sequencing will assist identifying markers associated with resilience to changing environments. | Reference genome (PacBio HiFi, HiC, transcriptome) | Jo Randall, Department of Agriculture and Fisheries, Northern Territory Government | DAF NT, AGRF |
| Oxleyan pygmy perch (Nannoperca oxleyana) | Freshwater | Nannoperca oxleyana is an endangered fish from NE NSW and SE Qld. NSW DPIRD is initiating a captive breeding program mixing various populations to establish new wild populations. DArT SNP data demonstrate lower levels of variation, thus having a chromosome scale genome and several short read genomes will greatly facilitate our understanding of genetic diversity across the genome and to provide a baseline against which future SNP work on stocked populations to better understand which parts of the genome appear to be driving stocking outcomes and to identify which populations are providing genetic variants that persist across multiple generations, vs those that contribute variants that do not persist. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Sam Davis, Fisheries NSW | Ucan, Monash |
| West Australian dhufish (WA dhufish) (Glaucosoma hebraicum) | Marine | The recovery of dhufish populations from overfishing has been influenced by geographic variation in key demographic processes such as reproduction and recruitment. Somatic growth is an important determinant of these traits and is itself influenced by environmental and genomic factors. There is need to understand the contribution of these factors and identify adaptive variation that is important for population demography, and subsequent stock recovery. Our findings will guide management arrangements that optimise the maintenance of phenotypic diversity across the species latitudinal distribution. Our results will provide insight into the effects of environmental change on one of the most important phenotypic traits of a harvested fish. | Population genomics (Illumina) | Sam Payet, Department of Primary Industries and Regional Development (DPIRD), Government of Western Australia | DPIRD WA, UniMelb |
| Freshwater Catfish (Tandanus tandanus) | Freshwater | Tandanus tandanus is a widespread species in eastern Australia that is common in coastal drainages, but has undergone decline in the Murray-Darling Basin with the species listed as protected in NSW, VIC and SA. There are now efforts being made either through hatchery production or translocation of adults in NSW, VIC and SA to reestablish populations in wild and semi wild habitats. We are currently working with the North Central Catchment Management Authority in Victoria and recently completed some work with NSW DPIRD to improve their genetic management of their breeding program which will also benefit programs in the other states. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Peter Rose, North Central Catchment Management Authority, Victoria | Ucan, Monash, Nature Glenelg trust, NCCMA VIC, NSW DPI |
| Southern Purple Spotted Gudgeon (Mogurnda adspersa) | Freshwater | M. adspersa is widespread in eastern Australia, while common in coastal drainages, it has undergone a massive decline in the Murray-Darling Basin, having been thought extinct in the southern half of the basin until 3 pops were discovered by chance in 1998, 2004 and 2019. The first 2 pops went extinct during the Millenium Drought. The species also declined in the 2019 drought with some pops in the northern half of the basin being lost. There are now major captive breeding efforts in SA, VIC and NSW to breed remnant pops which are being restocked into wild and semi wild habitats. Unmack has been doing SNPs with NSW DPIRD to improve their genetic management of their breeding program which will also benefit the programs in the other states. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Peter Rose, North Central Catchment Management Authority, Victoria | Monash, Ucan, Middle creek farm, NCCMA VIC, NSW DPI, Nature Glenelg trust, DAF Qld, BMRG, Usyd, |
| Agassizi's Glassfish (Ambassis agassizii) | Freshwater | There are now major captive breeding efforts in NSW and VIC along with interest in SA to breed remnant populations which are just starting to be restocked into wild and semi wild habitats. Unmack is currently working with NSW DPIRD using SNPs to improve their genetic management of their breeding program which will also benefit the programs in the other states. Generating whole genome data will improve our ability to understand which individuals are contributing more to future generations, which pops to mix, how DArT SNPs are distributed across the genome and how well they represent genetic diversity. It also provides an improved starting point for future grant requests that benefit from having a reference genome completed. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Sam Davis, Fisheries NSW | Monash, Ucan, Middle creek farm, NCCMA VIC, NSW DPI, Nature Glenelg trust, DAF Qld, BMRG, Usyd, |
| Pacific Blue Eye (Pseudomugil signifer) | Freshwater, Marine [freshwater] | P. signifer is widespread in fresh and estuarine coastal drainages of NSW and Qld and has extreme mtDNA (3-12% ATPase p-distances between lineages) and geographically variable morphology (fish size, fin size and colour). While both mtDNA and morphology are highly variable, it has been challenging to sort out their taxonomy as to how many species might be present. Having a reference genome, plus some short read data from across the species range will help clarify their underlying phylogenetic relationships and the degree of divergence. This resource will provide a solid basis for future research into their taxonomy, plus the species has a lot of potential for additional behavioural studies (several have been published in the past). | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Peter Unmack, University of Canberra | NT Museum and Art Gallery, Monash |
| Running River Rainbowfish (Melanotaenia sp) | Freshwater | RRRF have always been an enigmatic population, long recognised as being different. Michael Hammer examined rainbowfishes across the Burdekin System in 2015 to sort out its taxonomic status. We discovered another rainbowfish had been introduced into Running River. I organised a group of people to save the species through captive breeding and translocation. SNPs revelaed a complicated history of introgression with other rainbowfish species. Our goal is to use short read genomes to better characterise what unique genetic portions still exist in the RRRF genome and in other closely related, but more heavily introgressed populations to help with understanding the taxonomic uniqueness and evolutionary history of Burdekin System rainbowfishes. | Reference genome (PacBio HiFi), Population genomics (Illumina) | Peter Unmack, University of Canberra | Northern Territory Museum and Art Gallery, Monash |
| Honey Blue Eye (Pseudomugil mellis) | Freshwater | P. mellis is a highly endangered fish from SE Qld which has sadly been largely ignored by management agencies. Having a reference genome will facilitate future research and conservation actions which are likely to be reliant on captive breeding. The genome will also be quite valuable for evolutionary comparisons with other blue eye species. Blue eyes have an elevated rate of evolution (they are small, short lived, and often live in warm environments any of which can drive faster rates, mtDNA cytocrhome b is typically ~10% p-distant divergence between sister species in the family, vs its near sister family rainbowfishes which are often 2-4% divergent) which makes it more difficult to use one genome as a proxy for other related species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Peter Unmack, University of Canberra | Monash University |
| Yarra pygmy perch(YPP) (Nannoperca obscura) Southern pygmy perch (SPP) (Nannoperca australis) | Freshwater | The SPP and the YPP went extinct in the lower MDB. Individual of both species were rescue before the Millenium Drought and used for a captive breeding and reintroduction program with contrasting results. To improve the reintroduction success, genetic rescue would be implemented by mixing different lineages to reduce inbreeding and loss of genetic diversity. Whole genome resequencing will allow the detection of Run of Homozygosity and genetic load to assess the genomic diversity of each lineage and possible genetic incompatibilities among them. This will provide the information to maximize the adaptive potential of reintroduced lineages and implement the best conservation management strategies for each species in the lower MDB | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Jonathan Sandoval-Castillo, Flinders University | Flinders, MAG NT, UniAdel, Nature Glenelg trust, |
| Leafscale gulper shark (Centrophorus squamosus) Birdbeak dogfish/Brier shark (Deania calceus) | Marine | The Centrophoridae family (~15 deepwater species) face significant conservation challenges due to their slow reproductive rates, vulnerability to overfishing, and insufficient protection under international law. Valued for liver oil, many species have elevated extinction risk. Centrophoridae will be proposed for protection under CITES trade restrictions in 2025. For effective enforcement, member countries need traceability tools. Genomics can aid by providing reference nuclear and mitochondrial genomes to develop genus and species-specific assays, resolve taxonomic uncertainties, and assess global population structures. These tools will enable accurate monitoring, support policy enforcement, and inform sustainable management strategies. | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Madeline Green, Institute for Marine and Antarctic Studies, University of Tasmania | NIWA, New Zealand, CSIRO |
| Australian Cods (Maccullochella macquariensis, Maccullochella mariensis, Maccullochella ikei, Maccullochella peelii) | Freshwater | All cods are actively managed for conservation. One major issue is male sex bias in adult pops. We propose to build resources to identify genetic sex markers, hybridization, genomic regions with introgression, and to characterise genomic differences between the species. We propose to generate male (heterogametic sex) reference genomes from three species without assemblies to ensure the genetic integrity of broodstock and to inform conservation efforts. A second focus will be to use short read data from 3 females (homogametic sex) for genome subtraction to identify sex-specific markers. We will evaluate these across the four species to facilitate development of a rapid sex-detection assay. | Reference genome (PacBio HiFi, ONT, HiC, transcriptome), Population genomics (Illumina) | Matthew "Mac" Campbell, The University of Sydney | Ucan, DAF QLD, BMRG, DEECA, Usyd, DPI NSW |
| Black Slickhead (Xenodermichthys copei) Longfin Boarfish (Zanclistius elevatus) Brilliant Lightfish (Polymetme illustris) Little Conger (Gnathophis longicauda) Shortfinned Worm Eel (Scolecenchelys tasmaniensis) Basketwork Eel (Diastobranchus capensis) Cucumber Fish (Paraulopus nigripinnis) Silver Dory (Cyttus australis) Deepwater Burrfish (Allomycterus pilatus ) | Marine | Linking with global initiatives, these reference genomes enable both fundamental and applied research of scarcely-studied groups. Most of the aforementioned species represent the first-ever genomic resources for their families or genera. Using comparative whole-genome analyses, we will investigate trait evolution (e.g. jaw morphology in anguilliforms), identify genetic basis of adaptations (e.g. depth adaptation in deep-sea species such as Xenodermichthys copei, Polymetme illustris), resolve phylogenetic relationships, and inform sustainable management strategies. These data will provide essential baselines for conservation while advancing Australia's capacity in the deep-sea research and innovation. | Reference genome (PacBio HiFi, HiC, transcriptome) | William White, CSIRO Australian National Fish Collection. Hobart, Tasmania | CSIRO, Scripps-UCSD |
| Bull shark (Carcharhinus leucas) | Marine | Nationally, white, tiger, and bull sharks are responsible for the most shark bites, leading to increased calls for culling. Despite varying conservation statuses (vulnerable, near-threatened, least concern), all three species face population declines due to human activities- though the pressure is species dependent. This presents a unique opportunity to compare their conservation statuses and assess the potential effects of future declines such as culling, on genetic diversity. Genomic analyses, along with the generation of a reference genome for bull sharks, will provide valuable insights into their evolutionary history, the impact of culling on genetic diversity and survival, and create critical genomic resources for conservation. | Reference genome (PacBio HiFi, HiC, transcriptome) | Isabella Reeves, Flinders University | Flinders, ANU, JCU, DPI NSW, Uni Otago |
| Australian Angel shark (Squatina australis) | Marine | There are very few shark genomes available and most are poorly sequenced and annotated. Without annotated genomes it is difficult conduct other genomic analysis, such as metagenomics, viromics, metaboliomics, or proteomics. The genome would allow investigation of unique features associated with the evolution of these organisms and between the various levels of the holobiont. During our microbial and viral analysis of sharks in Australia, we have noticed that most are not sequenced and with a small amount of sequencing data we have seen that several single species are actually multiple species. Indeed conducting eDNA surveys off the coast of Australia is currently limited by the lack of genomic data on Australian species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Elizabeth Dinsdale, Flinders University | Flinders Uni |
| Jungle perch (Kuhlia rupestris) | Freshwater, Marine [freshwater] | The distinct southern strain of this species is extinct throughout most of its former range south of Mackay to the NSW border. The Queensland government has established hatchery methods and is currently trialling restocking in two impoundments. Having a reference genome provides a resource to enable genetic diversity to be managed through conservation restocking as the source breeding population is restricted to one small creek on K'Gari. | Reference genome (PacBio HiFi, HiC, transcriptome) | Tim Lucas, Fisheries Queensland | Monash University |
| Southern Eagle ray (Myliobatis tenuicaudatus) | Marine | There are very few shark genomes available and most are poorly sequenced and annotated. Without annotated genomes it is difficult conduct other genomic analysis, such as metagenomics, viromics, metaboliomics, or proteomics. The genome would allow investigation of unique features associated with the evolution of these organisms and between the various levels of the holobiont. During our microbial and viral analysis of sharks in Australia, we have noticed that most are not sequenced and with a small amount of sequencing data we have seen that several single species are actually multiple species. Indeed conducting eDNA surveys off the coast of Australia is currently limited by the lack of genomic data on Australian species. | Reference genome (PacBio HiFi, HiC, transcriptome) | Elizabeth Dinsdale, Flinders University | Flinders Uni |
| Swamp Eel (Ophisternon gutturale) | Freshwater | Swamp eels (family Synbranchidae) have a circumtropical distribution with a range of life history modes ranging from obligate freshwater, troglobiont, semi-terrestrial and estuarine. They are behaviourally and morphologically cryptic with a similar simple body form that hinders traditional systematic assessment. Molecular systematics has proved fruitful in uncovering hidden biodiversity and relationships of the group in Southeast Asia, and preliminary data for Australasian Ophisternon indicates a hyper-species complex, represented by two major lineages each with several candidate species. The availability of a full genome will allow a more robust and in-depth assessment of species boundaries and evolutionary processes. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Michael Hammer, Museum and Art Gallery of the Northern Territory (MAGNT) | Museum and Art Gallery of the Northern Territory, Deakin Uni |
| Fiddler ray (Trygonorrhina dumerilii) | Marine | There are very few shark genomes available and most are poorly sequenced and annotated. Without annotated genomes it is difficult conduct other genomic analysis, such as metagenomics, viromics, metaboliomics, or proteomics. The genome would allow investigation of unique features associated with the evolution of these organisms and between the various levels of the holobiont. During our microbial and viral analysis of sharks in Australia, we have noticed that most are not sequenced and with a small amount of sequencing data we have seen that several single species are actually multiple species. Indeed conducting eDNA surveys off the coast of Australia is currently limited by the lack of genomic data on Australian species. | Reference genome (PacBio HiFi, HiC, transcriptome) | Elizabeth Dinsdale, Flinders university | Flinders Uni |
| Edgbaston goby (Chlamydogobius squamigenus) Elizabeth Springs Goby (Chlamydogobius micropterus) | Freshwater | Edgbaston Goby are closely managed by Bush Heritage Australia and Unmack has been collaborating with them on collecting DArT SNPs for this species, plus some on Elizabeth Springs Goby. Both species are low in genetic diversity and require careful management to ensure no further losses of genetic diversity occur. Having reference genomes will greatly expand the value of our SNP datasets and improve our understanding of their genetic diversity and set us up to collect future data to allow us to explore historical changes in population size which is fundamental to understanding the evolutionary history of these species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Dean Gilligan, Bush Heritage Australia | Ucan, Monash |
| Mangrove Blue-eye (Pseudomugil halophilus) | Marine | The Mangrove Blue-eye has been hiding in plain sight for the last 150 years of Australian ichthyological exploration along the north-east coast of Australia. It has a specialised coastal fringing habitat in mangroves, and is morphologically conserved being similar in appearance to sympatric Pacific Blue-Eye (euryhaline), and Honey Blue-eye (obligate wetland habitat specialist). The evolutionary relationships and origins of this group remain unresolved, with the genus also appearing to be paraphyletic. A whole genome will establish a framework to better explore these relationships and for examining population genetics of the Mangrove Blue-eye across environmental gradients and spatial conservation units. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Michael Hammer, Museum and Art Gallery of the Northern Territory | Museum and Art Gallery of the Northern Territory, Monash |
| Snapper (Chrysophrys auratus) | Marine | In a past ARC Linkage (2019-2022) with the 5 major state fisheries agencies of Australia, we used ddRAD SNPs to clarify stock structure, connectivity, and parameters of economic relevance for snapper across the continent (e.g. uploaded PDFs). Here we request support for WGS data to characterise, for the first time, population-level adaptive diversity across equivalent latitudinal clines of temperature on the east and west coasts of Australia. We expect to find signal of parallel climatic evolution in genomic regions (including structural variations, SVs). Outputs will help clarifying stock resilience and will be used by our fishery agency collaborators (DPIRD NSW and DPIRD WA) for evidence-based stock management under climate change. | Population genomics (Illumina) | Luciano Beheregaray, Flinders University | DPIRD, DPI NSW, Plant and food research NZ, Flinders |
| Southern sandgobies (Nesogobius) | Marine | Nesogobius are cool temperate marine gobies distributed between Sydney-Perth and south around Tasmania. It is one of only two endemic southern Australian goby genera, having a relatively high species diversity as a radiation with species zoned across different depths/tidal ranges/microhabitats. There are 5 described and at least 7 undescribed taxa, and the project lead has been actively involved in their taxonomy with Dr Doug Hoese (Australian Museum). Preliminary genetic data indicates a potential early branching position for the genus, which requires much more robust data to confirm. A whole high quality reference genome will facilitate robust assessment of existing sequencing in study of species boundaries and relationships. | Reference genome (PacBio HiFi, HiC, transcriptome) | Michael Hammer, Museum and Art Gallery of the Northern Territory | Museum and Art Gallery of the Northern Territory, Monash |
| Maugean skate (Zearaja maugeana) | Marine | The Maugean Skate is arguably the world’s most endangered elasmobranch. While our understanding of the species biology, ecology, life history and population structure has significantly improved in recent years, there remain key knowledge gaps regarding current population level genetic characteristics and recent demographic history. This project seeks to understand those crucial parameters to inform effective conservation strategies and enhance restoration efforts. We are requesting support for whole genome (re) sequencing of multiple representative individuals from the current population | Population genomics (Illumina) | Jayson Semmens, Institute for Marine and Antarctic Studies, University of Tasmania | Utas, NRE Tas |
| Peppered Mudskipper (Apocryptodon madurensis) Scaleless Wormgoby (Caragobius urolepis) | Marine | Gobies from subfamilies Amblyopinae (worm gobies) and Oxudercinae (mudskippers) are wide-spread across the tropical Indo-pacific in estuarine and near shore habitats, with only limited Australian whole genome coverage, and some international genera represented. Targeted addition of 2 whole genomes from the group will assist local and broader evolutionary and biodiversity research in the group. Genetic and morphological data in progress highlights high cryptic diversity in northern Australia. The genera Caragobius and Apocrypton are key gaps in family representation and hold different ecological roles (in-fauna and semi-terrestrial respectively), and are accessible from the Darwin region | Reference genome (PacBio HiFi, HiC, transcriptome) | Michael Hammer, Museum and Art Gallery of the Northern Territory | Museum and Art Gallery of the Northern Territory, Monash |
| Redfin Blue-eye (Scaturiginichthys vermeilipinnis) | Freshwater | Redfin Blue Eye (RFBE) are closely managed by Bush Heritage Australia and Unmack has been collaborating with them on collecting DArT SNPs for this species and assisting Elise Furlan with novel nuclear focused eDNA approaches on this species. RFBE are low in genetic diversity and require careful management to ensure no further losses of genetic diversity occur. Having reference genomes will greatly expand the value of our SNP datasets and improve our understanding of their genetic diversity and set us up to collect future data to allow us to explore historical changes in population size which is fundamental to understanding the evolutionary history of this species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Dean Gilligan, Bush Heritage Australia | Ucan, Monash |
| Western pygmy perch (Nannoperca vittata) | Freshwater | The Warren-Donnelly catchments in southwest WA are highly impacted by agricultural supply, rising salinisation and declining water flows. Freshwater fauna in these areas, particularly poor dispersers like western pygmy perch, will be further threatened by climate change. Direct management of river flows is needed to maintain biodiversity, but little is known about the ecological needs for dispersal in these systems. Previous genomic work also suggested that N. vittata is a complex of multiple cryptic species; however, these catchments were not sampled and occur at the boundary of two of them. Genomic analyses are needed to understand connectivity, guide water management, and inform taxonomy of N. vittata in this critical part of its range. | Population genomics (Illumina) | Sean Buckley, School of Science, Edith Cowan University | DWER WA, DBCA, UWA, Murdoch |
| Australian Brook lamprey (Mordacia praecox) Short-headed lamprey (Mordacia mordax) | Freshwater | Lampreys exist in cryptic species pairs based on adult parasitic and non-parasitic feeding types. For most of their life history, there is currently no way to distinguish between the Mordacia praecox (EN) from the sympatric, M. mordax (LC). Recently, M. praecox was confirmed to occur in QLD, making it the only tropical lamprey globally. Preliminary genetic analyses have revealed there may be multiple non-parasitic species. High quality genome assemblies of Mordacia sp. will allow us to perform comparative genomics analyses and develop a molecular assay to discern between these two species and investigate the possibility of undescribed non-parasitic species. This will be of great significance for lamprey species pair research globally. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Ido Bar, Centre for Planetary Health and Food Security, Griffith University | Griffith, DES QLD, CSIRO |
| Black-stripe minnow (Galaxiella nigrostriata) | Freshwater | The Black-stripe minnow is an endangered freshwater fish endemic to the SW of Western Australia. Its currently fragmented distribution suggests extensive declines. There is an urgent need to develop strategies such as captive breeding and translocation. However, there are no genomic resources available to guide such programs. Here, we propose to (1) assemble a reference genome, and (2) undertake WGS across extant populations. These data will be used to assess genetic diversity, structure, and inbreeding, and guide sourcing of individuals for potential captive breeding or translocation. We will also use this species to assess how well our G. occidentalis data represent diversity in a threatened species. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Renee Catullo, University of Western Australia | DBCA, DWER WA, ECU, murdoch, WAM |
| Western Minnow (Galaxias occidentalis) | Freshwater | The western minnow is a non-threatened species that is broadly distributed across the SW, and therefore a feasible species to sample for assessing broad patterns of diversity across and within catchments. For this proposal, we will use sampling from all catchments, and at the ends of each catchment. Using these data, we will assess overall population structure, and how genetic diversity (e.g. allelic richness, inbreeding, etc) varies upstream and downstream. The goal of this initial dataset is to produce a broad-scale publication on diversity patterns that can then be used to apply for further funding, which will assess fine-scale within-catchment variation to understand how water management affects connectivity. | Population genomics (Illumina) | Renee Catullo, University of Western Australia | DBCA, DWER WA, ECU, murdoch, WAM |
| Spiny Chromis Damselfish (Acanthochromis polyacanthus) | Marine | The damselfish A. polyacanthus is ideal for studying population structure, and evolutionary history on the Great Barrier (GBR). Lacking a pelagic larval stage and being confined to natal reefs, A. polyacanthus populations are highly divergent. Evidence from mDNA, and whole genome (re)sequencing suggesting that colour morphs mask speciation. By sequencing additional populations from southern ‘dark’ morph, and using computational tools for demographic inference (e.g., SMC++, fastimcoal, and PSMC), we aim to test existing hypothesis surrounding historical evolutionary events and speciation between different A. polyacanthus colour morphs, and potentially classifying the southern ‘dark’ morph as new species of marine fish within Australia. | Reference genome (PacBio HiFi, transcriptome), Population genomics (Illumina) | Elliott Schmidt, James Cook University | JCU |
| Clown anemonefish (Amphiprion ocellaris) Orange clownfish (Amphiprion percula) | Marine | The recent publication of Clownfish genomes revealed they lack the genetic variation to adapt to climate change. Finding Nemo's success led to a decade of overfishing causing genetic drift that‚further reduced diversity and caused local extinctions. Captive breeding is necessary to continue supplying the industry, including genome-wide methods is particularly important for endangered/exploited species to characterise adaptive genetic variation and guide captive breeding and conservation efforts. Despite this, high-quality genomic data are limited; the initial genome was highly fragmented using one fish of unknown age and sex, re-assembly saw genome completeness improve by 16% integrating Nanopore long-reads and further work is needed. | Population genomics (Illumina) | Katarina Doughty, University of Western Australia | UWA, Living Oceans Pty |
| Flatheaded Galaxias (Galaxias rostratus) | Freshwater | The conservation stocking program needs a quality reference genome to assist with conservation actions as well as hatchery production. Some DArT SNP sequencing has been completed, but it would benefit greatly by being able to map those SNPs. | Reference genome (PacBio HiFi, HiC, transcriptome), Population genomics (Illumina) | Tarmo A. Raadik, Arthur Rylah Institute for Environmental Research, Department of Energy, Environment and Climate Action, Victoria | DEECA, Monash |
PARTNERS
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advisory committee members
Freshwater Fish Advisory Committee
Christopher Burridge | University of Tasmania |
Luciano Beheregaray (Chair) | Flinders University |
Mark Kennard | Griffith University |
Michael Hammer | The Museum and Art Gallery of the Northern Territory |
Peter Unmack | University of Canberra |
Sarah Richmond | Bioplatforms Australia |
Sophie Mazard | Bioplatforms Australia |
Marine Fish Advisory Committee
Campbell Davies | CSIRO |
Christine Dudgeon | University of Queensland |
Will White | CSIRO |
Yi-Kai Tea | Australian Museum |
Shannon Corrigan | Minderoo Foundation |
Sarah Richmond (Chair) | Bioplatforms Australia |
Sophie Mazard | Bioplatforms Australia |
KEY INFORMATION
ACKNOWLEDGEMENT INFORMATION
Bioplatforms Initiative DOI: https://doi.org/10.25953/ysny-p489
Umbrella Bioproject ID: PRJNA1098053
Please use this ID when submitting any derived data to a database that is a member of the International Nucleotide Sequence Database Collaboration (INSDC), such as GenBank/NCBI, ENA or DDBJ.
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Citation Guidelines
To cite the general initiative:
Australian Fish Genomics Initiative, 2024, https://doi.org/10.25953/ysny-p489
To cite a specific dataset:
The Australian Fish Genomics Initiative, 2024, https://doi.org/10.25953/ysny-p489, [year-of-data-download], [full dataset title], [dataset-access-URL], accessed [date-of-access].
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Acknowledgement Statement
We would like to acknowledge the contribution of the Australian Fish Genomics Initiative Consortium in the generation of data used in this publication. The Initiative is supported by funding from Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy (NCRIS).
If relevant, also credit other organisations involved in the collection of the particular dataset you are using, as listed in the ‘project_lead’ and ‘project_collaborators’ in the metadata record.
CONTACT US
Project Manager
Sophie Mazard – Bioplatforms Australia
smazard@bioplatforms.com
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com
DATA AND COLLABORATION POLICY
Data generated through this initiative is subject to the Data and Collaboration policy. Please review it here.