Australian bilby genome sequenced for the first time

An important breakthrough provides new biological information on the bilby.

A group of scientists, including researchers at UNSW Sydney, have sequenced the entire genome of the Australian bilby for the first time, publishing today in Nature Ecology and Evolution.  

This first mapping of the bilby’s genetic blueprint, led by Professor Carolyn Hogg at the University of Sydney, provides an important tool for conservation of the threatened species. Lesser known than other marsupials, bilbies are often referred to as the Australian Easter bunny and have ongoing cultural significance to Aboriginal Australian communities.  

Notable for their large ears and backward facing pouches, bilbies are burrowing nocturnal omnivores. They use their strong forelimbs and long claws to find food and turn over soil and organic matter, making them the ecosystem engineers of Australia’s deserts.  

There were once two bilby species, the Lesser bilby, which became extinct in the 1960s, and the Greater bilby that now exists in only 20 per cent of its former habitat range, mostly in the central deserts of Western Australia and the Northern Territory.  

Bilby populations went into steep decline after European arrival and the introduction of feral cats and foxes, as well as rabbits competing for food sources. Bilby populations are often managed in the wild by Indigenous rangers, while about 6000 live in fenced sanctuaries, islands and zoos.  

This first complete map of their genome has provided biological information on how they grow and evolve.

“The bilby genome project continues our work with Professor Hogg, with whom we previously collaborated on the koala genome project,” says Professor Marc Wilkins, a co-author on the paper from the School of Biotechnology and Biomolecular Sciences (BABS). “Along with further genome projects, including the cane toad and the Queensland fruit fly, these are substantial contributions to conservation of endangered species and also understanding the genetics of pests of economic impact.”

Mapping a genome

Using DNA from a deceased zoo bilby, the collaborative team sequenced the genome of the surviving Greater bilby. The team also created the first genome for the extinct Lesser bilby from the skull of a specimen collected in 1898. 

A significant amount of the genetic data was generated by the Ramaciotti Centre for Genomics at UNSW. “The assembly, annotation and interpretation of a new genome requires unparalleled expertise and effort,” says Dr Martin Smith, the Director of the Ramaciotti Centre. “Our team supported this milestone by meticulously producing an extensive volume of DNA sequencing data using our state-of-the-art genomics platforms. The Centre is delighted to add the bilby to the list of iconic Australian animal genomes.”

Prof. Hogg said: “The Greater bilby reference genome is one of the highest quality marsupial genomes to date, presented as nine pieces, representing each of the bilby chromosomes. It offers insights into biology, evolution and population management.”  

A reference genome is the equivalent of having a puzzle box lid; it’s a way of knowing what all the DNA puzzle pieces mean. For example, it helps us understand what gives bilbies their unique sense of smell and how they survive in the desert without drinking water.  

The reference genome has also helped us understand bilby sex determination. “Bilbies are really strange because males have two Y chromosomes. This contrasts most other mammals who only have one Y chromosome. The extra Y chromosome provided us with the opportunity to study some of the earliest stages of sex chromosome evolution,” says Associate Professor Paul Waters, also from the School of BABS, who carried out research on the sex chromosome of the bilby as part of this project.  

Managing bilby populations

Importantly, the genome is being used to manage the bilby metapopulation in zoos, fenced sanctuaries and islands. The research team selected individuals for translocation and release to maximise their genetic diversity and improve the population’s ability to adapt to a changing world.

The team has also used the genome to develop a more precise scat testing method to complement existing traditional land-use practices by Indigenous rangers.  

“We know a lot about bilbies – where they live, what they eat, and how to track them,” said ranger Scott West from the Kiwirrkurra Indigenous Protected Area in Western Australia.  

“It’s good to use iPads for mapping, and cameras to monitor them. The DNA work also helps check if bilbies are related, where they are from and how far they travelled. Using old-ways and new-ways together helps us get good information about bilbies and how to look after them. This is what two-way science is.”  

Dr Brianna Coulter, a field ecologist at UNSW’s Wild Deserts, says: “The bilby reference genome will help us make better informed genetic management decisions for translocated populations, such as the bilbies we have translocated to Wild Deserts, our UNSW, Ecological Horizons and NSW NPWS partnership project.”