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World-first mapping of complete Koala genome brings hope for the icon's future

By: Claire Vince, Category: Science, Date: 03 Jul 2018

Australian Museum scientists are co-leading groundbreaking genomic research of one of Australia’s most iconic species – the koala.

Professor Rebecca Johnson and Koala at the announcement of the successful mapping of the complete Koala genome

Professor Rebecca Johnson and Koala at the announcement of the successful mapping of the complete Koala genome
Photographer: Nick Langley © Australian Museum

Today is a significant day for Australian science. A team of Australian and international scientists known as the Koala Genome Consortium, led by Professor Rebecca Johnson, Director of the Australian Museum Research Institute, and Professor Katherine Belov, University of Sydney, have made a significant breakthrough in successfully sequencing the full Koala genome. The findings have been published today in Nature Genetics.

Considered to be the most complete marsupial genome sequenced to date, it is as accurate as that of the human genome. The highly detailed 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 the iconic Koala ,” Professor Johnson said.

“This milestone has come from our vision to use genomics to conserve this species. The genetic blueprint has unearthed a wealth of data regarding the Koala ’s highly specialised diet of eucalyptus leaves, their immune system, population diversity and evolution.”

Co-lead author at the University of Sydney, Professor of Comparative Genomics, Katherine Belov said, “The genome provides a springboard for the conservation of this biologically unique species.”

Five years in the making

This ground-breaking milestone is the culmination of five exciting and challenging years of research conducted by 54 scientific collaborators from 29 institutions across seven countries. It has been a truly remarkable feat of collaboration focused on the common goal of revolutionising the conservation and management outlook for threatened Koala populations and opening doors for the continued discovery through genomic research on Australian mammals.

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 genes of this unique species,” said Professor Marc Wilkins, Director, Ramaciotti Centre for Genomics, UNSW.

Evolving a taste for eucalyptus

Consortium members from the Earlham Institute (Norwich, UK) identified that Koala s have two large expansions in a gene family known to be integral to detoxification. 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 Koala s 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.”

Dr Will Nash in the Haerty Group at Earlham Institute, said: “Gene duplication can lead to copies of genes associated with specific functions being retained in the genome. In the Koala, the largest group of retained copies make an enzyme that breaks down toxins. This means the Koala has evolved an excellent toolkit to deal with eating highly toxic eucalypts, one made up of lots of copies of the same (or very similar) tools.”

The amazing science of mother’s milk

According to Professor Belov, another important discovery was the characterisation of the composition of Koala milk. Like all marsupials, Koala s do the majority of their development in the pouch. They are born without an immune system after 34-36 days gestation and spend around 6 months developing in the pouch.

“We characterised 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,” Professor Belov said. “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.”

“Thanks to the high-quality genome, the team was able to analyse 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 Koala s,” Professor Belov said.

New weapons in the fight against Chlamydia

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. The complete Koala genome has been instrumental in showing that an individual Koala can have many (more than a hundred) insertions of KoRV into its genome, including many versions of KoRV,” Professor Peter Timms, University of the Sunshine Coast said.

“This information will enable to determine which strains of KoRV are more dangerous and to assist with our development of a KoRV vaccine,” he said.

Conservation of habitat

One of the biggest threats 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 Koala s 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 1000 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.”

A precious icon

All of the sequence data generated by the Koala Genome Consortium has been deposited into public databases and made freely available to scientists around the world. “Not only does open data promote the best interests of science, it also maximises the benefits that the Koala populations, and the public, receive from such research,” Professor Johnson said.

The Koala (Phascolarctos cinereus) is a native tree-dwelling Australian marsupial that is one of the world’s most fascinating and iconic mammals. Not only is the Koala synonymous with Australia it is also a powerful international symbol for the preservation and conservation of our natural world.

Wild Koalas are currently found in eucalypt forest and woodlands across Eastern Australia (Victoria, New South Wales and Queensland) and have been translocated to other sites, such as south eastern South Australia and onto some islands such as Kangaroo Island, South Australia and French Island,Victoria.

Their unique and highly specific diet of eucalyptus (gum) tree leaves, has resulted in Koala s being especially vulnerable to habitat loss due to the clearing of native vegetation for agriculture and urban development. The Australian Federal government lists Koala populations in Queensland, New South Wales and Australian Capital Territory as ‘Vulnerable’ under national environment law.

“Our next efforts must be in the application of these findings to genetically manage Koala populations, advance the treatment of the diseases affecting Koala s, with the goal of conserving this very important species,” Professor Johnson said.