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

All’s whale that ends whale

The gray whale, Eschrichtius robustus, is a member of the baleen whale family. Their name comes from their mottled skin with gray and white patches, due to being covered in barnacles, whale lice, and other parasites. (Actually barnacles may have a mutualistic relationship with their host whales, providing protection from attack from killer whales [1].) Female gray whales are usually larger than males, reaching sizes of approximately 14.9 meters, and weighing up to 41 tonnes [2].

Gray whales have the longest annual migration of any mammal, making 10,000-12,000-mile round trips around the North Pacific Ocean. During their migration, gray whales stick close to the shores, preferring shallower waters [3]. Their close proximity to land and their natural curiosity cause them to be frequently spotted by whale watching tours.

Gray whale breaching by Eric Neitzel, [CC BY-NC-ND 2.0], via flickr.com

Once at the brink of extinction in the early 1800’s, conservation efforts and hunting bans have allowed the eastern population of gray whales to return to pre-whaling levels! In 1994, gray whales were officially removed from the endangered species list, though the Western North Pacific population is still endangered [5]. All gray whales are still protected under the MMPA! As whales play a large role in the oceans’ ecosystems, preserving the gray whale species will have boundless effects on other marine life.

Today we share the chromosome length assembly of the gray whale, with contig N50 = 67Kb and scaffold N50 = 103 Mb. This is another $1K genome assembly, for procedure details, see Dudchenko et al., 2018. This is the third baleen whale (Mysticeti) in our collection so don’t forget to check out Bryde's whale and the North Atlantic right whale as well!

This work was performed under Marine Mammal Health and Stranding Response Program (MMHSRP) Permit No. 18786-03 issued by the National Marine Fisheries Service (NMFS) under the authority of the Marine Mammal Protection Act (MMPA) and Endangered Species Act (ESA). The specimen used in this study was collected by Pam Tuomi (Alaska Sealife Center) from Girdwood, Alaska and provided by the National Marine Mammal Tissue Bank, which is maintained by the National Institute of Standards and Technology (NIST) in the NIST Biorepository, and which is operated under the direction of NMFS with the collaboration of USGS, USFWS, MMS, and NIST through the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project.

Post by: Ruqayya Khan and Ben Neely

The panda dolphin

The Commerson’s dolphin (Cephalorhynchus commersonii) aka skunk dolphin aka panda dolphin is best known for its distinctive, black and white body that consists of black fins, flippers and head, with white covering all other regions. These dolphins are small in size and found largely across the southwest Atlantic Ocean, with some populations also seen in the Indian Ocean. Other than their vastly different geographic habitats, Commerson’s dolphins found in the Indian Ocean also differ physically from their Atlantic counterparts. The dolphins seen in the Indian Ocean tend to have more grey patterns along their body and are also usually larger in size. [1]

Given their small size, these dolphins are extremely agile and register swimming speeds as fast as 11 to 13 kmph, often seeing riding waves surrounding high-speed boats. They are friendly to other relatives and like to associate with the Peale’s dolphin (Lagenorhynchus australis) when performing spectacular acrobats and playful swimming routines!

Photograph by GP0STRFPH, Greenpeace UK [CC BY 2.0], via flickr.com

Typically, Commerson’s dolphins exist in groups of 2-3 individuals but are also known to travel and socialize in groups as big as 100 individuals. Although their life spans in the wild average at around 10 years of age, one captive individual at SeaWorld (San Diego) lived for a record-breaking 25.8 years! Previously, these dolphins were often intentionally captured by fishermen for use as bait, but the practice has since been outlawed, allowing populations level to rise again. Yet, accidental entanglement in fishing nets continues to be a threat to these dolphins. [2]

Today we release a chromosome-length assembly for the Commerson’s dolphin species, our seventh assembly in the Delphinidae (oceanic dolphins) family (see our assemblies page here). This is a de novo assembly with contig N50 = 92Kb and scaffold N50 = 104Mb. See Dudchenko et. al, 2018 for details on the protocol. We thank SeaWorld for their help with the sample!