Koala Genome Consortium - Australian Museum koala research

The Australian Museum is a co-leader in the Koala Genome Consortium project to Unlock the koala genome

Koala asleep in tree

HOWARD HUGHES © Australian Museum

Tuesday 9th April, 2013, Sydney, NSW: Today, Australian Museum CEO, Mr. Frank Howarth PSM, announced that a consortium of Australian scientists led by Dr Rebecca Johnson of the Museum and Professor Peter Timms of the Queensland University of Technology (QUT) has achieved a world-first major breakthrough by completing an initial sequencing of the koala genome – the genetic blueprint for koalas.

Mr. Howarth congratulated the scientists working on this landmark achievement, which promises to lead to a new understanding of koala biology, transform how we study and manage this iconic species, and provide new ways to diagnose and treat the diseases affecting them.

“Prior to this ground-breaking study, virtually nothing was known about the immune system of Australia’s ‘honorary citizens.’ For the first time, we now have an insight into how and why the two major diseases threatening the koala, Chlamydia and Koala retrovirus (KoRV), have had such a devastating effect on our iconic native species.” Mr. Howarth said at today’s launch of the Koala Genome Consortium.

The Koala Genome Consortium is jointly led by Scientists at the Australian Museum and Queensland University of Technology (QUT).

The Australian Museum koala genome research team led by Rebecca Johnson (Head of the Australian Museum’s ‘Australian Centre for Wildlife Genomics’) and includes researchers Don Colgan Mark Eldridge, Matthew Hobbs and Andrew King.

This is one of the first mammalian genomes to be completely sequenced in Australia (from sample extraction right through to genome sequence) thanks to generous funding support from the Australian Museum Foundation, Bioplatforms Australia and the Queensland University of Technology, with invaluable technical expertise and resources from the Ramaciotti Centre for Gene Function Analysis the UNSW Systems Biology Initiative and the National Computational Infrastructure Specialised Facility (NCI-SF) in Bioinformatics.

 

The koala genome, announced today, has been obtained from a female koala ‘Pacific Chocolate’, from Port Macquarie (NSW), who was euthanased on 27th June 2012 due to severe chlamydial infection. She was 7-8 years old and had become infertile as a result of the chlamydial infection as well as suffering complications from the disease. She had been found on Pacific Drive, Port Macquarie and had been treated at the Port Macquarie Koala Hospital.

The research to date has been funded by Bioplatforms Australia (BPA), the Australian Museum Foundation, Queensland University of Technology and the ARC Linkage Scheme. BPA was established by the Commonwealth Government in 2007 to help achieve a coordinated and strategic approach to supporting research infrastructure in Australia.This research also has the assistance of resources provided at the National Computational Infrastructure Specialised Facility (NCI-SF) in Bioinformatics through the National Computational Merit Allocation Scheme supported by the Australian Government.

Dr Rebecca Johnson from the Australian Museum’s Australian Centre for Wildlife Genomics said, “Analysis of this huge data set is already revealing an extensive repertoire of koala genes, with more than 12,000 identified so far. This fantastic resource opens the way to exciting new research possibilities incorporating the rich collection of historic samples housed in natural history museums around the world. The thousands of new genetic markers in this genomic data will allow the Museum to analyse the genetic structure of koala populations at a level of detail comparable to most human forensic analyses, and this will be a major focus of our future work.”

The sequencing of the koala genes (or transcriptome) is a major breakthrough for Koala research, For the first time scientists working on Koala biology will have access to a complete set of molecular tools for their research. Currently there are only a handful of koala genes in the public databases but our study has already identified over 12,000 koala genes with more to come. The koala transcriptome data has already uncovered genes in koala that are associated with human diseases such as bowel and breast cancer. The Australian Museum’s research focus is largely on the evolution of species. By analysing these genes across a range of species we are able to get an idea when they arose in evolutionary time.

Koalas are the sole surviving species of a previously more diverse marsupial Family and have no close relatives making them out on an evolutionary limb even amongst Australia’s unique marsupials. Since koalas have been evolving independently for 35-40 million years they have acquired many highly specialised and unique characteristics that are of great interest to scientists throughout the world. These include a highly sensitive sense of smell, impressive powers of digestion and ability to detoxify the potentially poisonous compounds naturally found in gum tree leaves.

Australian Museum Senior Research Scientist Dr Mark Eldridge said “the koala genome project had already identified thousands of unique koala genes including some associated with the koala’s remarkable ability to survive on its specialised diet of eucalyptus leaves. We should also now be able to identify those genes that enable the koala to survive in such different environments as temperate Victoria and tropical north Queensland. This will give us clues as to how well equipped koalas are to adapt to future environmental change”.

Australian Museum scientist Dr Don Colgan, also expressed his excitement at the new koala transcriptome and genome data saying “once we have the assembled genome data, it will be the foundation for studies of variation that show how koalas can be helped to respond to climate change”

QUT’s Professor Timms said part of the data is helping researchers understand why Queensland and New South Wales koala populations have been crippled by the spread of Chlamydia while Victorian populations remain virtually unaffected. “We know koalas are infected with various strains of Chlamydia, but we do not know why some animals go on to get severe clinical disease and some do not,” Professor Timms explained.


While the consortium leading the project already contains more than 12 scientists, veterinarians and bioinformaticians, the team have only just embarked on this voyage of discovery. Australian and International experts are invited to participate in a larger new Koala Genome Consortium which will supplement existing national and international koala research programs. To ensure this sea of data is fully utilized and have real world outcomes an additional $5 million of funding will need to be sourced over the next 5 years.

Professor Timms pointed out that “Funding to date has resulted in a rich koala genetic bank. However, we require more help to explore and analyse the data fully to ensure the continued survival of this iconic species.” To improve the completeness and accuracy of the genome sequence this project requires an additional $5 million of funding to cover the laboratory and bioinformatic costs of completing the first draft of the genome. This will lead to substantial flow-on benefits to the broader koala and scientific community.

Mr Howarth said “The Australian Museum plays an important role in advising government and industry on population genetic health of many native Australian animals, and for over a decade has been providing advice based on population genetic data for some NSW koala populations. Today’s announcement represents a major advance in saving the NSW and Queensland koalas from these terrible diseases and securing the future for this iconic species.”


Mr. Howarth acknowledged and thanked existing funders: the Australian Museum Foundation, Bioplatforms Australia, ARC Linkage Grant Scheme (awarded to QUT), QUT as well as UNSW’s Ramaciotti Centre for library preparation, sequencing and outstanding technical expertise along with the staff and volunteers of the Port Macquarie Koala Hospital and Australia Zoo Wildlife Hospital.


While more than 12 scientists, veterinarians and bioinformaticians already work in the consortium, the task is much larger than they can accomplish and will require many more researchers to assist with analysing the data. Funding is also critical. While the funding to date (around $150,000) has resulted in a rich koala genetic bank, if we are to use these data to answer key koala survival questions, then more funding is need. It is planned to expand the consortium and hold a workshop to develop the best approaches to analysing the data and hence ensuring the continued survival of this iconic species.
The Australian Koala Genome Consortium will hold its first workshops to map out the assembly and annotation program for the draft koala genome in the latter half of 2013.
The Australian Koala Genome Consortium will soon call for expressions of interest from all interested groups in a diverse range of scientific disciplines to ensure the koala genome is annotated to the highest quality and the maximum information possible can be derived from the data to benefit this important and iconic species

Anyone wishing to donate to or partner in this important research cause please visit www.koalagenome.org .

Media contacts:

Christine Callen, marketing 0422 441 446, Claire Vince, publicist 0421 617 019

  • Dr Rebecca Johnson, 0412476200, rebecca.johnson[at]austmus.gov.au
  • Dr Mark Eldridge, 02 9320 6320; 0409 121 097, mark.eldridge[at]austmus.gov.au
  • Dr Don Colgan, 02 9320 6030, don.colgan[at]austmus.gov.au
  • Dr Matthew Hobbs, matthew.hobbs[at]austmus.gov.au
  • Mr Andrew King, andrew.king[at]austmus.gov.au

Visit - http://koalagenome.org for more information on this exciting project.


Dr Rebecca Johnson , Acting Head, Science Services & Infrastructure
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