Something mice

The Australian desert mouse, Pseudomys desertor, is a species of rodent endemic to the great arid interior of Australia. When the first desert mouse specimens were collected in 1857 by Australian zoologist Gerard Krefft on the Blandowski Expedition, they were quite common. The species no longer occurs anywhere near where Krefft found them at the intersection of Victoria and New South Wales, but the specimens live on in the Museums Victoria collection (NMV C147 to C149). Extinct in Victoria and critically endangered in New South Wales, the desert mouse is believed to be reasonably common across the arid interior of Australia. These and other historical specimens provide a window into the changing diversity of this once widespread species.

The bright chestnut brown fur interspersed with long dark guard hairs gives the Australian desert mouse a spiny appearance. Its belly fur is a light grey-brown. The tail looks scaly and slightly bi-coloured, with length equal to or shorter than the animal's head-body length. A defining feature of the desert mouse is its pale orange eye-ring, which may be used to distinguish it from the Western chestnut mouse Pseudomys nanus where their habitat overlaps in the northern Tanami Desert.

Pseudomys desertor, the brown desert mouse. Photo Credits and acknowledgements - Source: Atlas of Living Australia / Photographer: Margarita Steinhardt

The animals thrive throughout the arid zone of Australia, and the desert mouse also inhabits the north dry savanna region of Queensland. Its preferred habitat ranges from sand dunes with spinifex to rocky hillsides, which it uses to create shallow burrows.

Fossilized remains of the desert mouse have been found from Cape Range National Park and the Nullarbor Plain in Western Australia to the northern Flinders Ranges of South Australia, and Lake Victoria in New South Wales. When combined with modern records, these fossils suggest that the species once had an even more extensive range across arid Australia.

As the name suggests, the desert mouse has quite low water requirements. (Check out another rodent with desert adaptations in our collection, here!) Desert mice happily eat seeds and invertebrates when leaves and shoots are less widely available. They are nocturnal and spend the day in their burrows or sheltering underneath spinifex clumps. They are mostly solitary.

The reproduction rate of the desert mouse is very high, even when compared with other species in the Pseudomys genus. This allows populations to increase rapidly after periods of suitable rainfall and the pups will themselves become reproductively mature in about ten weeks.

To support the ongoing conservation efforts, DNA Zoo teamed up with Museums Victoria Senior Curator of Mammals Kevin C. Rowe and Oz Mammal Genomics to get a genome for the species assembled. Today, we are happy to release the chromosome-length assembly for the desert mouse.

The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using ~8.5x Oxford Nanopore long reads polished with short-insert Illumina data (46x coverage). The raw sequencing data for the draft assembly was generated by Oz Mammal Genomics. The draft was scaffolded into 24 chromosomes with ~20X 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 detail!

We gratefully acknowledge the collaboration and samples provided by Kevin C. Rowe, Museums Victoria. The sample generation for draft assembly was supported by Oz Mammals Genomics, a collaborative at Bioplatforms Australia initiative building genomic resources for Australian marsupials, bats & rodents. The draft genome assembly was supported by ShanghaiTech High Performing Computing Platform and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, China. The Hi-C work was supported by resources provided by DNA Zoo Australia, the University of Western Australia (UWA) and DNA Zoo, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

The following people contributed to the project: Erez Aiden, Olga Dudchenko, Zhenzhen Yang, Ashling Charles, Ruqayya Khan, David Weisz, Kevin Rowe & Parwinder Kaur.

Blog post by Parwinder Kaur.

Citations

Ruan, J. and Li, H. (2019) Fast and accurate long-read assembly with wtdbg2. Nat Methods doi:10.1038/s41592-019-0669-3

Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., Aiden, E.L., 2017. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95. https://doi.org/10.1126/science.aal3327.

Dudchenko, O., Shamim, M.S., Batra, S., Durand, N.C., Musial, N.T., Mostofa, R., Pham, M., Hilaire, B.G.S., Yao, W., Stamenova, E., Hoeger, M., Nyquist, S.K., Korchina, V., Pletch, K., Flanagan, J.P., Tomaszewicz, A., McAloose, D., Estrada, C.P., Novak, B.J., Omer, A.D., Aiden, E.L., 2018. The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv 254797. https://doi.org/10.1101/254797.

Durand, Shamim et al. “Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments.” Cell Systems 3.1 (2016): 95–98.

James T. Robinson, Douglass Turner, Neva C. Durand, Helga Thorvaldsdóttir, Jill P. Mesirov, Erez Lieberman Aiden, Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data, Cell Systems, Volume 6, Issue 2, 2018