The Australian lemming

They don’t jump of cliffs but eat grasses just like their Arctic relatives: meet the Tooarrana aka the broad-toothed rat aka Mastacomys fuscus!

Photo Description - Mastacomys fuscus, Broad-toothed Rat. Location: Australia, Victoria, Alpine National Park, Davies Plain. Survey: ALB 2013 0925. Alpine Bioscan. Photo Credits and acknowledgements - Source: Museums Victoria / Photographer: Heath Warwick

If you like to enjoy yourself by going for a walk near green vegetation, streams and waterfalls, you may find yourself share a similar taste with broad-toothed rat. These adorable creatures with a gentle demeanor are nocturnal medium-sized rodents with a short-tail, a broad face and a big belly. As a herbivore feeding mainly on stems, seeds of grasses and sedges, they are active in runways underneath the snow in the winter.

The animals thrive in alpine and sub-alpine areas and due to climate change have experienced a significant decline. As a result, the broad-toothed rat was classified as near threatened in the IUCN Red List of Threatened Species 2016.

Things have gotten even worse for Tooarrana after the catastrophic bushfire season 2019/2020. See below, for example, a photo of what was a thriving broad-toothed rat habitat for generations, now charred.

An image of what some of the broad-toothed rat sites in the burn scar looked like a few weeks ago, including the one in which the material for this study was collected. You can see the runways used by the rats for generations revealed on the charred ground, where before the fire they would have been covered by grasses, heath, and shrubs.

Under the Saving Our Species program, a targeted strategy for managing the broad-toothed rat has been developed, and 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 to help with the conservation efforts. Today, we are happy to release the chromosome-length assembly for the species.

The draft genome assembly was created using the wtdbg2 assembler (Ruan and Li, Nat Methods, 2019), using Oxford Nanopore reads (23.5Gbp, ~3.5 Million nanopore reads with read N50 of 15.9kb) polished with short-insert size Illumina reads (138Gbp, 459,921,452 PE 150bp).

The draft was scaffolded to 24 chromosomes using a total of 454,485,855 151bp PE Hi-C reads (137Gbp) using 3D-DNA and Juicebox Assembly Tools. See our Methods page for more detail!

Over the next year Museums Victoria will resequence 50 broad-toothed rat genomes and map them to the newly created reference. This will help monitor the population and inform the species management plans.

Read more about Tooarrana in this wonderful article by Joe Hinchliffe!

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, Parwinder Kaur, Ruqayya Khan, Kevin Rowe, David Weisz & Zhenzhen Yang.

Blog by: Zhenzhen Yang & Parwinder Kaur

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

Citations

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

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