Koala hugs for Australia Day!

The koala is recognized worldwide as a symbol of Australia, who got their name from the word Dharug gula, meaning no water. It was at one time thought, since the animals were not observed to come down from trees often, that they were able to survive without drinking. The secret lay in their diet: the eucalyptus leaves. The leaves have a high-water content, so the koala does not need to drink often. But the notion that they do not need to drink water at all is a myth [1].

Koala (Phascolarctos cinereus) Photo Credits & acknowledgements – Parwinder Kaur, [CC BY 2.0]

Koalas typically inhabit open eucalyptus woodlands. They are super cute, cuddly and fluffy, yet very territorial wild species. Koalas are evolutionarily and biologically distinct from other marsupials. The modern koala is the only living representative of the marsupial family Phascolarctidae, a family that once included several genera and species. During the Oligocene and Miocene, koalas lived in rainforests and had less specialised diets [2]. During the Miocene, the Australian continent began drying out, leading to the decline of rainforests and the spread of open Eucalyptus woodlands. The genus Phascolarctos split from Litokoala in the late Miocene [2][3] and had several adaptations that allowed it to live on a specialised eucalyptus diet [4].


Unlike kangaroos and eucalyptus-eating possums, koalas are hindgut fermenters, and their digestive retention can last for up to 100 hours in the wild, or up to 200 hours in captivity. They can eat highly toxic eucalyptus leaves that would kill most other mammals, but they are picky eaters, so very prone to habitat loss. They are able to digest the toxins present in eucalyptus leaves due to their expansion of cytochrome P450 gene family of metabolic enzymes, which breaks down these poisons in the liver [5].


Koalas are listed as a vulnerable species by the International Union for Conservation of Nature [6]. The animal was hunted heavily in the early 20th century for its fur, and large-scale cullings in Queensland resulted in a public outcry that initiated a movement to protect the species. Sanctuaries were established, and translocation efforts moved to new regions koalas whose habitat had become fragmented or reduced. Among the many threats to their existence are habitat destruction caused by agriculture, urbanization, droughts and associated bushfires, some related to climate change.


The animals are particularly vulnerable to bushfires due to their slow movements and the flammability of eucalyptus trees. The koala instinctively seeks refuge in the higher branches, where it is vulnerable to intense heat and flames. Bushfires also fragment the animal's habitat, which restricts their movement and leads to population decline and loss of genetic diversity [7].

This koala mum and her joey were rescued during a wildfire by Jimboomba Police and Wildcare volunteers in the Gold Coast Hinterland Bushfires. Photo Credits and acknowledgements – Darren, Jimboomba Police

The chromosome-length assembly we share today is based on a draft assembly phaCin_unsw_v4.1 submitted to NCBI by The Earlham Institute, UK with full refseq representative genome data (Johnson et al., Nat. Genet. 2018). Please visit The Koala Genome Consortium website and learn about the efforts by the Koala Genome Project, a pioneering collaborative research led by Australian geneticist Rebecca Nicole Johnson AM, with far-reaching and significant implications for the conservation of Australian koalas!


The above draft was scaffolded with in situ Hi-C reads generated by DNA Zoo labs using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details.


We gratefully acknowledge the collaboration with Natasha Tay, Harry Butler Institute, Murdoch University, and samples provided by the Ranger Red's Zoo & Conservation park. The Hi-C work was enabled by resources provided by DNA Zoo Australia, the University of Western Australia (UWA) and by DNA Zoo, Aiden Lab at the Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.


A high-quality genome sequence is an essential resource required to implement genomics data into conservation management initiatives. More than 80% of the current 200 Australian national vertebrate recovery plans have genetic action listed in the species recovery plan with only less than 15% with any genomic data available. The genomic resources for understanding genetic diversity is of utmost importance in species conservation.


This chromosome-length genome assembly enables a highly detailed 3D view of the genome architecture for koala, karyotype evolution studies, identification of new genome linked markers and learning how the overall structure of genes evolve from a zoonotic point of view. Having koala DNA organized into 8 chromosomes (see map below) in the present release provides a cost-effective method for fast and reliable analyses options for conservation management initiatives. We hope the improved assembly will also offer further insights into the species’ genetic susceptibility to diseases like koala retrovirus (KoRV) and Chlamydia, serve as a basis for innovative vaccines, and facilitate new conservation management solutions that incorporate the species’ population and genetic structure, such as facilitating gene flow via habitat connectivity or translocations.

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, Ashling Charles & Parwinder Kaur.


Blog by: Parwinder Kaur


Citations

1. "Bigger and better 'Blinky Drinkers' to quench koalas' thirst this summer". NSW Environment & Heritage. Archived from the original on 22 July 2019.


2. Louys, J.; Aplin, K.; Beck, R. M. D.; Archer, M. (2009). "Cranial anatomy of Oligo-Miocene koalas (Diprotodontia: Phascolarctidae): Stages in the evolution of an extreme leaf-eating specialization". Journal of Vertebrate Paleontology. 29 (4): 981–92. doi:10.1671/039.029.0412. S2CID 86356713.


3. Black, K.; Archer, M.; Hand, S. J. (2012). "New Tertiary koala (Marsupialia, Phascolarctidae) from Riversleigh, Australia, with a revision of phascolarctid phylogenetics, paleoecology, and paleobiodiversity". Journal of Vertebrate Paleontology. 32 (1): 125–38. doi:10.1080/02724634.2012.626825. S2CID 86152273.


4. Tyndale-Biscoe, p. 226 Archived 3 June 2016 at the Wayback Machine.


5. Koalas are eating their forests into extinction — even feasting on poisonous eucalyptus plants National Post, 4 July 2018.


6. Woinarski, J. & Burbidge, A.A. 2020. Phascolarctos cinereus (amended version of 2016 assessment). The IUCN Red List of Threatened Species 2020.


7. Moyal, pp. 209–11 Archived 11 June 2016 at the Wayback Machine.

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