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!

Don't rein on our parade

Reindeer (Rangifer tarandus L. 1758), or caribou, is a prominent semi-domesticated cervid species (family Cervidae, subfamily Capreolinae). Reindeer is one of the few modern hoofed species in which domestic and wild forms coexist on the same territory. It exists in the northern boreal, tundra, and subarctic zone of two continents, Eurasia and North America, and nearby islands. The reindeer in the distant past made it possible for humans to explore the North, and currently remains the most important biological resource for more than twenty nations of Eurasia and North America. Reindeer were domesticated at least 3000 years ago. Reindeer are bred and hunted for meat, skins, and milk and are also used for riding and as pack transport (Corlatti and Zachos, 2022).

IMG_1499. Photo by Hazel Watson, via flickr.com [CC BY-NC 2.0]

It is generally recognized that there are two ecological forms: tundra and taiga; some authors distinguish, in addition, mountain. The intraspecific taxonomy of Rangifer tarandus is highly controversial. Various authors distinguish up to fourteen reindeer subspecies: two extinct and twelve modern (Holand, I Mizin, RB Weladji, 2022).

Today, we share a chromosome-length assembly of the reindeer based on the Zoonomia draft RanTarSib_v1_BIUU (GCA_004026565.1) [Zoonomia Consortium, 2020]. The chromosome-length upgrade was done with Hi-C generated using cultured cells from the primary fibroblast cell line (passages 4-7). Hi-C libraries were constructed by Guzel Davletshina, Natalia Lemskaya, and Polina Perelman.

The primary fibroblast cell line was established from the ear biopsy by Anastasia Proskuryakova. The fibroblast cell line was cultivated by Katerina Ivanova. Biopsy from a three-year-old female was kindly provided by Primorsky Safari-Park (Director Dmitry Mezentsev, https://safaripark25.ru/) and was collected by Vasilina Belik. According to the habitat (Russian Far East), the studied reindeer likely belongs to the R. t. phylarcus subspecies. This subspecies inhabits Siberia, east of the river Lena, including Transbaikalia, the Amur region, the coast of the Sea of Okhotsk, the Kamchatka and Sakhalin (Harding, 2022). The biopsy collection was organized by Olga Uphyrkina (Far East Biodiversity Center). The scaffolding was done using 3D-DNA and Juicebox Assembly Tools.

The assembly (see interactive contact map below) is consistent with the standard cervid karyotype with 2n=70. Interestingly, reindeer have huge sex chromosomes (X and Y) enriched with repetitive sequences (Graphodatsky et al., 2020). A comparative chromosome map of the reindeer with dromedary homologies (Proskuryakova et al., 2022) identified the conservation of chromosomes in the Capreolinae subfamily at large scale. We are excited to see how whether if this conservation is confirmed at a finer scale, the analysis that is now enabled with chromosome-length assemblies across the subfamily.

We thank Dr. A.S. Graphodatsky, N.S. Serdyukova, Yu. Butakova for thelp with this assembly.

Citations:

1. Atlas of mammalian chromosomes (2nd edition). eds. Graphodatsky AS, Perelman PL, O’Brien SJ. Wiley-Blackwell, USA, 2020, 1008 p.

2. Holand O., Mizin I., Weladji R.B. Reindeer Rangifer tarandus (Linnaeus, 1758). Terrestrial Cetartiodactyla, 2022. 248-269

3. Harding, Lee E., 2022. Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies. ZooKeys: 117-151.

4. Proskuryakova A.A., Ivanova E.S., Perelman P.L., Ferguson-Smith M.A., Yang F., Okhlopkov I.M., Graphodatsky A.S. Comparative Studies of Karyotypes in the Cervidae Family. Cytogenic and Genome Research, 2022.