Mongoose on the loose

The small Indian mongoose (Urva auropunctata) may be a small carnivorous species, but it has managed to have an incredibly large ecological impact! The Indian mongoose's native habitat is widespread across South Asia, from Iraq to Myanmar. However, in the late 19th and early 20th century, the small Indian mongoose was introduced into Hawaii, the Caribbean, the Adriatic, and Japan to serve as a predator against rats and snakes. Unfortunately, the Indian mongoose's ability to thrive in a variety of environments and opportunistic hunting style lead to massive devastation on the introduced habitats.

Small Indian mongoose by James Bailey, [CC BY-NC], via iNaturalist.org

Today, we release the chromosome-length assembly for the small Indian mongoose. This is a short-read genome assembly, with a contig N50 = 80 Kb and a scaffold N50 = 133 Mb. The sample used to generate this assembly was a primary fibroblast cell line provided to us by the T.C. Hsu CryoZoo from the M.D. Anderson Cancer Center. Thank you to Drs. Asha Multani, Sen Pathak, and Richard Behringer in the Department of Genetics at the MD Anderson Cancer Center as well as Dr. Liesl Nel-Themaat and Arisa Furuta for their help with this sample!

Interestingly, in initial studies of the eutherian small Indian mongoose the Y chromosome could not be identified in somatic cells. The male chromosome number is uniquely odd, 2n = 35, whereas that of females is 2n = 36. Further studies suggested that this unique karyotype resulted from a translocation of the ancestral Y chromosome to an autosome (Murata et al., 2016)!

We now confirm this finding and identify the autosome of interest (luckily our fibroblasts turned out to be male). The last chromosome in our assembly (HiC_scaffold_18) appears in two versions. One of these version reported in the default fasta (Urva_auropunctata_HiC.fasta) is the canonical autosomal version. Each female Indian mongoose would have two of these. Males, on the other hand, would have only one of these. The other copy, reported separately in our assembly as Urva_auropunctata_Y.fasta, has a completely different sequence on it's q-tip. Check out the full release page for links to the relevant files, and check out the the contact map below showing 18 'canonical' chromosomes of the small Indian mongoose Urva auropunctata.

Rally for the rakali

The rakali is an Australian native rodent first described in 1804. It's scientific name, Hydromys chrysogaster, translates to "golden-bellied water mouse”. Rakali is the name given to the species by the Aboriginal people from the Murray River area. The species is also known as rabe or water-rat. It is a distinctive Australian rodent specialised for an aquatic existence, with broad partially webbed hind-feet, water-repellent fur, and abundant whiskers. It is the largest rodent in Australia, often weighing more than 1 kilogram!

The Australian water rat (Hydromys chrysogaster). Photo Credits and acknowledgements - Lizette Salmon, via iNaturalist.com (CC BY-NC 4.0)

Among murid rodents, semiaquatic species have evolved at least three times, including (1) Hydromys and relatives on New Guinea, (2) Nilopegamys and relatives of Africa, and (3) Waiomys of Sulawesi, Indonesia. The rakali is one of four species in the genus Hydromys, and it is the only one with a range extending beyond Papua New Guinea and Indonesian West Papua.

Having adapted to a unique niche of a semiaquatic and nocturnal lifestyle, this species lives in burrows on the banks of rivers, lakes and estuaries. The rakali have a diverse diet of aquatic insects, fish, small vertebrates, birds' eggs and water birds. There is some sexual dimorphism present in the rakali, with females being generally smaller than males. However, the thick and muscular tails, which help serve as a rudder when swimming, remain the same size in both genders.

At the beginning of the century, the rakali was considered a pest and were widely hunted for their soft fur which caused the wild population to drastically decrease. Humans have been their greatest predator, with rakali requiring protection by legislation in 1938. Since this legislation, wild populations have recovered in all Australian states except for Western Australia where the rakali is still at a “near threatened” status.

To support ongoing conservation efforts, DNA Zoo teamed up with Museums Victoria Senior Curator of Mammals Kevin C. Rowe to release the chromosome-length assembly for the rakali, Hydromys chrysogaster. The genome draft was generated with short-insert size Illumina reads [481, 563, 388 PE reads] and scaffolded to chromosome length with Hi-C [770, 408, 993 PE reads]. See our Methods page for more assembly details. Browse the 24 chromosomes (2n=48) of the rakali in the interactive Juicebox.js session below:

This 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.

Jird is the word

Though the name of the Libyan jird, Meriones libycus, implies it is somehow special to Libya, this adaptable rodent can be found all across Northern Africa and even into western China! From hot deserts, tropical shrub-lands, and even domestic gardens, this species of jird can make pretty much any environment inhabitable [1]. Because of its mainly herbivorous diet, it can make its home as long as sufficient amounts of vegetation is present.

Libyan jird by Raouf Guechi, [CC BY-NC], via iNaturalist.org

The Libyan jird is a social animal that tends to form small colonies, but it has been reported that some prefer to live individually. They live in burrows made up of a complex network of tunnels which may extend up to 1.5 metres underground and several metres outwards. This little creature likes to plan ahead, and tiny “warehouses”, chambers which colonies may use store up to 10 kg of seed, are also included as part of the burrow’s construction [2]. They sometimes travel locally from burrow to burrow, and when doing so, they stick their tails up in the air and run quickly, spending as little time in the open as possible [3].

The diet of the Libyan jird primarily consists of seeds, leaves, and little fruits. They have a preference for grass seeds, although they aren’t particularly picky. They have been known to consume insects in some cases. In areas under human cultivation such as farms or gardens, they will happily feed on any crop. The Libyan jird is known to devastate agricultural areas near their habitats, especially potato and tomato crops. For this reason, they are considered as serious pests by farmers [4].

The Libyan jird is highly abundant and found across a wide range, and as such is considered as a species of ‘Least Concern’ by IUCN. Libyan jirds are among the several species of gerbils which are kept as pets, although it is not known if this has an impact on the population.

Today, we release the chromosome-length assembly for the Libyan jird, Meriones libycus! This was a $1K assembly, for more details on our assembly procedure, please see our Methods page. The sample used for this assembly was a primary fibroblast cell line provided by the T.C. Hsu Cryo-Zoo, originally frozen back in 1988. We thank Drs. Asha Multani, Sen Pathak, Richard Behringer, Liesl Nel-Themaat and Arisa Furuta in the Department of Genetics at the MD Anderson Cancer Center for their help with this sample!

We here at the DNA Zoo think rodents are rad! We're happy to welcome the Libyan jird to our released collection, bringing our total to 26 chromosome-length rodent assemblies. Browse the 22 chromosomes (2n=44) of the Libyan jird in the interactive Juicebox.js session below!