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!

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!