Happy Birthday to Happy Quokka!

With their round cheeks and happy smiles, Quokkas aka Setonix brachyurus have been dubbed the most cheerful animal on the planet. They eat flowers and carry their babies in pouches. They are adorable. No wonder the #QuokkaSelfie is going viral on Instagram and Twitter. Check those by @chrishemsworth @MargotRobbie and many more!

Setonix brachyurus, Quokka. Location: Australia, WA, Rottnest Island. Photo Credits: Microsoft Australia.

With the onset of Spring in September the adorable quokka joeys are ready to hop out from their mom’s pouches and into the big wide world. Time to have a birthday party!

After the inaugural Quokka Birthday in 2019, we are celebrating the 2nd Quokka Birthday today with the release of a chromosome-length genome assembly for these much-loved members of the kangaroo family.

Quokkas are listed as “vulnerable” by the IUCN and the Australian Department of Environment and Energy. The IUCN estimates that there are between 7,500 – 15,000 mature adults in the wild. The vast majority of these lives on Rottnest Island. There's also a protected population on Bald Island, and a few scattered colonies on mainland Australia.

The biggest threat to quokkas is deforestation. Humans are tearing down trees to build cities; weather changes are having ripple effects on vegetation, erosion, and rainfall. Wildfires are also a problem. E.g., in 2015, a wildfire in Western Australia decimated 90% of the local quokka population, with the estimated quokka numbers dropping from 500 to just 39. We hope that the new genome assembly will help monitor the population and inform the species management plans.

The genome assembly shared today was generated using two samples: one from Rottnest Island and one coming from a mainland quokka. This is a $1K genome assembly. See our Methods page for more details on the procedure!


Quokkas belong to the Macropodidae family of marsupials that includes kangaroos and wallabies. This is the 5th macropod in the DNA Zoo collection, after the tammar wallaby, Western grey kangaroo, Eastern grey kangaroo and red kangaroo. See below how the chromosomes in the new genome assembly relate to those of the tammar wallaby below! Looks like the genomes are highly syntenic, but 3 chromosomes in the tammar wallaby correspond to two distinct chromosomes in the quokka, chr #1 (chr #1+#10 in quokka), chr #3 (#5+#7 in quokka) and chr #6 (#6+#8 in quokka), explaining the difference in the karyotype.

Whole-genome alignment plot between the tammar wallaby chromosome-length genome assembly (me-1k, 2n=16) and the quokka genome assembly (Setonix_brachyurus_HiC, 2n=22). The chromosomes are largely syntenic with three chromosomes in tammar wallaby corresponding to two separate chromosomes each in the quokka.

If you are curious to know more about Rottnest Island Kingdom of the Quokka, please watch this Trailer from Sea Dog TV International on Vimeo. Better still, book a trip to Rottnest Island, Western Australia!


We gratefully acknowledge the collaboration and samples provided by Cassyanna Gray, Conservation Officer, Rottnest Island Authority, and Natasha Tay, Murdoch University. The work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA) and DNA Zoo, Aiden lab, Baylor College of Medicine (BCM). We are grateful for the computational support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia. Additional computational resources and support was received via Microsoft AI for Earth grant.


The following people contributed to the project: Parwinder Kaur, Olga Dudchenko, David Weisz and Erez Aiden.

For more detail visit https://www.dnazoo.org/assemblies/Setonix_brachyurus.

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