Earresistable puzzle: decoding the plains vizcacha

The South American plains vizcacha (Lagostomus maximus, Desmarest, 1817) is a rodent that inhabits the Southern area of the Neotropical region, mainly distributed in Argentina, from the North of Patagonia throughout the Pampean region and reaching the South of Bolivia and Paraguay (Jackson et al. 1996). The species belongs to the order Caviomorpha, suborder Hystricomorpha, family Chinchillidae (Voloch et al. 2013, Steppan and Schenk 2017), which comprises three living species: the chinchilla (Chinchilla lanigera), the mountain vizcacha (Lagidium viscascia), and the plains vizcacha (Lagostomus maximus).

The South American plains vizcacha, drawing by Patricia Saragüeta

Three subspecies of L. maximus are recognized: L. m. petilidens (Hollister, 1914), distributed in southern Buenos Aires, La Pampa, and Río Negro provinces in Argentina, L. m. maximus (Desmarest, 1817), in central Argentina, and L. m. immollis (Thomas, 1910), spreading from northern Argentina to Paraguay and Bolivia (Llanos and Crespo 1952, Redford and Eisenberg 1992). Its widespread distribution in the Argentinean pampas contributes to the cultural symbolic value of this species.

Phenotypically, plains vizcachas show a strong occipital crest, a noticeable facial pattern consisting of two parallel black bands, one passing through the eyes and the second across the nose, separated by a white stripe, two pairs of bi-laminate molars, hind limbs with three digits, and a strong tail used as a third leg (Pocock 1922, Jackson et al. 1996). Sexual dimorphism is very pronounced. Males are much larger, have a bigger head, and a more pronounced facial mask than females. This large herbivore species is highly social and shows polygynous behavior. It lives in communal burrow systems and indulges in nocturnal foraging outings (Llanos and Crespo 1952).

The South American plains vizcacha, photo by by Adrián Grilli

Like other packrats, Vizcachas in North Patagonia are in the habit of collecting “souvenirs”. For this reason, they function as a marker species in Paleoecology in South America, revealing the secrets of peculiar places such as the Huemul cave (Llano 2020). It is very difficult to determine the rodent species inhabiting these caves; then, genomic information could contribute to precise the species in the past of the Earth.

Female plains vizcacha is a seasonal breeder that shows unusual reproductive features, distinguishing it from other mammals, representing the highest polyovulation rate so far recorded for a mammal (Weir 1971) and the second longest gestation for a rodent, only exceeded by the pacarana (Dinomys branickii), another caviomorph rodent. Neonates are precocious and, despite suckling for a couple of weeks, can feed and move independently from birth. The unusual physiology of the ovary makes L. maximus a unique alternative research model, especially to understand the regulatory mechanisms of oogenesis (Leopardo and Vitullo, 2017).

Today we release the chromosome-length assembly for the South American plains vizcacha. The sample used for this genome assembly came from an adult female plains vizcacha from ECAS (Estación de Cría de Animales Silvestres, Wild Animal Breeding Station, Fauna and Flora Department, Ministry of Agrarian Development, Buenos Aires Province, Argentina). The capture of the specimen was approved by the Fauna and Flora Department, Ministry of Agrarian Development and CICUAE (Comité Institucional de Cuidado y Uso de Animales de Experimentación) at Universidad Maimónides. The sample was collected by Dr. Alfredo Vitullo and his scientific team at CEBBAD (Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo, Universidad Maimónides, Buenos Aires, Argentina) and processed by Clara Campos at Saragüeta´s team at IBYME-CONICET (Instituto de Biología y Medicina Experimental, Buenos Aires, Argentina). Browse the Hi-C contact map for the 28 L. maximus chromosomes below, and visit the assembly page for more details about the data model and sequencing.

Blog post by Patricia Saragüeta, IBYME-CONICET, Buenos Aires Argentina, saraguetalab@gmail.com

Brewing genomes

Australia produces high quality barley, with annual production averaging over 9 million tonnes/year. It is a widely grown crop (second in size only to wheat) and occupies a large geographic area – around 4 million hectares – and it is dispersed from southern Queensland through to Western Australia.

Australia has an enviable reputation for producing a reliable supply of high-quality barley in a contaminant-free climate. Australian barley is highly sought after by the malting, brewing, distilling, Shochu (Japanese distilled spirit) and feed industries and is well known for its low moisture content and low foreign material.

Since its domestication in the Fertile Crescent about 10 000 years ago, barley accompanied the spread of agriculture into Europe during the 5th and 6th millennia BC. It was subsequently introduced to North America and Australia by European settlers in the 17th and 18th centuries.

The Australian growing season is different from that in many European and North American countries, and the breeding activities are expected to have shaped the genomes of Australian barley cultivars and led to significant phenotypic and genetic divergence from the counterparts grown in other agroclimatic regions. Of special interest is selection for gene variants associated with fast development, that is early flowering, allowing the crops to escape terminal heat during the maturation stage.

To better understand the gentic basis for adaptation of Australian barley cultivars we sequenced and de novo assembled the genomes of two early Australian barley varieties, namely “Clipper” and “Stirling” in collaboration with Prof. Chengdao Li, Director of the Western Crop Genetics Alliance at Murdoch University.

A collage of the two historical barley varieties sequenced, Stirling (upper left) and Clipper (lower right). Photos by Rex Rowles (Mortlock Malt) and Thomas Ryan (Barossa Valley Craft Malt), used with permission.

The genomes were assembled using HiFi+Hi-C sequencing strategy. The assembly length of the Clipper and Stirling genomes are 4.28 Gb and 4.26 Gb with a contig N50 of 39.4 Mb and 36.9 Mb, respectively. In-situ Hi-C sequencing anchored 97% of sequences to seven chromosomes in both assemblies. The interactive contact map of the chromosomes is included below. Visit the assembly pages for Hordeum vulgare cv. Stirling and Hordeum vulgare cv. Clipper for more details!

Funding was provided by the Grain Research and Development Corporation Australia. E.L.A. was supported by the Welch Foundation (Q-1866), a McNair Medical Institute Scholar Award, an NIH Encyclopedia of DNA Elements Mapping Center Award (UM1HG009375), a US-Israel Binational Science Foundation Award (2019276), the Behavioural Plasticity Research Institute (NSF DBI-2021795), NSF Physics Frontiers Center Award (NSF PHY-2019745), and an NIH CEGS (RM1HG011016-01A1). For more details read our paper:

Hu, H., Wang, P., Angessa, T.T., Zhang, X.-Q., Chalmers, K.J., Zhou, G., Hill, C.B., Jia, Y., Simpson, C., Fuller, J., Saxena, A., Al Shamaileh, H., Iqbal, M., Chapman, B., Kaur, P., Dudchenko, O., Aiden, E.L., Keeble-Gagnere, G., Westcott, S., Leah, D., Tibbits, J.F., Waugh, R., Langridge, P., Varshney, R., He, T. and Li, C. (2023), Genomic signatures of barley breeding for environmental adaptation to the new continents. Plant Biotechnol. J. https://doi.org/10.1111/pbi.14077

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!