Mala (rufous hare-wallaby)

An important ancestral figure in the mythology of the Warlpiri people, the last wild mala (rufous hare-wallaby, Lagorchestes hirsutus) population in central Australia went extinct in the early 1990s, succumbing to the impacts of destructive wildfires and feral predators like foxes and cats. These small macropods are now making a comeback behind the conservation fences, thanks to captive breeding programs.

Photo 60046491, (c) Michael Hains, some rights reserved [CC BY-NC], via iNaturalist.org

The mala is a small marsupial covered in a greyish-orange fur. It grows to about 30cm tall. If you spot a smaller one it is likely to be male. On average they weigh only 1-2kg! The animals resemble hares in looks (hence the hare-wallaby), but with larger hind legs and a long thin tail, used for balance. Their scientific name ‘Lagorchestes hirsutus’ means ‘shaggy dancing hare’. This refers both to the shaggy fur on their lower back and the similarities the wallaby has to hares.

Mala prefers to go out at night and will hide underground during the day throughout most of summer. Their diet consists of seeds, fruits and leaves, with no water required. This is because they are typically found in semi-arid climates an obtain the moisture they need from their food. Females breed throughout the year (no set breeding season) and may have up to three young, which the mother carries around in her pouch. Joeys will be kept in their mother’s pouch for around 125 days.

They primarily use body language to communicate with each other. However, when frightened they may scream. Or rather, they produce a high-pitched squeak. In sanctuaries, the wallabies tend to have a lifespan of up to 13 years, which is longer than in the wild.

The rufous hare-wallaby is an important animal to Aboriginal culture. For the Anangu, or Aboriginal people, the Mala or "hare wallaby people" are important ancestral beings. Mala Tjukurpa, the Mala Law, is essential to culture and celebrated in dance and stories.

Rufous hare-wallaby listed as an endangered in WA, extinct in NT, endangered in SA and endangered species status nationally in Australia.

Today, we share the chromosome-length genome assembly for rufous hare-wallaby. The sample for the genome assembly was provided by Natasha Tay, Harry Butler Institute, Murdoch University. This is a $1K genome assembly, with contig N50=57kb, and scaffold N50=401Mb. See our Methods page for more detail on the assembly procedure. Check out the interactive Hi-C contact map for 10 chromosomes of the rufous hare-wallaby below and on the relevant assembly page.

The 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.

A high-quality genome sequence is an essential resource required to implement genomics data into conservation management initiatives. More than 80% of the current 200 Australian national vertebrate recovery plans have genetic action listed in the species recovery plan with less than 15% of them having any genomic data available. Reach out if you have access to sample to help us address the gap!

A spectacular bear assembly

The spectacled bear (Tremarctos ornatus) is the only bear native to South America. It is the last remaining short-faced bear (subfamily Tremarctinae). The species is classified as Vulnerable by the IUCN because of habitat loss.

Handsome Chester, photo by Valerie [CC BY-NC-ND 2.0], via flickr.com

The species is of course famous in literary circles as much as in conservation ones thanks to Michael Bond's much-loved Paddington, whose adventures have featured in twenty books, three TV series and two feature films to date. (Interestingly, Bond originally imagined Paddington to have 'travelled all the way from darkest Africa', before being advised that there were no bear species in Africa! So the bear became one from 'darkest Peru').

Today, we share the chromosome-length genome assembly for the spectacled bear, based on a sample provided to us by the San Antonio Zoo. This is a $1K-model genome assembly, with contig N50=117kb and scaffold N50=105Mb. Read more about the $1K genomes on our Methods page.

This is our 5th genome in the Ursidae family (bears), after the Malayan sun bear, the American black bear, grizzly and polar bear. Unlike all the other bears who all have a karyotype of 2n=74, the spectacled bear is 2n=52. See below how the chromosomes of the spectacled bear relate to the very conservative karyotype of all other bears, suggesting multiple fusion events associated with the spectacled bear chromosomes as compared to the 'main' Ursidae karyotype!

Whole-genome alignment plots between the chromosome-length spectacled bear assembly and those of other bears in the DNA Zoo collection: left to right, Ursus americanus, Ursus arctos, Helarctos malayanus and Ursus maritimus. The Helarctos malayanus alignments are filtered at a higher threshold to account for shorter phylogenetic distance between the species.

Don't forget to check out the interactive map for the 2n=52 chromosomes below and on the corresponding assembly page!

Clever clovers

Sustainable agricultural production entails growing food without damaging the underlying soil. Legumes are of great interest for such efforts: because they produce their own nitrogen via symbiotic nitrogen fixation, legumes can actually improve the soil.

Among legumes, pasture or forage legumes tend to be more resilient to stress and more capable of thriving in marginal land. These forage legumes are highly valued feed for extensive livestock production. There is an increasing interest worldwide in using annual forage legumes as cover crops to supply soil nitrogen. Symbiotic nitrogen fixation in legumes leads to high protein fodder content and rejuvenated soils for a sustainable feed system.

Photo Description – The subterranean clover (Trifolium subterraneum) cv Daliak. Photo Credits and acknowledgements – Dr Parwinder Kaur [CC]

Clovers are among the most effective to break the ‘infernal circle of the fallow’ a technique known to the Germans as ‘Besömmerung’. Subterranean clover (Trifolium subterraneum L.) makes the greatest contribution to livestock feed production and soil improvement in terms of total worldwide usage among annual clovers, particularly in Australia, where it is sown over 29 million hectares. The self-reseeding ability and grazing tolerance of subterranean clover, even under suboptimal and variable environmental conditions, contribute to its widespread distribution.

Subterranean clover is a diploid (2n = 2x = 16), predominantly inbreeding, annual species with a relatively small genome size of 540 Mbp (1C = 0.55 pg DNA) that can be readily hybridized, and exhibits wide diversity for both qualitative and quantitative agronomic and morphological characters. Within the genus Trifolium, it is established as a reference species for genetic and genomic studies.

Today, we add the subterranean clover chromosome-length resource to the DNA Zoo website. The assembly is described in more detail in our 2018 preprint on the subject.

The Hi-C 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. The following people contributed to the Hi-C chromosome-length upgrade of the project: Christopher Lui, Melanie Pham, Olga Dudchenko, Erez Aiden & Parwinder Kaur.