Koala Genome Sequenced

The Koala Genome Consortium, a research group that includes 54 scientists from 29 different institutions across seven countries, has produced the first high-quality genomic sequence for the koala (Phascolarctos cinereus), a tree-dwelling Australian marsupial that is one of the world’s most fascinating and iconic mammals.

Koalas (Phascolarctos cinereus). Image credit: Holger Detje.

The koala, which first appeared in the fossil record 350,000 years ago, is the only extant representative of the marsupial family Phascolarctidae and its closest living relatives are the wombats. It is found in coastal areas of Australia’s eastern and southern regions, inhabiting Queensland, New South Wales, Victoria, and South Australia.

The animal is about 24 to 33 inches (60-85 cm) long and weighs up to 14 kg in the southern part of its range, but only about half that in subtropical Queensland to the north.

Virtually tailless, the body is stout and gray, with a pale yellow or cream-colored chest and mottling on the rump. The broad face has a wide, rounded, leathery nose, small yellow eyes, and big fluffy ears.

The koala typically lives in open eucalypt woodlands and forests, and the leaves of these trees make up most of its diet.

While the species was previously classified as ‘Least Concern’ on the IUCN Red List of Threatened Species, it was uplisted to ‘Vulnerable’ two years ago.

Current threats to koalas include continued habitat destruction, fragmentation, and modification, bushfires, and disease, as well as drought associated mortality in habitat fragments.

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 genome provides a springboard for the conservation of this biologically unique species,” said Professor Katherine Belov, from the University of Sydney.

“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 specialized diet of eucalyptus leaves, but also provides important insights into their immune system, population diversity and the evolution of koalas,” added Professor Rebecca Johnson, director of the Australian Museum Research Institute.

The team 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.

“We then assembled the genome with supercomputers, allowing the Consortium to then study over 20,000 genes of this unique species,” said Professor Marc Wilkins, Director of the Ramaciotti Centre for Genomics at the University of New South Wales.

The researchers 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.

“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,” Professor Johnson said.

Another important discovery was the characterization of the composition of koala milk.

Like all marsupials, koalas do the majority of their development in the pouch. They are born without an immune system after 34-36 days gestation and spend six months developing in the pouch.

“We characterized the main components of the mothers’ milk — which is crucial for koala joeys — born the size of a kidney bean and weighing half of one gram. We identified genes that allow the koala to finetune milk protein composition across the stages of lactation, to meet the changing needs of their young,” Professor Belov said.

“Thanks to the high-quality genome, we were able to analyze and discover koala-specific milk proteins that are critical for various stages of development. It also appears these proteins may have an antimicrobial role, showing activity against a range of bacterial and fungal species, including Chlamydia pecorum, the strain known to cause ocular and reproductive disease in koalas.”

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.

“In addition to Chlamydia, the other major infection that is threatening the species is koala retrovirus (KoRV), however very little is presently known about it,” said Professor Peter Timms, from the University of the Sunshine Coast.

“The complete koala genome has been instrumental in showing that an individual koala can have many insertions of KoRV into its genome, including many versions of KoRV. This information will enable to determine which strains of KoRV are more dangerous and to assist with our development of a KoRV vaccine.”

One of the most threatening processes to koala survival is loss of habitat through land clearing and urbanization 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.

“For the first time, using over 1,000 genome linked markers, we are able to show that New South Wales and Queensland populations show significant levels of genetic diversity and long-term connectivity across regions,” Professor Johnson said.

“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.”

The findings are published in the journal Nature Genetics.

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Rebecca N. Johnson et al. Adaptation and conservation insights from the koala genome. Nature Genetics, published online July 2, 2018; doi: 10.1038/s41588-018-0153-5