Mapping DNA to protect an iconic Australian species

Project Leader: Associate Professor Parwinder Kaur, Australian DNZ Zoo

The Australian DNA Zoo node has mapped the first-ever genome of Australia’s cutest mammalian critter: the quokka aka Setonix brachyurus. A genome is the library of DNA for an animal or species.

DNA Zoo is a watershed initiative, leading the world in rapid generation and release of high-quality genomic resources. DNA Zoo Australia at The University of Western Australia is the Australian node of the global project.

These efforts will promote and enable evidence‑based decision making in all aspects of biodiversity and environmental research, policy and operational outcomes.

 

 
team members
 
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core hours allocated in Magnus
Partner Institution: University of Western Australia System: Zeus, Data Portal, Magnus, Topaz Areas of science: Genetics and Zoology Applications used: Juicer, 3D-DNA, W2Rap-contigger, Maker annotations, LAST

The Challenge

Mapping an animal’s genome can help conservationists understand more about their life code, health and diet, as well as help develop treatments for any diseases that may endanger the animal population.

For quokkas, this effort was doubly important. Rottnest Island in Western Australia, a popular tourist destination is home to the only remaining high-density sub-population of the quokka. While the mainland quokka populations continue to decline, the Rottnest Island sub-population is well managed and may be the only source of reproductive potential for the species in the future.

Because of their limited habitat, quokkas are very vulnerable to natural disasters. In 2015, the quokka population around Northcliffe, Western Australia was almost decimated, going from 500 animals to 39, following a large bushfire. If a disease or natural disaster were to occur on Rottnest, quokkas might face extinction.

Associate Professor Parwinder Kaur is the Director of the Australian DNA Zoo node and a passionate advocate of the quokka. She led the team that successfully mapped a chromosome-length sample of the quokka genome.

“This project gives us insurance for the future. Anything can happen any time; any disease could come and wipe out the population. But now we have the DNA code, we’re better equipped to deal with future problems,” Parwinder said.

Like humans, a quokka’s genome consists of approx. 3 billion bases. Each base is a protein that acts as a building block of our DNA strand. While a coiled DNA strand is nearly ten times smaller than the width of a human hair, this strand is so long that uncoiled it would reach two metres. Because of this huge amount of data, the DNA Zoo team used the Pawsey Supercomputing Centre to process and store the quokka genome.

“There’s no technology that can accurately read such a long information train, so we have to chop it down. We chop it into millions of pieces. Then we read each piece hundreds of times to make sure each letter is correct,” Parwinder said.

The Solution

By cutting up the genome into many smaller segments and parallel processing it in 3D, the DNA Zoo team was able to accurately read a quokka genome. They were interested in creating a chromosome-length copy of the quokka genome for a more meaningful handle on the biology.

Chromosomes are major segments of your DNA, inherited from your mother and father. Humans have 23 chromosome pairs, while quokkas have 11. By mapping a chromosome-length strand of DNA, the DNA Zoo team were able to map the first quokka genome in history.

“Mapping this genome, we were working from a blank slate. We had no other quokka DNA to compare it to.” Parwinder said.

To accurately read this chromosome, each DNA base had to be read 50-to-100 times to make sure it was accurately recorded. Pawsey systems were a vital part of processing these multiple readings of the huge DNA strand.

“To accurately read a single animal’s genome, we’re looking at roughly 172GB of data. On a desktop computer, a single run of this data may have taken years. With Pawsey, it was close to a week. It’s not just checking the data, there are a lot of mathematical equations and comparisons to other genomes that need to be made to ensure accuracy. That’s why Pawsey was critical to this project,” Parwinder said.

“The DNA Zoo team uses Pawsey to process and store the data.”

The Outcome

The quokka joins a list of 118 mammal species with their high quality genomes mapped by DNA Zoo. Mapped genomes are used by local conservation teams to protect vulnerable species, to guide population management and breeding strategies.

With humans occupying an ever-increasing portion of the Earth, species like the quokka are pushed to smaller habitats or forced into human spaces. This can make the species vulnerable to extinction. With many mammals and insects, occupying human spaces may also mean more diseases can be spread between humans and animals. We have seen the devastating effect this can have with the SARS-CoV-2 coronavirus.

“We have a duty to protect these species but it’s also in our own best interest. If we can keep their populations healthy, we protect ourselves from zoonotic diseases. By mapping their genomes we may also discover superpowers these animals have that can be used in our own medicines,” Parwinder said.

“Quokkas, for example, can halt their pregnancies when the environment doesn’t suit having a joey. Understanding the genetics behind that could help our own reproductive science.”

As the world’s climate changes and more species than ever face the threat of extinction, projects like DNA Zoo are vital to maintaining those vulnerable animal populations that remain. Pawsey’s support is enabling researchers to map dozens of endangered mammal species, helping protect them for future generations.

“We have a duty to protect these species but it’s also in our own best interest. If we can keep their populations healthy, we protect ourselves from zoonotic diseases” Parwinder said.
Associate Professor Parwinder Kaur, Australian DNZ Zoo,
Project Leader.