The cat's out of the bag

The Pallas’s cat (Otocolobus manul) aka manul is a small wild cat similar in size to a domestic cat. It has a stocky build and a long, thick coat which helps protect it in its frosty habitat. These cats were named in 1776 after Peter Pallas, the eighteenth-century German zoologist. The word ‘manul’ comes from the Mongolian language. The scientific name of Pallas’s cat, Otocolobus, is from Greek and means 'ugly-eared' (gasp!).

Otocolobus manul, by flickr user Kouyuzu (CC BY-NC-SA 2.0)

Pallas’s cats are found in Turkmenistan, Iran, Kyrgyzstan, Kazakhstan, Bhutan, Nepal, India, Pakistan, Afghanistan, China, Mongolia, and Russia. They inhabit arid, montane shrublands and grasslands, rocky outcrops, scree slopes, and ravines in areas, where the continuous snow cover is below 15-20 cm (6-8 in). In the central part of their range, they live in hilly landscapes, high plateaus, and intermontane valleys that are covered by dry steppe or semi-desert vegetation, such as low shrubs and xerophytic grasses.

The manul has many unusual properties. For example, its fur changes color depending on the season, in winter being a frosted gray and in spring a gray/fox-red. The pupils of its large eyes, unlike those of other small cats, contract to small circles instead of slits!

Secretive and solitary, Pallas’s cats move slowly but purposefully, concealing themselves within their environment and blending into the background. They are mainly crepuscular but, in some areas, they may also be active during the day. In the daytime, Pallas's cats shelter in rock crevices or small caves, the most common place being the abandoned burrows of marmots. They are adept predators and hunt by stalking and then ambushing prey. Pallas’s cats growl or yelp when excited, sounding like a small dog. They can also purr!

Currently, this species is classified as Least Concern (LC) on the IUCN Red List but its numbers today are decreasing. Major threats to this animal are the large-scale poisoning of vole and pika populations, which are important prey items for Pallas’s cats. Habitat fragmentation and development as well as domestic dogs are other increasing threats to Pallas’s cats. They have also been hunted for many years for their luxurious fur, but international trade in their skin has declined in recent years.

Today, we share a short-read chromosome-length genome assembly for the Pallas's cat generated using primary fibroblasts. We thank the Brookfield Zoo T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center for providing a sample for this work and the Pawsey Supercomputing Centre and the DNA Zoo Australia team at the University of Western Australia for computational support! Check out the interactive Hi-C contact map for the species below!

Hopperation wallaroo genome annotation

This post is about the common wallaroo (Osphranter robustus) or, in the language of Indigenous Australians, Nurungga. The name “wallaroo” comes from "wadlu waru", meaning wallaby urine. Early settlers to Australia tried to pronounce the indigenous language but ended up saying “walla waroo”, leading to the name “wallaroo”.

Osphranter robustus. Photograph by Bob McDougall, via inaturalist.org (CC BY-NC)

Wallaroos are typically distinct species from kangaroos and wallabies. With its stocky build, coarse, shaggy fur, and short thick tail, the common wallaroo resembles Australian kangaroos in body shape. Its genetic makeup however says it is a closer relative to some wallabies.

This common wallaroo is listed as “least concern” in population conservation status. It is well suited to the Australian landscape conditions, and can be found throughout most of Australia, except for Tasmania. They are often spotted around rocky hills, caves, and rock formations with large overhangs to provide shade during the daytime. They can also be found in shrubland areas near food and water sources. They are herbivorous, preferring to eat soft-textured grasses and shrubs. Unlike some of its relatives, common wallaroos are primarily solitary and only form loosely packed gatherings around valued food sources.

Common wallaroos are polygamous, and a male common wallaroo will mate with multiple females. They have no mating season and produce young all year round; because of this, a female common wallaroo is almost constantly breeding. It is not uncommon for a female to have three babies at different stages of development, one waiting to be born in the uterus, one in the pouch and one at her feet. The common wallaroo has a life expectancy of 22-24 years and weighs between 16-35 kilograms.

Today, we share a chromosome-length genome assembly [2n=14] for the common wallaroo (Osphranter robustus). This is a short-read genome assembly from a primary fibroblast cell line. We gratefully acknowledge T.C. Hsu Cryo-Zoo at the University of Texas MD Anderson Cancer Center for providing the samples for this assembly! We also thank the Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational support for this genome assembly. Check out the contact map below showing the 7 chromosome-length scaffolds below!

Don’t desert us!

The addax (Addax nasomaculatus) is considered the most desert adapted antelope on the planet but is also among the most endangered, with less than 100 individuals left in the wild. Although the species was once found across the Sahelo-Saharan region of North Africa, they are now only present in a small area of Niger. Addax are able to live in extreme conditions and can face temperatures between -5 and 60 °C. They have large, flat hooves that allow them to walk across the desert without sinking into the sand and they rarely need to drink, since they obtain most of their liquids from the plants they eat, including wild melons. The primary threats faced by addax are hunting and changes in habitat use and their survival in the wild now relies on a series of large-scale reintroductions.

Addax (Addax nasomaculatus) by Josh more, [CC BY-NC-ND 2.0], via flickr.com

Fortunately, since the 1920s, addax have successfully been managed in captive populations across the globe. These insurance populations have proved invaluable for reintroductions and translocations into Tunisia, Morocco and Chad and will continue to represent a crucial component of addax management going forward. As part of this, researchers and conservationists are integrating genetic information into planning and decision making (Dicks et al. 2023). The availability of high quality genetic and genomic resources can therefore directly support addax conservation.

Today, we share a chromosome-length assembly for addax created using a combination of PacBio HiFi and Illumina Hi-C sequencing. PacBio HiFi sequencing was carried out at the University of Louisville Sequencing Technology Center from a male addax fibroblast cell line donated by the San Diego Frozen Zoo and contigged using HiFiasm (Cheng et al., 2021). The HiFi sequencing was made possible thanks to support from the Environment Agency – Abu Dhabi to the University of Edinburgh and the Royal Zoological Society of Scotland. Hi-C sequencing was carried out by the DNA Zoo using a blood sample donated by a female individual from SeaWorld.

Previously we shared an addax genome assembly using a draft generated by Hempel et al., 2021. The new genome assembly dramatically improves the contiguity of the assembly, boosting contig N50 from 10kb to 65.7Mb. We hope that this improved chromosome-level assembly will serve as an important backbone for future studies investigating this beautiful species of antelope on the brink of extinction.

Check out the chromosome-length contact map of the new addax reference below, and follow the assembly link for more details and info!