– ABOUT
amphibian AND REPTILE GENOMICS
Established in 2020, the Amphibian and Reptile Genome Initiative is building a robust foundation of genomic data to advance the understanding and conservation of Australia’s unique reptiles and amphibians. By leveraging Australia’s distinctive strengths in biodiversity research, the initiative accelerates genomics research and addresses critical conservation needs. It fosters a collaborative network of museums, universities, research organisations, and government agencies, while raising awareness about the importance of genomics in the conservation of Australian species.
The initiative is centred on three core programs: comparative genomics and evolution, phylogenomics, and taxonomy and conservation genomics. These programs aim to develop high-quality reference genomes, establish a comprehensive phylogenetic framework, and create genomic datasets for threatened species. The Amphibian and Reptile Genome Initiative supports conservation, taxonomic clarification, and evolutionary research on Australia’s reptiles and amphibians. Find out more on the initiative’s website.
OBJECTIVES
The creation of referential genomic data resources of Australian reptiles and amphibians will:
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- Build genomic data to enhance the understanding and conservation of Australia’s reptiles and amphibians.
- Advance global research in reptile and amphibian genomics.
- Use genomics to address conservation needs and biodiversity issues.
- Create a sustainable collaborative network among Australian institutions.
- Raise awareness of reptile and amphibian diversity and the role of genomics in their conservation.
DATA
For further information and to view and access initiative data, please go to the Bioplatforms Australia Data Portal.
PROJECTS
| Project name | Project Summary | Species name | Project aim | Project lead | Partners |
|---|---|---|---|---|---|
| Shingleback Lizard - Tiliqua rugosa | Reference Genome (HiFi, Hi-C, PromethION), resequencing (Illumina) and transcriptomes (Illumina) | Mike Gardner | Flinders University, SA Museum | ||
| Eastern water dragon - Physignathus lesueurii | Reference Genome (HiFi, Hi-C) and transcriptomes (Illumina) | Cecile Frere | |||
| Eastern three-lined skink - Bassiana duperreyi | Reference Genome (HiFi, Hi-C, PromethION), resequencing (Illumina) and transcriptomes (Illumina) | Arthur Georges, Janine Deakin | |||
| Pig nosed turtle - Carettochelys insculpta | Reference Genome (Hi-C, PromethION), resequencing (Illumina) and transcriptomes (Illumina) | Arthur Georges, Matt Young | |||
| Dtellas - Gehyra lapistola (australis) | Reference Genome (Hi-C) | Emily Roycroft | |||
| Dtellas - Gehyra paranana (nana) | Reference Genome (Hi-C, PromethION) and resequencing (Illumina) | Emily Roycroft | |||
| Dtellas - Gehyra moritzi (variegata) | Reference Genome (Hi-C) | Emily Roycroft | |||
| Dtellas - Gehyra purpurascens | Reference Genome (Hi-C) | Emily Roycroft | |||
| Bungle Bungle Ranges gehyra - Gehyra ipsa | Reference Genome (Hi-C) | Emily Roycroft | |||
| Northern spotted rock dtella - Gehyra nana | Reference Genome (Hi-C) | Emily Roycroft | |||
| Ghost gecko - Gehyra lauta | Reference Genome (Hi-C) | Emily Roycroft | |||
| East Arnhem land gehyra - Gehyra arnhemica | Reference Genome (Hi-C) | Emily Roycroft | |||
| Plain tree gehyra - Gehyra gemina | Reference Genome (Hi-C) | Emily Roycroft | |||
| King's Rock Gehyra - Gehyra koira | Reference Genome (Hi-C) | Emily Roycroft | |||
| Relictual Karst Gehyra - Gehyra calcitectus | Reference Genome (Hi-C) | Emily Roycroft | |||
| Western Kimberley Tree Gehyra - Gehyra chimera | Reference Genome (Hi-C) | Emily Roycroft | |||
| Olive headed sea snake - Hydrophis major | Reference Genome (HiFi, Hi-C) and transcriptomes (Illumina) | Kate Sanders | |||
| delicate skink - Lampropholis delicata (eugongylus) | Reference Genome (HiFi, Hi-C, PromethION), resequencing (Illumina) and transcriptomes (Illumina) | Oliver Griffith | |||
| Central bearded dragon - Pogona vitticeps | Reference Genome (Hi-C, PromethION) | Janine Deakin, Arthur Georges | |||
| Investigating hybridisation and climate adaptation in skinks through genomic analysis | This project aims to generate a Pseudemoia entrecasteauxii genome to investigate hybridisation with the endangered alpine bog skink (P. cryodroma) and develop molecular markers for population genetics. These markers will allow mapping of adaptive loci under selection, aiding comparisons across skink populations in different climates. | Southern grass skink - Pseudemoia entrecasteauxii | Reference Genome (HiFi, Hi-C), resequencing (Illumina) and transcriptomes (Illumina) | Oliver Griffith | University of Melbourne, The University of Sydney, La Trobe, Monash Univerity, Museums Victoria, University of Tasmania. |
| Ornate burrowing frog - Platyplectrum ornatum | Reference Genome (Hi-C, PromethION) | Renee Catullo | |||
| Fletcher's frog - Lechriodus fletcheri | Reference Genome (Hi-C) | Renee Catullo | |||
| Three-toed skink - Saiphos equalis | Reference Genome (HiFi, Hi-C), resequencing (Illumina) and transcriptomes (Illumina) | Camilla Whittington | |||
| Green-eyed treefrog - Litoria serrata | Reference Genome (HiFi, Hi-C), size estimate (Illumina) and transcriptomes (Illumina) | Megan Higgie | |||
| Broad-shelled river turtle - Chelodina expansa | Reference Genome (Hi-C, PromethION), resequencing (Illumina) and transcriptomes (Illumina) | Arthur Georges | |||
| Murray River Turtle - Emydura macquarii | Reference Genome (PromethION, Hi-C), resequencing (Illumina) and transcriptomes (Illumina) | Arthur Georges | |||
| Southern ornate nursery frog - Cophixalus australis | Reference Genome (HiFi, Hi-C), resequencing (Illumina) and transcriptomes (Illumina) | Conrad Hoskin | |||
| Southern Gastric-brooding Frog - Rheobatrachus silus | Reference Genome (HiFi) and resequencing (Illumina) | Steve Donnellan | |||
| Northern Gastric-brooding Frog - Rheobatrachus vitellinus | Resequencing (Illumina) | Steve Donnellan | |||
| Orange-crowned toadlet - Pseudophryne occidentalis | Resequencing (Illumina) | Steve Donnellan | |||
| Eungella leaf-tailed gecko - Phyllurus nepthys | Reference Genome (HiFi, Hi-C) and transcriptomes (Illumina) | Conrad Hoskin | |||
| Bynoe's gecko - Heteronotia binoei | Reference Genome (HiFi, Hi-C) | Kate O'Hara | |||
| Pygopodidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Typhlopidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Pygopodidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Carphodactylidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Eugongylus | Exon Capture (Illumina) | Elizabeth Broady | |||
| Elapidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Diplodactylidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Dragon | Exon Capture (Illumina) | Elizabeth Broady | |||
| Sphenomorphine | Exon Capture (Illumina) | Elizabeth Broady | |||
| Elapidae2 | Exon Capture (Illumina) | Elizabeth Broady | |||
| Gekkonidae | Exon Capture (Illumina) | Elizabeth Broady | |||
| Gap filling | Exon Capture (Illumina) | Elizabeth Broady | |||
| Gehyra spp. | Population Genetics (DArT) | Renee Catullo | |||
| A genomic approach to assess the diversity of the water and olive pythons (Liasis) | olive pythons (Liasis) | Population Genetics (DArT) | Renee Catullo, Joanna Sumner | ||
| A look under the carpet: a genomic approach to assess the diversity of the carpet pythons (Morelia spilota complex) | carpet pythons (Morelia spilota complex) | Reference Genome (HiFi) and Population Genetics (DArT) | Stephen Sarre | ||
| Clarifying the taxonomy of Collared Burrowing frogs (Cyclorana brevipes complex) species from central and eastern Australia | Collared Burrowing frogs (Cyclorana brevipes complex) | Population Genetics (DArT) | Paul Oliver, Conrad Hoskin | ||
| Conservation and genes under selection in the alpine tree frog (Litoria verreauxii alpina) | alpine tree frog (Litoria verreauxii alpina) | Population Genetics (DArT) | Renee Catullo | ||
| Conservation and taxonomy of geckos (Oedura lineata and Strophurus taenicauda subspecies) in Brigalow remnants of the central-eastern QLD | Oedura lineata and Strophurus taenicauda | Population Genetics (ddRAD) | Conrad Hoskin, Craig Moritz | ||
| Conservation genomic-informed management of threatened ‘sky island’ Cophixalus nursery frogs | Nursery frog - Cophixalus spp. | Population Genetics (DArT) | Arthur Georges | ||
| Cryptic Crypto’s: Deciphering cryptic diversity to promote evolutionary and conservation research on Cryptoblepharus skinks | Resequencing (Illumina) | Arthur Georges | |||
| Developing Genetic Tools to Increase Spotted Tree Frog Resilience to Chytridiomycosis | Population Genetics (DArT) | Graeme Gillespie, Renee Catullo | |||
| Elucidating unrecognised restricted-range species of arid-zone Diplodactylus geckos | Population Genetics (DArT) | Mitzi Pepper | |||
| Generating a reference genome for the Common Eastern froglet (Crinia signifera) for comparative analysis of immunity in amphibians | Population Genetics (DArT) | Damien Esquerre | |||
| Generating a reference genome for the Common Eastern froglet (Crinia signifera) for comparative analysis of immunity in amphibians | Population Genetics (DArT) | Damien Esquerre | |||
| Generating a reference genome for the Common Eastern froglet (Crinia signifera) for comparative analysis of immunity in amphibians | Population Genetics (DArT) | Ian Brennan | |||
| Generating a reference genome for the Common Eastern froglet (Crinia signifera) for comparative analysis of immunity in amphibians | Resequencing (Illumina) | Sofia Hayden, Sally Potter | |||
| Genetic assessment of high priority bushfire-affected frogs | Reference Genome (HiFi) | Matt West | |||
| Genetic assessment of high priority bushfire-affected snakes | Population Genetics (ddRAD) | Callum McDiarmid | |||
| Genetic distinctiveness and diversity of the Pedra Branca skink | Population Genetics (ddRAD) | Megan Higgie | |||
| Impacts of changing environments on south-eastern Australian dragon lizards | Resequencing (Illumina) | Steve Donnellan | |||
| Population genetic structure of the Howard River Toadlet, Uperoleia daviesae | Population Genetics (DArT) | Steve Donnellan, Harry Hines | |||
| Protecting and connecting sea snake populations across northern Australia | Population Genetics (DArT) | Geoff White, Chris Burridge | |||
| Reproductive isolation and cryptic diversity in the spotted snow skink | Population Genetics (DArT) | Eric Wapstra, Chris Burridge. Paul Sanders | |||
| Resolving species boundaries among Amalosia geckos across the Australian savannas | Population Genetics (DArT) | Steve Donnellan, Hartvigsen-Power, Hutchinson | |||
| Resolving taxon boundaries and estimating genetic risk for reptiles impacted by 2019/20 fires - Egernia saxatilis complex | Population Genetics (DArT) | Stephen Zozaya, Conrad Hoskin | |||
| Resolving taxon boundaries and estimating genetic risk for reptiles impacted by 2019/20 fires - leaftail geckos (Saltuarius, Phyllurus) | Resequencing (Illumina) | Wendt, Brannelly | |||
| Species Delimitation and Phylogeography in eastern Australian skink species complexes | Population Genetics (DArT) | Steve Donnellan | |||
| Species Delimitation and Phylogeography of the Australasian Chelidae | Population Genetics (DArT and ddRAD) | Bail Hoskin and Kate Sanders | |||
| Taxonomic comparison of Kangaroo Island and mainland populations of amphibian and reptiles – evaluation of the conservation impact of the 2019-20 bushfires | Reference Genome (HiFi) | Tiffany Kosch | |||
| Taxonomic resolution of central Australian Pseudophryne (Myobatrachidae), rare mesic relicts in the dry heart | Transcriptomes (Illumina) | Tiffany Kosch | |||
| The Devil You Know: Investigating Population Structure of Moloch horridus | Reference Genome (Illumina) | Tiffany Kosch | |||
| Uncovering diversity in the ‘dead heart’ of Australia: systematics and taxonomy of arid zone geckos | Reference Genome (Hi-C) | Tiffany Kosch | |||
| Understanding the diversity and connectivity of populations of Lampropholis skinks from the east coast of Australia | Population Genetics (ddRAD) | Mitchell and Catullo | |||
| Understanding the diversity and connectivity of threatened Sunset frog (Spicospina flammocaerula) populations from the peatlands of southwest Australia | Population Genetics (DArT) | Peter McDonald, Paul Oliver | |||
| Yellow-spotted Bell Frog (Litoria castanea) and Peppered Tree Frog (Litoria piperata) | Reference Genome (HiFi) and resequencing | Rachael Dudaniec |
PARTNERS
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advisory committee members
- Distinguished Prof Arthur Georges (University of Canberra)
- Dr Renee Catullo (University of Western Australia)
- Dr Jane Melville ( Museums Victoria)
- Dr Jodi Rowley (Australian Museum)
- Prof Scott Keogh (Australian National University)
- Dr Margaret Byrne (Dept of Biodiversity, Conservation and Attractions)
- Andrew Gilbert (Bioplatforms Australia)
CONTACT US
Project Manager
Sophie Mazard – Bioplatforms Australia
smazard@bioplatforms.com
General Manager – Science Programs
Sarah Richmond – Bioplatforms Australia
srichmond@bioplatforms.com