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!

Nosy knowtrias

Also known as the nutria, the coypu (Myocastor coypus [Molina, 1782]), is a large amphibious rodent from about 5 to 7 kg (Woods et al. 1992). Native to South America, its range includes Argentina, Chile, Paraguay, Uruguay, as well as the southern parts of Bolivia and Brazil. It is associated with aquatic habitats and primarily feeds on vegetation along the river banks (Woods et al. 1992). Coypu shares some ecological adaptations with another amphibious species, the beaver (e.g., it can remain submerged for about 10 min!). The two species however are phylogenetically distant. The main external morphological difference between the beavers and the coypu is probably the tail that is flat in the formers.

Underwater picture of a wild coypu (Myocastor coypus) taken with an underwater camera trap. Photo by Quentin Martinez and Cécile Molinier.

In the late 19th and early 20th centuries, coypus have been exported for fur production to Europe, North America, Asia, and Africa. Due to accidental escapes and voluntary releases, the species is now considered as one of 100 of the world's worst invasive alien species (GISD 2021). At high densities, their burrows present along the river banks may impact the overall wetland ecosystems. The expansion of the coypu seems to be limited by the extreme temperature of cold winters. However with the overall global warming, some models predict a massive worldwide expansion of the species (Jarnevich et al. 2017).

We are still discovering new things about this species. As an example, recent evidence shows that the coypu may have reduced olfactory capabilities in comparison to its close terrestrial relatives (Martinez et al. 2020). Indeed, it was found that the relative size of their olfactory organs is reduced, including the loss of two olfactory turbinals, a nasal structure involved in olfaction. In order to investigate the olfactory question from a genomics perspective and test if there is a relation between the morphology and the genome (Martinez et al. 2023), today we release the chromosome-length assembly for the coypu Myocastor coypus.

The new genome assembly via Hi-C upgrade of a draft generated by combining Nanopore long reads with Illumina short reads, made by Marie-Ka Tilak, Quentin Martinez, Rémi Allio, Pierre-Henri Fabre and team from Institut des Sciences de l'Évolution de Montpellier (ISEM) and Université de Montpellier (UM).

This project was funded by l‘Agence Nationale de la Recherche (Défi des autres savoirs, Grant DS10, ANR-17-CE02-0005 RHINOGRAD 2017 granted to Pierre-Henri Fabre). We thank the other collaborators of this project: Cécile Molinier, Benoit de Thoisy and Vincent Goanec.

In accordance with the local program for pest management and in collaboration with Régis Gibert and Nathalie Vazzoler-Antoine the original sample comes from a wild Myocastor coypus (34130, Lansargues, France). The sample (QM1153) used fot assembly is now part of the ISEM collection. Browse the 20 chromosome-length scaffolds of the new assembly using the interactive map below!

References:

GISD. Of the World's Worst Invasive Alien Species. Global Invasive Species Database. http://www.iucngisd.org/gisd/100_worst.php. 100, (2021).

Jarnevich, C. S., Young, N. E., Sheffels, T. R., Carter, J., Sytsma, M. D., & Talbert, C. (2017). Evaluating simplistic methods to understand current distributions and forecast distribution changes under climate change scenarios: an example with coypu (Myocastor coypus). NeoBiota, 32(1), 107.

Martinez, Q., Clavel, J., Esselstyn, J. A., Achmadi, A. S., Grohé, C., Pirot, N., & Fabre, P. H. (2020). Convergent evolution of olfactory and thermoregulatory capacities in small amphibious mammals. Proceedings of the National Academy of Sciences, 117(16), 8958-8965.

Martinez Q, Courcelle M, Douzery E, Fabre PH. When morphology does not fit the genomes: the case of rodent olfaction. Biol Lett. 2023 Apr;19(4):20230080. doi: 10.1098/rsbl.2023.0080. Epub 2023 Apr 12. PMID: 37042683; PMCID: PMC10092080.