Victoria’s faunal emblem - fairy (Leadbeater's) possum

The Leadbeater's possum (Gymnobelideus leadbeateri) was named in 1867 after John Leadbeater, the then taxidermist at the Museum Victoria [1]. (They also go by the common name of fairy possum [2].) These cute little fairies which are just 33 cm (13 inches), tail included in body length, are rarely seen being nocturnal, fast-moving, and living in tree hollows of some of the tallest forest trees in the world [3]. They live in small family colonies of up to 12 individuals and mate twice per year, with a maximum of two joeys being born to each monogamous breeding pair in colony [4].

Leadbeater's possum (Gymnobelideus leadbeateri), image by Arabella Eyre, Zoos Victoria

The Leadbeater’s possums belongs to the Petauridae family together with the gliding possums. In contrast to other members of the family, Leadbeater’s possums do not glide, and are thought to represent an ancestral form that evolved about 20 million years ago [5].

The State of Victoria, Australia, made the Leadbeater's possum its faunal emblem on 2 March 1971 [6], and since then this emblematic species has almost gone extinct! It is now listed as critically endangered, largely restricted to small pockets of alpine ash, mountain ash, and snow gum forests in the Central Highlands of Victoria, Australia, north-east of Melbourne, with a single isolated population in lowland floodplain forest [7, 8, 9]. In the highlands, the February 2009 Black Saturday bushfires destroyed massive part of the reserve system of Leadbeater's possums' habitat, and the wild population is thought to have been drastically reduced in size.

The availability of suitable habitat is critical for saving the species from looming extinction. Intensive population recovery measures, including translocation, will be required to save the last lowland population. The loss of hollow-bearing trees is the possums' biggest threat in highland habitats, along with bushfire. Suitable hollows can take 190 years to develop in living trees, and old trees with suitable hollows have decreased due to logging and bushfires in the wild over the last three decades of the 20th century [10]. The animal’s vulnerability to fire makes climate change a severe danger.

To support ongoing conservation efforts led by Zoos Victoria, DNA Zoo has been working with Paul Sunnucks and Alexandra Pavlova at Monash University to get a chromosome-length assembly genome for a female belonging to the sole remaining population of fewer than 30 individuals of lowland Leadbeater’s possum, which experience harmful effects of inbreeding [11].

The chromosome-length assembly we share today is based on the draft assembly available on NCBI was generated by Han Ming Gan, Stella Loke and Yin Peng Lee of Deakin Genomics Centre, and the Monash University team, with funding from Zoos Victoria and Australian Research Council funded project LP160100482 (Gymnobelideus leadbeateri isolate B50252). The draft genome assembly was created using MaSuRCA v. 3.3.4 (Zimin et al. 2013), using Oxford Nanopore MinION reads polished with short-insert size Illumina NovaSeq reads.

The draft was scaffolded to 11 chromosomes with 250M Hi-C reads generated by DNA Zoo labs from a liver sample from the same isolate, obtained from Leanne Wicker and Dan Harley (Zoos Victoria), using 3D-DNA (Dudchenko et al., 2017) and Juicebox Assembly Tools (Dudchenko et al., 2018). See our Methods page for more details!

The Hi-C work was supported by resources provided by DNA Zoo Australia, Faculty of Science, The University of Western Australia (UWA), DNA Zoo, Zoos Victoria and Monash University, with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia.

See below how the chromosomes from the new Leadbeater's possum genome assembly related to those of another notable Australian mammal from our collection, the tammar wallaby. That's about 55MY of evolution separating the species [12]. Check out the assembly page for the $1K tammar wallaby genome assembly here!

Whole genome alignment plot between the Leadbeater's possum (LBP_v1_HiC) and the tammar wallaby (me-1k)

The following people contributed to the Hi-C chromosome-length upgrade of the project: Erez Aiden, Olga Dudchenko, David Weisz, Ruqayya Khan & Parwinder Kaur.

Blog by: Parwinder Kaur and Olga Dudchenko

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

Don't worry be capy!

The capybara is the largest living rodent in the world! Their scientific name, Hydrochoerus hydrochaeris, comes from the Greek words “hydor” meaning water and “choiros” meaning pig. Native to South America, these oversized rodents are well adapted to life on land and in water. Capybaras can be found inhabiting flooded grasslands, swamps, as well as the banks of rivers and lakes. One can say capybaras were made to swim with their webbed feet and their wiry, quick-drying hair that’s perfectly suited for moving land and water frequently [1].

Image by Karsten Paulick from Pixabay [Pixabay License], via pixabay.com

Capybaras are very social animals, living in groups ranging from 3 to 30 individuals [2]! They are very communicative, producing various types vocalizations. Similar to beavers, the front teeth of the capybara never stop growing [3]. Capybaras must continually gnaw and chew on grasses and aquatic vegetation to keep their teeth size in check. Just like their close relatives, the guinea pigs, capybaras must eat their feces to get beneficial bacteria to help their stomach break down the fiber in their meals.

Today we share the chromosome-length assembly for the capybara. This is a $1K genome assembly with a contig n50 of 79 Kb and a scaffold n50 of 71 Mb. Check out Dudchenko et al., 2018 for procedure details. Thank you to Pop from the Houston Zoo for providing us with the sample to make this assembly possible! See Pop bonding with his keeper here!

Capybaras are legal to own as pets in some states in the US, and owning a capybara is a relatively recent trend in the pet world. This has already had some consequences: did you know that the state of Florida is dealing with a problem of invasive capybaras, most likely due to them escaping or being released by irresponsible owners?

Some may say that the capybara is basically an oversized guinea pig, but the genomics says otherwise. Just look at the many rearrangements between the two species! Check out our assembly page for the domestic guinea pig here.

Whole genome alignment plot for the capybara against the domestic guinea pig (Cavpor3.0_HiC).

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