The Koala Genome

After five years of pioneering collaborative research the koala genome has been sequenced!

The koala – a treasured and quintessentially Australian species – is under threat from habitat loss, predator attack and disease, and there are concerns that its genetic diversity is decreasing and its population health is, as a result, in danger.

Researchers at the Australian Museum are working with koala specimens like this one to sequence the approximately 20,000 genes in the koala. Assembling the koala genome will open up opportunities for medical treatments, provide knowledge about how koalas evolved, and indicate how best to conserve the species. It will also allow scientists to look at disease resistance and susceptibility, and compare current genetic diversity to that of koalas collected in the past.

Dr Rebecca Johnson: This study is the first time that the entire genome of the Koala has been mapped and described. We found that the Koala genome is actually a little bit bigger than the human genome and we found over 26,000 genes that belong to the Koala.

This discovery is important because koalas really are an iconic species. They're recognised around the world. Unfortunately they are in danger: lots of their populations are vulnerable and in need of protection, and this genome gives us the data to help us make really informed decisions for their conservation.

Koalas are at risk due to a number of factors and these include habitat loss, urbanisation and disease, and the genome allows us to get right down at the DNA level to help us understand how all those different factors are affecting this really important species.

Koalas have a diet that is predominantly eucalyptus leaves and in fact it's very high in toxins in the form of plant secondary metabolites, to the point where most mammals would find the level fatal. Koalas don't, and the genome has given us insight into why not, because koalas seem to have many more detoxification genes than other species and these genes are in fact metabolic enzymes allowing them to modify these toxic molecules and excrete them, probably through their urine.

The genome’s allowed us to reconstruct population size right back through evolutionary time and what we've discovered is that koala populations peaked probably around 50,000 years ago and then between 30 and 40,000 years they've really dropped off to much, much lower numbers.

We already know that koalas - they're marsupials - they have very specific developmental requirements in the pouch because they do so much of their developing there. They're born at 35 days and so for the next six months they do a lot of growth in the pouch. Through the genome we've actually identified some milks that seem to be novel to the koala, which obviously are very important for their development. In addition to that, we already knew that koalas are born without an immune system and the genome, because it's a very high quality genome, has allowed us to characterise, in great detail, a lot of their immune genes.

This is the first time a mammalian genome has been entirely sequenced in Australia. It's also only the fourth marsupial to have been sequenced globally.

We established the Koala Genome Consortium because there were significant interests in conservation and understanding disease in this very important species. The consortium started off with a handful of researchers here in Australia, it's since expanded to include 54 researchers from seven different countries around the world representing 29 institutions.

It sounds simple on paper to sequence a genome but in fact it's a very complex task and it does represent a major breakthrough. It took us five years. We launched in 2013 and so in 2018 we have an incredibly high-quality genome for a very iconic marsupial that can be used as a springboard for so many new studies.

The applications for a genome once it's been sequenced are almost endless and for koala we've already seen the importance of genetic information recognised and incorporated into management of koalas in New South Wales. So it's already known that koalas are probably very efficient at processing pain relief medication for example, and now we've got the genome, that completely confirms that they have this super detox ability, so future applications will probably really assist with veterinary care pain relief in this species, to make sure that they're there they have adequate medications in the future.

In addition to that, they're often given very high dosages of anti-chlamydia medication, so the antibiotics important for treatment of chlamydia, and again the genome has helped us to understand that probably this is because they're really efficient at detoxification, and this can now be used to assist with improved medications for some of the well known diseases in koalas.

The next phase in the koala genome work that we're doing is really focused on conservation and it's using the historical specimens that we have here in the museum to understand what's changed in the last 200 years since humans really started impacting their environment and doing things like hunting koalas and reducing their populations. So our next steps are taking the past, to inform the future, to ensure that we have the best conservation strategy possible for this really important species.

Frequently asked questions

The Koala Genome Consortium and the subsequent Koala Genome Project has been the culmination of five years of pioneering collaborative research, the outcomes of which have far-reaching and significant implications for the conservation of Australian koalas. Below we answer some of the more common questions asked about the project and its anticipated impacts.

Led by Australian Museum Research Institute Director Dr Rebecca Johnson, a small group of Australian scientists with a passion for koalas gathered together in 2013 to share current knowledge and ideas about koala populations, genetics and diseases. Their collective aim was to steer their research towards ensuring the long-term survival of this important marsupial. They also recognised the importance of increasing Australia’s genome sequencing capability, since no de novo mammal genome had ever been sequenced and assembled by a solely Australian led group. It was from this small group that the Koala Genome Consortium was born.

In 2018 Consortium now comprises of 54 scientists from 29 different research institutions across seven countries. The group have strong links with international and domestic partners and end-users, including wildlife hospitals and governments responsible for managing koala conservation.

This is the first Australian-led big genome project. The Consortium sequenced the genomes of three animals, one using state of the art long-read sequencing technology from Pacific Biosciences (also known as ‘PacBio sequencing’). This technique delivers very long and uninterrupted sequences, and has produced the best quality marsupial genome to date, of comparable quality to the human genome (the human genome project took 13 years and cost US$3billion to complete).

The koala genome is slightly larger than the human genome (3.5Gb v 3.2Gb) and has a similar number of genes. We report 26,558 koala genes, an update on our original discovery of 15,500 Koala genes (Hobbs et al 2014). The long-read genome allowed the consortium to discover many genes that contribute towards the koala’s unique biology.

The Australian Museum’s collection of mammals was formed in the mid-1800s and has grown to become one of the most comprehensive collections in the world. The collection currently contains approximately 48,000 specimens from over 100 different countries.

The Australian Museum Koala collection currently comprises over 290 specimens dating from the late 1870s. There are over 100 skins, 130 skulls and approximately 50 spirit preserved specimens in the collection which are available to researchers both within Australia and overseas. Many of the early specimens are ex captives from Zoos. More recently, specimens are received after they have been found dead on the road or euthanised due to severe injuries or disease

Many specimens in the collection have great historical as well as scientific value having formed the basis of the original description of a particular species when it was first named. There are over 570 of these specimens known as “type” specimens” in the collection including the only known specimens of a number of species.

One of the most important specimens is the “type” specimen of a Koala subspecies from Victoria, Phascolarctos cinereus victor, described in 1935 by the museum’s mammal curator at the time, Ellis Troughton. Other significant specimens in the collection include those donated in the 1950s from the now endangered population on Barrenjoey Peninsula in Sydney’s north.

The Koala collection has formed the basis of a number of recent research projects. DNA extracted from historical specimens from the late 1800s and early 1900s was used to examine the origins and evolution of retroviruses which increase Koala’s susceptibility to infections such as Chlamydia. Specimens used in the Koala genome sequencing project are also lodged in the collection.

The koala is recognised worldwide as an iconic Australian species, and there is anxiety in Australia and internationally that this unique species is declining in the wild.

The koala is of interest to scientists, policy makers and the public because of their biological uniqueness, the high level of attention they receive for conservation, and their attraction to the visitor economy (koala-related tourism estimated at over AUD$1.5 billion per annum).

Koalas are evolutionarily distinct. They are the only living representative of the marsupial family Phascolarctidae, the last of up to 20 species recognised in the fossil record.

Koalas are biologically unique. They can eat highly toxic eucalyptus leaves that would kill most other mammals, but they are picky eaters, so very prone to habitat loss. With increasing threats of predation and habitat loss through urbanisation, koalas are particularly vulnerable to deleterious effects of fragmented habitat and population bottlenecks, and are further threatened by disease, low genetic diversity and climate change. Worryingly, some koala populations are expected to decline across Australia by up to 50% over the next three generations (approx. 20 years), so maintaining healthy populations will require significant conservation intervention measures.

New information from the Koala Genome Project is critical in understanding and communicating the threats that modern populations face.

We use a technique that estimates demographic history over thousands of generations from genome sequence. Looking back >100,000 years, koalas were at their peak population size of 50,000 – 86,000 animals. At around 30-40,000 years ago the population underwent a rapid decrease, then stabilised to about 10% of their previous numbers. This rapid decline coincided with the time that other Australian species, especially the megafauna, underwent widespread extinction, pointing to a significant climatic or habitat change.

Those stable population numbers were again dramatically reduced by European settlement around 200 years ago, when millions of koalas were hunted for their skins, resulting in extinctions and severe bottlenecking in southern Australia. This is the koala population we are now faced with conserving in the current day.

One of the biggest modern threats to koala survival is land clearing. This has led to loss of habitat, and loss of connectivity between habitats. One of the long-lasting outcomes has been reduced genetic diversity and possibly inbreeding. This is complicated by the wide geographic distribution of koalas throughout Australia, covering many bio-regions and four Australian states.

Good news has come from our populations studies using new genome markers. Using genome linked markers, we show, for the first time, that NSW and Queensland populations retain significant levels of genetic diversity and still show long term connectivity across regions. Ensuring this genetic diversity is conserved, is the key to the long term survival of this species, and genetic monitoring must accompany conservation measures to protect habitat, and reduce dog attacks, vehicle strikes and disease.

This work represents the new generation of science based conservation policy as it has been integrated as an important pillar into the NSW Koala Strategy 2018. Sequencing the koala genome represents a paradigm shift for Koala research and conservation efforts.

The genome sequence of the koala tells us more about their immunity and resilience to disease - one of the biggest threats to populations.

The long-term survival of the koala is significantly threatened by disease, so characterizing the immune system of the koala is important for management. Our long-read genome allowed characterisation of koala immune genes, many for the first time. These gene families are notoriously difficult to characterise because there are many copies with similar sequence, but they can be assembled, counted and identified by long read sequencing.

Once these genes were assembled we could compare the ones that were expressed in animals with symptoms of ocular chlamydia with those expressed in the healthy animals. Several of these animals were also involved in a chlamydial vaccine trial, with some showing ‘strong’ or ‘weak’ immune response to the vaccine. The genome has provided the first insights into the genetic basis for this response, and will provide essential information for future successful vaccine development.

New findings on koala reproduction enlighten us further about the uniques and specialised development that takes place in young.

Koalas are induced ovulators, which means they only ovulate in response to mating. Genes known to be involved in male induced ovulation were found in the koala genome (also highly conserved in other induced ovulators such as camels and llamas) suggesting a role for male koalas in inducing ovulation.

Like all marsupials, koalas do most of their development in the pouch. They are born after 34-36 days gestation and spend ~6 months developing before emerging from the pouch. As for other marsupials, the development of koala young depends on a supply of milk that changes in composition during pouch life. Thanks to the high-quality genome, we were able to analyse and discover koala-specific milk proteins that are critical for various stages of development. Excitingly, these proteins seem to have an antimicrobial role, showing activity against a range of bacteria and fungal species, including the strain of Chlamydia pecorum known to cause ocular and reproductive disease in koalas. This would be vital in the early stages of development, when the koala young lack a functional immune system.

What does the koala genome tell us about their interesting taste for low calorie, high toxin plants?

Koalas eat a diet largely of eucalyptus leaves (20 of the >600 species), which have a high level of toxins. The consortium found that koalas have two large expansions in a gene family known to be integral to detoxification, the Cytochrome P450 gene family of metabolic enzymes, which oxidise molecules that can then be excreted as water soluble metabolites. These detox genes are expressed in many koala tissues, especially the liver. The evolution of these extra detox genes is undoubtedly what allowed koalas to become dietary specialists, and thus evade competition from other species which could not detoxify as effectively.

There must have been strong selection for koalas to be able to metabolise this food source. The Consortium found that koala detox genes have experienced diversifying selection (creating more detox genes via expansion through tandem duplicates) and purifying selection (which keeps the genes functioning, presumably because they play a very important role).

Knowledge of the koalas’ detox genes is important for veterinary care of koalas because this gene family is known to metabolise non-steroidal anti-inflammatory drugs (typically used in pain relief) and possibly antibiotics used to treat koala diseases like chlamydia.

In addition to this, Eucalyptus leaves are very low in calories, so koalas typically need to eat 600-800g per day. They are often touted as the most expensive animal to feed in captivity outside of Australia. The koala genome offers us clues to the basis of koala ‘choosiness’.

The consortium found that koalas have an expanded ‘bitter taste’ repertoire of 24 genes, the most of any Australian marsupial. Bitter taste receptors recognise structural toxins (such as terpenes, phenols and glycosides which are found in high levels in Eucalyptus), so this would allow them to optimise their leaf choice by targeting nutrients and minimising toxins.

Koalas derive most of their water from their diet, eating only leaves with more than 55% water content. The genome points to the koala’s ability to ‘water taste’ as it has a duplication in the aquaporin 5 gene thought to be a central component to sense water concentration.

This project was made possible by access to infrastructure provided by Bioplatforms Australia through funding from the Australian Government National Collaborative Research Infrastructure Strategy; access to technology through NCI, Amazon Web Services and Pacific Biosciences. Stakeholders such as Featherdale Wildlife Park, The Koala Hospital in Port Macquarie, and Australia Zoo Wildlife Hospital provided access to live animals; and funding was obtained from various grants including the Australian Museum Foundation, the Australian Research Council, and the NSW Environmental Trust.

Our team

Companion papers

Johnson R.N. et al. (2018). Adaptation and conservation insights from the koala genome. Nature Genetics, 50 (8), 1102–1111. https://doi.org/10.1038/s41588-018-0153-5
Nyari, S. et al. (2019) Therapeutic effect of a Chlamydia pecorum recombinant major outer membrane protein vaccine on ocular disease in koalas (Phascolarctos cinereus) PLOS ONE, 14 (1) https://doi.org/10.1371/journal.pone.0210245
Olagoke, O. et al. (2018). Induction of neutralizing antibody response against koala retrovirus (KoRV) and reduction in viral load in koalas following vaccination with recombinant KoRV envelope protein. Npj Vaccines, 3(1), 30. https://doi.org/10.1038/s41541-018-0066-4
Brandies, P.A. et al. (2018). Disentangling the mechanisms of mate choice in a captive koala population. PeerJ 6:e5438 https://doi.org/10.7717/peerj.5438
Löber, U. et al. (2018). Degradation and remobilization of retroviruses by recombination during the earliest stages of genomic invasion. Proceedings of the National Academy of Sciences August 21, 2018 115 (34) 8609-8614; first published August 6, 2018 https://doi.org/10.1073/pnas.1807598115
Hobbs, M. et al. (2017). Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Scientific Reports, 7:15838 doi:10.1038/s41598-017-16171-1.
Cheng, Y. et al. (2017). Characterisation of MHC class I genes in the koala. Immunogenetics. doi: 10.1007/s00251-017-1018-2.
Jones, E. A. et al. (2017). Characterization of the antimicrobial peptide family defensins in the Tasmanian devil (Sarcophilus harrisii), koala (Phascolarctos cinereus), and tammar wallaby (Macropus eugenii). Immunogenetics, 69, 3:133-143. doi: 10.1007/s00251-016-0959-1.
Dennison, S. et al. (2017). Population genetics of the koala (Phascolarctos cinereus) in north-eastern New South Wales and south-eastern Queensland. Australian Journal of Zoology, DOI: org/10.1071/ZO16081.
Duchêne, D. A. et al. (2017). Analysis of phylogenomic tree space resolves relationships among marsupial families. Systematic Biology, syx076, https://doi.org/10.1093/sysbio/syx076
Neaves, L. E. et al. (2016). Phylogeography of the Koala, (Phascolarctos cinereus), and harmonising data to inform conservation. PLoS One 11, e0162207, doi:10.1371/journal.pone.0162207.
Bragg J. G. et al. (2016). Resources for phylogenomic analyses of Australian terrestrial vertebrates. Molecular Ecology Resources.: doi:10.1111/1755-0998.12633
Morris, K. M. et al. (2016). Characterisation of the immune compounds in koala milk using a combined transcriptomic and proteomic approach. Scientific Reports, 7, 6:35011. doi: 10.1038/srep35011.
Morris, K. M. et al. (2015). Identification, characterisation and expression analysis of natural killer receptor genes in Chlamydia pecorum infected koalas (Phascolarctos cinereus). BMC Genomics, 16:796.doi: 10.1186/s12864-015-2035-x.
Cui, J. et al. (2015). SNP marker discovery in koala TLR genes. PLoS ONE 10(3): e0121068. doi:10.1371/journal. pone.0121068.
Morris, K. M. et al. (2014). The koala immunological toolkit: Sequence identification and comparison of key markers of the koala (Phascolarctos cinereus) immune response. Australian Journal of Zoology, 62, 3, pp. 195-199.
Hobbs, M. et al. (2014) A transcriptome resource for the koala (Phascolarctos cinereus): insights into koala retrovirus transcription and sequence diversity. BMC Genomics, 15:1 doi:10.1186/1471-2164-15-786.