By sequencing the genome of the endangered Southern Corroboree Frog, we could save it

Ever since I first learned about the devastating disease killing frogs worldwide, I knew I wanted to be part of the solution.

In the 1980s, mysterious die-offs started occurring in frogs in Australia and the Americas. During this time, hundreds of frogs were found dead or reported missing.

Declines in Australia started in Queensland and moved up and down the east coast.

Then, in 1998, during her PhD studies, Associate Professor Lee Berger discovered the pathogen that causes amphibian chytrid fungus disease, found to be responsible for the mass deaths of many frog species in Australia and worldwide.

Since then, the fungus has decimated populations of a tiny black and yellow Australian frog.

The Southern Corroboree Frog (Pseudophryne corroboree; Myobatrachidae) is now classed as functionally extinct, meaning it can no longer survive without support in the wild, only in zoos.

But with our latest study, we hope we now have the genetic tools to help the Corroboree Frog overcome the fungus and return to its habitat in the Snowy Mountains.

Sciences & Technology

Captive breeding to prevent extinction

After nearly 10 years of work, our research team has produced the first genome sequence – the genetic blueprint – of the Southern Corroboree Frog.

Understanding its genetics will help our team develop innovative breeding strategies to support its survival.

Blueprint to fight infection

Despite their small size, Corroboree Frogs have remarkably large genomes, nearly three times the size of the human genome. Measured in DNA base pairs, the Corroboree Frog genome is nearly nine billion base pairs or 9 gigabases, where ours is around 3.1 gigabases.

Interestingly, Corroboree Frogs have only 12 pairs of chromosomes compared to our 23, meaning their chromosomes are exceptionally large, with the biggest being five times the size of the largest human chromosome.

This makes it one of the largest genomes of any Australian frog and significantly larger than many other species of Australian ground frogs.

Amphibian genomes are notoriously difficult to sequence due to their sheer size, but the reasons behind why they are so large remain unclear.

We also found that more than 80 per cent of its genome is made up of non-coding DNA – genetic material that doesn’t directly code for proteins, and we aim to explore what this might mean for the species, and for other amphibians.

A decade in the planning

Sequencing the Corroboree Frog genome was an international effort nearly a decade in the making. It began when I first reached out to researchers at the Vertebrate Genomes Project at Rockefeller University (USA) to explore the possibility of sequencing the genome.

After extensive discussions about funding, selecting the right DNA-donor frog from Melbourne Zoo’s conservation breeding program and navigating logistical challenges to transport the invaluable samples to the USA, sequencing finally commenced in early 2021.

Environment

Hope for endangered frogs

Seeing the first assembled genome data was an incredible moment for me – after years of effort, we finally had a complete genetic blueprint of this iconic species.

This project is a testament to the power of collaboration, persistence and scientific innovation.

Thanks to our amazing team, we achieved a high-quality genome, assembled with exceptional completeness, down to piecing together the DNA sequences into their full chromosomes – the thread-like structures that house the DNA in the cell.

Now, my research group, in collaboration with Melbourne Zoo, Taronga Conservation Society Australia and NSW Department of Climate Change, Energy, the Environment and Water, is using this genome to investigate how and why individual frogs and populations respond differently to chytridiomycosis infection.  

Targeted breeding for Corroboree Frog survival

The genome will allow us to understand down to the gene level which factors increase or decrease susceptibility to the chytrid disease. This will help us to develop approaches to increase the frequency of potential genes that may boost the immune system to fight it.

Our goal is to apply this knowledge to selectively breed Corroboree Frogs for increased disease resistance, giving them a fighting chance to persist in the wild once again.

Beyond Corroboree Frog conservation, this genome is also an incredible resource for studying amphibian genetics more broadly.

As part of the Amphibian Genomics Consortium, an international initiative dedicated to advancing amphibian genomics, researchers will use this data to explore genetic factors linked to disease resistance, climate adaptation and evolutionary history.

Sciences & Technology

Using genetics to conserve wildlife

These insights could help inform conservation strategies for other frogs threatened by chytridiomycosis and other environmental challenges by enabling the identification of genes that impact resilience to major threats.

We also plan to compare the Corroboree Frog genome with those of other amphibians to uncover broader patterns of resilience.

Our ultimate goal is to translate these findings into real-world conservation action, helping to secure a future for this remarkable species in the wild.

The research team consisted of three researchers from the University of Melbourne (Tiffany Kosch,  Lee Berger, Lee Skerratt), nine researchers from the Vertebrate Genomes Laboratory (Erich Jarvis, Linelle Abueg, Guilio Formenti, Tatiana Tilley, Nivesh Jain, Brian O'Toole, Conor Whelan, Oliver Fedrigo, Jennifer Balacco), two people from Zoos Victoria (Deon Gilbert, Damian Goodall), David Hunter (NSW-DCCEEW), Michael McFadden (Taronga Conservation Society Australia), Ira Cooke James Cook University), Andrew Crawford (Universidad de los Andes), and three researchers from the Wellcome Sanger Institute (Joanna Collins, Bethan Yates, Matthieu Muffato)