Scientists assemble the cane toad genome

An international research team, led by UNSW, has unlocked the DNA of the cane toad. Published in the journal GigaScience, the breakthrough will help scientists gain a better understanding of what makes Australia’s most infamous amphibian tick.

As explained by project leader Prof Peter White, from UNSW, “There are major gaps in our understanding of cane toad genetics, and up until now no-one had put the genome together.” A decade ago, Western Australian researchers tried to sequence the cane toad genome, but they encountered obstacles and didn’t complete the project.

For this project, the researchers worked at the Ramaciotti Centre for Genomics at UNSW, which has played a role in decoding the genomes of other iconic Australian species, including the koala. Lead author Dr Rich Edwards explained, “By using the cutting-edge sequencing technology and expertise available at UNSW, we sequenced 360-odd billion base pairs and assembled one of the best-quality amphibian genomes to date.

“We managed to decipher more than 90% of the cane toad genes using technology that can sequence very long pieces of DNA, which makes the task of putting together the genome jigsaw much easier.”

Having a draft cane toad genome is expected to help to close key knowledge gaps and accelerate cane toad research. More toads can now be sequenced at a fraction of the cost, and the genome is freely available — anyone can access it now and conduct further research.

“Future analysis of the genome will provide insights into cane toad evolution and enrich our understanding of their interplay with the ecosystem at large — it will help us understand how the toad spreads, how its toxin works, and provide new avenues to try to control its population,” said study co-author and cane toad expert Professor Rick Shine from the University of Sydney.

“Very few amphibian genomes have been sequenced to date, so this is also great news for amphibians. Having a reference genome could provide valuable insights into how invasive species evolve to adapt to new environments.”

Having the genome will also help researchers to find new options for controlling the toad population. Professor White noted, “Current measures like physical removal haven’t been successful, but new methods to teach native species not to eat the toad — called taste aversion — give new hope. However, we need more approaches to control this invasive species.”

One such alternative measure is biocontrol, ie, using a virus to help control the toad population — for which the toad’s genetic material is essential. As explained by UNSW PhD student Alice Russo, “To find a virus for biocontrol, we need access to the toad’s DNA and RNA.

“DNA contains ancient fragments of viruses — the DNA of every animal can sometimes catalogue past infections.”

While viruses have previously been used to control the European rabbit population, the issue with cane toad viruses is that they could potentially infect native amphibians — which is why researchers are seeking to find a cane toad-specific virus.

In a paper published in the Journal of Virology, Russo and her colleagues describe how they sampled cane toads from different Australian locations and, using a combination of DNA and RNA sequencing, found three new viruses.

“Up until we published this paper, only one family of viruses was known to affect the cane toad,” Russo said. “This is the first paper that has found different viruses, which is very promising.

“This paper has opened the door: we found a retrovirus, a picornavirus and a circovirus which are genetically similar to viruses infecting frogs, reptiles and fish. For two of them, we found a full genome — both could potentially be used as biocontrol agents.”

Knowing these new viral sequences will help inform future studies which will investigate their prevalence and potential as agents for biocontrol. And while there’s a lot more work to be done, Professor White said these two papers are “the first — but most important — steps in finding an effective way to control the cane toad”.

Image credit: UNSW.