How scientists built a chromosome-level genome to rescue a critically endangered species from fungal extinction
In Australia's Snowy Mountains, a striking black-and-yellow amphibian—the Southern Corroboree Frog (Pseudophryne corroboree)—once thrived in alpine peat bogs. Today, this iconic species is functionally extinct in the wild, decimated by the deadly chytrid fungus Batrachochytrium dendrobatidis. First detected in the 1980s, this pathogen suffocates frogs by destroying their skin and has driven over 90 amphibian species to extinction globally 4 9 . But hope emerges from a decade-long international effort: the first chromosome-level genome assembly for this critically endangered frog, offering a roadmap for its resurrection 1 6 .
The Southern Corroboree Frog is listed as Critically Endangered by the IUCN, with fewer than 50 individuals estimated in the wild.
The Corroboree frog's genome stunned scientists with its complexity:
| Feature | Value | Significance |
|---|---|---|
| Total assembly size | 8.87 Gb | Largest Australian frog genome sequenced |
| Contig N50 | 6.8 Mb | Indicates high continuity |
| Chromosomes | 12 | 92.3% of genome mapped to chromosomes |
| BUSCO completeness | 89.8% | High gene-space coverage |
Researchers discovered that resistance to chytridiomycosis is heritable and polygenic—controlled by many genes. This finding enables selective breeding of resilient frogs 9 . Genome-wide association studies identified variants linked to immune responses, paving the way for CRISPR-based interventions to edit susceptibility genes 9 .
A male captive-bred frog (Zoo ID: B50597) from Melbourne Zoo was euthanized ethically. Kidney, liver, and other tissues were flash-frozen for analysis 1 8 .
The VGP Pipeline 2.0 integrated data, followed by manual curation correcting 280 structural errors 8 .
| Chromosome | Length (Mb) | GC Content (%) |
|---|---|---|
| 1 | 1251.52 | 45.5 |
| 4 | 947.25 | 45.5 |
| 7 | 518.98 | 46.0 |
| 12 | 177.84 | 46.5 |
Critical tools and materials that powered this genome project:
| Reagent/Technology | Role | Outcome |
|---|---|---|
| PacBio Sequel IIe | HiFi sequencing | Produced long, accurate reads (Q20+) |
| Arima-HiC 2.0 kit | Chromatin conformation capture | Scaffolded sequences into chromosomes |
| QIAGEN RNAeasy Protect Kit | RNA extraction from tissues | Enabled transcriptome annotation |
| MagAttract HMW DNA Kit | Isolated intact DNA strands | Preserved high molecular weight DNA |
| VGP Pipeline 2.0 | Genome assembly integration | Automated error correction |
Melbourne Zoo's captive population is being screened for resistant alleles. Frogs with protective variants ("Ellies") are prioritized for breeding 9 .
CRISPR-Cas9 experiments aim to introduce resistance genes from resilient relatives like the Common Eastern froglet 9 .
The Southern Corroboree frog's genome is more than data—it's a genetic ark for species recovery. As scientists refine breeding and gene-editing protocols, the goal is clear: return this jewel of the Snowy Mountains to its peat-bog home. For conservationists, this work proves that when genomics and ecology converge, extinction is not an endpoint—it's a challenge to overcome.
"What we learn from the Corroboree frog could save hundreds of other amphibians. This is genomics as a lifeline."