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Preliminary Koala Genome Results Presented at PAG

SAN DIEGO (GenomeWeb) – At the Plant and Animal Genome conference here this weekend, a representative from the Koala Genome Consortium outlined progress being made in an ongoing effort to sequence and analyze the koala genome and transcriptome.

Speaking during a session on population and conservation genomics, the Australia Museum Research Institute's Rebecca Johnson provided background for the project — which kicked off in 2013 — as well as an overview of preliminary results obtained using DNA and RNA sequences from two geographically separated koala representatives.

With their existing data set, the researchers are starting to piece together clues to biology and genetic diversity of the koala, Phascolarctos cinereus. They are also assessing the koala's immune gene repertoire since the animals are prone to chlamydial infections that can cause eye damage and fertility problems.

Together with colleagues at the Australian Museum's Australian Centre for Wildlife Genomics and the Queensland University of Technology, Johnson is leading a team that's working to produce a de novo genome assembly for the koala, along with transcriptome sequences representing more than a dozen koala tissues.

Other collaborators on the project include investigators based at the Port Macquarie Koala Hospital, the Australia Zoo Wildlife Hospital, and the University of New South Wales.

Koala populations present complex management issues, Johnson said, noting that the animals experienced a population bottleneck following historical fur trading in Australia. At the moment, populations in Southern Australia remain relatively robust, while populations in the north are more prone to decline.

In an effort to track down genetic features that might prove useful for future conservation efforts, the researchers used Illumina paired-end sequencing to tackle samples from a healthy male koala from Queensland named "Birke," who was euthanized after a dog attack, and from "Pacific Chocolate," a female koala from New South Wales who was sacrificed due to severe chlamydia infection.

Although genome annotation and analysis is still underway, the team has uncovered some 15,000 apparent protein-coding genes in Birke's 3.09 billion base genome assembly and in the 3.37 billion base assembly of Pacific Chocolate's genome.

The group eventually expects to find an estimated 20,000 or so koala genes as they incorporate long read sequences and BioNano mapping information into the koala genome.

Genome comparisons with other marsupials are tricky, Johnson said, since other species sequenced so far are very distantly related to the koala. Nevertheless, the available data points to koala genome expansions involving genes that code for alpha amylase and aldehyde reductase — enzymes suspected of aiding in the koala's ability to digest starch and dodge potentially poisonous compounds in eucalyptus plants.

The researchers took a look at koala immune genes, too. There, they saw signs of relatively robust Toll-like receptor genes. Those genes, which contribute to innate immunity and pathogen immunity, displayed far higher diversity in the koala genome than that described for Toll-like genes in the genome of the endangered Tasmanian devil.

Along with candidate protein-coding genes, meanwhile, the available koala transcript sequences revealed the presence of an endogenous retrovirus in the koala genome that resembles the gibbon ape leukemia virus and the feline leukemia virus.

The koala retrovirus (KoRV), described in a koala transcriptome paper published in BMC Genomics in September, appears to exist in both an endogenous form that's integrated into the koala genome and an exogenous form that can be transmitted from one animal to the next, Johnson noted.

She and her colleagues are gearing up to release a draft version of the koala genome later this year.

They are also interested in using that initial genome sequence as a resource to develop tools to conserve koala populations and maintain as much of the animals' genetic diversity as possible, including tools to assess genomic SNP patterns and/or the presence of KoRV sequences.

"Version [one] of the genome release will form the foundation of evolutionary genetic studies of marsupials in general, thorough analysis of koala immune genes, and importantly the opportunity for genome-level investigation of the koala retrovirus," Johnson and her co-authors noted in an abstract for the PAG presentation.