A short furrytail

Off the coast of southern California, there is a group of small islands - Channel Islands. About 7000 years ago, mainland grey foxes (Urocyon cinereoargenteus) got onto these islands (and we still do not know how exactly). The foxes thrived, and are now their own separate species called the island fox (U. littoralis).

Island fox by Christian Schwarz, [CC BY-NC], via inaturalist.org

Over the centuries, the foxes got smaller in size; average weight is only about 2 kg (~4 lb) making them the smallest fox in North America! They also lost a few tail vertebrae making their tails shorter. The island foxes are docile and are not afraid of humans. They enjoy life in woods, grasses, and on the beaches of islands by hunting mostly at dawn and dusk on small mammals (deer mice), insects (crickets), lizards, birds (and their eggs), and frogs.

The Santa Catalina Island fox (U. littoralis catalinae) is one of six subspecies of the island gray fox. The Santa Catalina population was almost wiped out in 1999 by the devastating outbreak of canine distemper virus. The epidemic left less than 100 foxes alive. The severe bottleneck has decreased the levels of genetic diversity in the fox population and increased the frequency of potentially deleterious variants. It is likely that these variants are responsible for the unusually high occurrence of ear tumors (ceruminous gland carcinoma) in these foxes after the distemper epidemic (Hendricks et al., 2022).

Over the last two decades enormous conservation efforts of Santa Catalina Island Conservancy together with the National Park Service, The Nature Conservancy, and the Institute for Wildlife Studies brought the number of foxes back to over 2000. Catalina Island fox survival is a remarkable tribute to well-planned science-based conservation strategies: fox vaccinations, captive breeding, radio-collar monitoring, predator control (Golden eagle), strict limits on mainland-derived pets, wildlife, parasites, and human impact monitoring etc. We hope that the genome assembly we share today will contribute to these conservation efforts including long-term monitoring of the carcinoma alleles as well as overall genetic diversity, and provide crucial information for the long-term persistence of the threatened fox population.

The ear sample that was used for this genome assembly was kindly provided by Julie King from the Catalina Island Conservancy and was collected with Winston Vickers. The primary fibroblast cell line ULI-623 was established by Polina Perelman from the biopsy of the 10-year-old female Catalina Island fox #36966 (affected by ceruminous gland carcinoma) at the Laboratory of Genomic Diversity led by Stephen O’Brien. Passage #3 was used to construct the short-read DNA-Seq and Hi-C libraries. We thank Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, and David Goldman for preserving LGD cell line collection.

Browse the 33 chromosomes of the island fox in the interactive Juicebox.js session below, and check out the assembly page for more information about this genome!

References

https://www.catalinaconservancy.org/

Hendricks SA, King JL, Duncan CL, Vickers W, Hohenlohe PA, Davis BW. Genomic Assessment of Cancer Susceptibility in the Threatened Catalina Island Fox (Urocyon littoralis catalinae). Genes (Basel). 2022 Aug 22;13(8):1496. doi: 10.3390/genes13081496.

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.