Rally for the rakali

The rakali is an Australian native rodent first described in 1804. It's scientific name, Hydromys chrysogaster, translates to "golden-bellied water mouse”. Rakali is the name given to the species by the Aboriginal people from the Murray River area. The species is also known as rabe or water-rat. It is a distinctive Australian rodent specialised for an aquatic existence, with broad partially webbed hind-feet, water-repellent fur, and abundant whiskers. It is the largest rodent in Australia, often weighing more than 1 kilogram!

The Australian water rat (Hydromys chrysogaster). Photo Credits and acknowledgements - Lizette Salmon, via iNaturalist.com (CC BY-NC 4.0)

Among murid rodents, semiaquatic species have evolved at least three times, including (1) Hydromys and relatives on New Guinea, (2) Nilopegamys and relatives of Africa, and (3) Waiomys of Sulawesi, Indonesia. The rakali is one of four species in the genus Hydromys, and it is the only one with a range extending beyond Papua New Guinea and Indonesian West Papua.

Having adapted to a unique niche of a semiaquatic and nocturnal lifestyle, this species lives in burrows on the banks of rivers, lakes and estuaries. The rakali have a diverse diet of aquatic insects, fish, small vertebrates, birds' eggs and water birds. There is some sexual dimorphism present in the rakali, with females being generally smaller than males. However, the thick and muscular tails, which help serve as a rudder when swimming, remain the same size in both genders.

At the beginning of the century, the rakali was considered a pest and were widely hunted for their soft fur which caused the wild population to drastically decrease. Humans have been their greatest predator, with rakali requiring protection by legislation in 1938. Since this legislation, wild populations have recovered in all Australian states except for Western Australia where the rakali is still at a “near threatened” status.

To support ongoing conservation efforts, DNA Zoo teamed up with Museums Victoria Senior Curator of Mammals Kevin C. Rowe to release the chromosome-length assembly for the rakali, Hydromys chrysogaster. The genome draft was generated with short-insert size Illumina reads [481, 563, 388 PE reads] and scaffolded to chromosome length with Hi-C [770, 408, 993 PE reads]. See our Methods page for more assembly details. Browse the 24 chromosomes (2n=48) of the rakali in the interactive Juicebox.js session below:

This work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at 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.

Jird is the word

Though the name of the Libyan jird, Meriones libycus, implies it is somehow special to Libya, this adaptable rodent can be found all across Northern Africa and even into western China! From hot deserts, tropical shrub-lands, and even domestic gardens, this species of jird can make pretty much any environment inhabitable [1]. Because of its mainly herbivorous diet, it can make its home as long as sufficient amounts of vegetation is present.

Libyan jird by Raouf Guechi, [CC BY-NC], via iNaturalist.org

The Libyan jird is a social animal that tends to form small colonies, but it has been reported that some prefer to live individually. They live in burrows made up of a complex network of tunnels which may extend up to 1.5 metres underground and several metres outwards. This little creature likes to plan ahead, and tiny “warehouses”, chambers which colonies may use store up to 10 kg of seed, are also included as part of the burrow’s construction [2]. They sometimes travel locally from burrow to burrow, and when doing so, they stick their tails up in the air and run quickly, spending as little time in the open as possible [3].

The diet of the Libyan jird primarily consists of seeds, leaves, and little fruits. They have a preference for grass seeds, although they aren’t particularly picky. They have been known to consume insects in some cases. In areas under human cultivation such as farms or gardens, they will happily feed on any crop. The Libyan jird is known to devastate agricultural areas near their habitats, especially potato and tomato crops. For this reason, they are considered as serious pests by farmers [4].

The Libyan jird is highly abundant and found across a wide range, and as such is considered as a species of ‘Least Concern’ by IUCN. Libyan jirds are among the several species of gerbils which are kept as pets, although it is not known if this has an impact on the population.

Today, we release the chromosome-length assembly for the Libyan jird, Meriones libycus! This was a $1K assembly, for more details on our assembly procedure, please see our Methods page. The sample used for this assembly was a primary fibroblast cell line provided by the T.C. Hsu Cryo-Zoo, originally frozen back in 1988. We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample!

We here at the DNA Zoo think rodents are rad! We're happy to welcome the Libyan jird to our released collection, bringing our total to 26 chromosome-length rodent assemblies. Browse the 22 chromosomes (2n=44) of the Libyan jird in the interactive Juicebox.js session below!

The three muskaroos

Today, DNA Zoo Australia is celebrating!!! We are very happy to announce the receipt of funding from Lotterywest to build a comprehensive genomic resource especially for Western Australia, the WA Genome Atlas.

Australia is one of 17 “megadiverse” countries that comprise a large proportion of the Earth’s biological diversity and house a multitude of unique and endemic species. Southwest Australia specifically is the world’s first recognised global biodiversity hotspot. The WA Genome Atlas initiative supported by Lotterywest will establish a transdisciplinary hub of excellence to genetically characterise, record and support our unique biodiversity, and fill a gap in genetic knowledge required for ambitious ecosystem and species conservation.

To mark the occasion, the DNA Zoo is releasing the world’s first chromosome-length genome assemblies for three marsupials, the Western brush wallaby (Notamacropus irma) endemic to Western Australia, and it's cousins the swamp wallaby (Wallabia bicolor) and Matschie's tree-kangaroo (Dendrolagus matschiei)!

Photo collage featuring the Western brush wallaby photo by Jukka Jantunen, CC BY-NC 4.0; Swamp wallaby photo by James Bailey, CC BY-NC 4.0 and Matschie's tree-kangaroo photo by Wally Gobetz, CC BY-NC-ND 2.0 [www.flickr.com]

The western brush-wallaby (Notamacropus irma) used to be very common in Western Australia but hunting for its pelt by early settlers and habitat destruction has resulted in reduced numbers. Sadly, these wallabies are most commonly seen around the outskirts of Perth – lying on the side of the road after being struck by a car. Several orphaned joeys have been taken to Perth Zoo after their mothers were killed on roads. (Please take extra care when driving near bushland, especially at dusk and dawn!)

Visit the assembly page for Notamacropus irma here and browse the contact matrix for the eight chromosomes below. Thanks to Natasha Tay, Harry Butler Institute, Murdoch University, for assistance with the sample!

The swamp wallaby (Wallabia bicolor) is a small, stocky wallaby with dark brown fur, often with lighter rusty patches on the belly, chest and base of the ears. Its population is similarly decreasing due to habitat destruction and, to a lesser degree, killing by farmers. Fortunately, Wallabia bicolor is still common, and the issues it faces are not currently considered threats to its survival. Several physical and behavioral characteristics make the swamp wallaby different enough from other wallabies that it is currently placed apart in its own genus, but its phylogenetic placement is debated. We hope the chromosome-length genome assembly we present today will help to resolve this controversial taxonomy for the species.

Visit the assembly page for Wallabia bicolor here and browse the contact matrix for the five chromosomes below. Thanks to Ranger Red’s Zoo & Conservation Park for their help with the sample used for this assembly!

Finally, give it up for the Matschie's tree-kangaroo (Dendrolagus matschiei), a strikingly beautiful endangered tree kangaroo found only in Papua New Guinea. Habitat loss and over harvesting are the main threats to the species. We are happy to have an opportunity to add a chromosome-length genome assembly to support the research on Matschie's tree-kangaroo!

Check out the assembly page for Dendrolagus matschiei here, and browse the contact matrix for the seven chromosomes below. We are grateful to the T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center that contributed the fibroblasts for this genome assembly.

This work was enabled by resources provided by DNA Zoo Australia, The University of Western Australia (UWA) and DNA Zoo, Aiden Lab at Baylor College of Medicine (BCM) with additional computational resources and support from the Pawsey Supercomputing Centre. The WA Genome Atlas project leading the West Australian node of the global DNA Zoo initiative is proudly supported by Lotterywest.