Koala Genome Sequenced for First Time

A team of Australian and international scientists, co-led by the Australian Museum Research Institute and the University of Sydney, has completed a world-first full sequencing of the koala genome. 

Considered to be the most complete marsupial genome sequenced to date, it is in terms of quality on par with the human genome. The highly accurate genomic data will provide scientists with new information that will inform conservation efforts, aid in the treatment of diseases, and help to ensure the koala’s long-term survival. 

The consortium of researchers - comprising 54 scientists from 29 institutions across seven countries - have sequenced more than 3.4 billion base pairs and more than 26,000 genes in the koala genome; the koala genome is slightly larger than the human genome.  

Unlocking the genomic sequence gives scientists unprecedented insights into the unique biology of the koala. 

The Koala Genome Consortium announced the establishment of the project in 2013 with its first unassembled draft genome. The collective aim was to steer their research towards ensuring the long-term survival of this important marsupial while simultaneously increasing Australia’s genomics capability. 

Since then, researchers have assembled this large marsupial genome into the most complete and accurate marsupial genome to date and annotated its 26,000 genes for analysis.  

The koala genome has been sequenced to an accuracy 95.1 percent, which is comparable to that of the human genome. A team of Australian and international scientists, led by Professor Rebecca Johnson, Director of the Australian Museum Research Institute and Professor Katherine Belov, University of Sydney, have made a significant break-through successfully sequencing the full koala genome, with the findings published today in Nature Genetics.

Considered to be the most complete marsupial genome sequenced to date, it is in terms of quality, on par with the human genome. The highly accurate genomic data will provide scientists with new information that will inform conservation efforts, aid in the treatment of diseases, and help to ensure the koala's long-term survival.

"The Koala Genome Consortium has been an ambitious journey affording us great insights into the genetic building blocks that make up a koala - one of Australia's, as well as the world's, most charismatic and iconic mammals," Professor Johnson said.

"This milestone has come from our vision to use genomics to conserve this species. The genetic blueprint has not only unearthed a wealth of data regarding the koalas unusual and highly specialised diet of eucalyptus leaves, but also provides important insights into their immune system, population diversity and the evolution of koalas," she said.

The Australian led consortium of scientists comprised 54 scientists from 29 different institutions across seven countries. They have sequenced over 3.4 billion base pairs and more than 26,000 genes in the Koala genome - which makes it slightly larger than the human genome. Unlocking the genomic sequence gives scientists unprecedented insights into the unique biology of the koala.

Professor Johnson said the uneven response of koala populations throughout their range was one of the major challenges facing broad scale management of the species.

"The genome enables a holistic and scientifically grounded approach to koala conservation," she said. "Australia has the highest mammal extinction record of any country during the Anthropocene.

"Koala numbers have plummeted in northern parts of its range since European settlement, but have increased in some southern parts, notably in Victoria and South Australia."

Director and CEO, Australian Museum, Kim McKay, AO congratulated Professor Johnson and the team on this achievement.

"Today we celebrate the completion of the highest quality, marsupial genome sequencing undertaken to date. This work was brought about through the meticulous efforts not only of Professor Johnson and Professor Belov, but also the contributions from many other Australian Museum scientists, as well as scientists from around the nation and the world. It will usher in a new era in our understanding and conservation of the iconic koala," she said.

Professor Jennifer Graves, AO, Distinguished Professor of Genetics, La Trobe University and winner of the 2017 PM's Prize for Science, said: "We could never have imagined, when we were pioneering koala genetics in the 1980s, that one day we'd have the entire koala genome sequence. This opens up all sorts of ways we can monitor the genetic health of koala populations."

The Koala Genome Consortium announced the establishment of the project in 2013 with its first unassembled draft genome. The collective aim was to steer their research towards ensuring the long-term survival of this important marsupial while simultaneously increasing Australia's genomics capability.

Since then, researchers have worked tirelessly to assemble this genome into the most complete and accurate marsupial genome to date and annotate its 26,000 genes for analysis. The koala genome has been sequenced to an accuracy of 95.1%, which is comparable to that of the human genome.

The 3.4 billion base pairs of the published Koala genome were sequenced at the Ramaciotti Centre for Genomics, at the University of New South Wales, using new sequencing technology.

"We then assembled the genome with supercomputers, allowing the Consortium to then study the >20,000 genes of this unique species," said Professor Marc Wilkins, Director, Ramaciotti Centre for Genomics, UNSW.

Consortium members from the Earlham Institute (EI), (Norwich, UK) identified that koalas have two large expansions in a gene family known to be integral to detoxification, the Cytochrome P450 gene family of metabolic enzymes. They found these genes to be expressed in many koala tissues, particularly in the liver; indicating they have a very important function in detoxification and likely allowed koalas to become dietary specialists.

As Professor Johnson explains, "this probably helped them to find their niche to survive, as they could rely on a food source that would have less competition from other species who were not able to detoxify as effectively."

Chlamydia causes infertility and blindness and has severely impacted koala populations in New South Wales and Queensland. Using information gained from the koala genome, scientists hope to develop a vaccine to fight diseases like Chlamydia.

One of the most threatening processes to koala survival is loss of habitat through land clearing and urbanisation which results in a reduction of habitat connectivity, reduced genetic diversity and puts koalas at high risk of inbreeding. The results of inbreeding can be highly detrimental to survival of those koala populations as it leads to reduced genetic diversity.

Professor Johnson added: "For the first time, using over 1000 genome linked markers, we are able to show that NSW and QLD populations show significant levels of genetic diversity and long-term connectivity across regions.

"Ensuring this genetic diversity is conserved in concert with other conservation measures to protect habitat, reduce vehicle strikes, dog attacks and disease, are the keys to the long-term survival of the koala."

This article has been republished from materials provided by the University of Sydney. Note: material may have been edited for length and content. For further information, please contact the cited source.

Reference: Johnson, R. N., O’Meally, D., Chen, Z., Etherington, G. J., Ho, S. Y. W., Nash, W. J., … Belov, K. (2018). Adaptation and conservation insights from the koala genome. Nature Genetics, 1. https://doi.org/10.1038/s41588-018-0153-5