Digging up mole-rat assembly data

The Cape dune mole-rat, Bathyergus suillus is the largest of the African mole-rats in the family Bathyergidae. It is a truly subterranean mammal that attains a body mass of up to 2 kg and uses its claws and extrabuccal teeth to excavate its burrow system.

Cape dune mole-rat, photo by Nigel Bennett (University of Pretoria)

It is a strictly solitary species with plural occupancy of burrows occurring during the breeding season and when the female has young. It is a seasonal breeder that cues its breeding to the rainfall of the southern hemisphere winter. The Cape dune mole-rat is endemic to South Africa being found in the coarse sands of the western and southern Cape of South Africa where is excavates it deep foraging tunnels in search of corms, tubers, bulbs as well as undermining aboveground vegetation.

Today we release the chromosome-length genome assembly for the Cape dune mole-rat (Bathyergus suillus) generated using a sample from a captive female animal from South Africa collected by Nigel Bennett at the University of Pretoria. Read about the exciting research on physiology and behavior of the African mole-rats on the Bennett lab website here. We also thank Wook Namkoong and Jenny Tung (Duke University, Max Planck Institute for Evolutionary Anthropology) for their help with sample shipment.

Check out the interactive contact map for the Hi-C data remapped to the final genome (2n=56) assembly below, and read more about African mole-rats in this book by Chris G. Faulkes and Nigel C. Bennett:

Bennett, N.C and Faulkes, C.G. Ecology and Eusociality of African mole-rats. Cambridge University press. 273pp.

Don’t go chasing waterbuck

Corey Kirkland, Marta Farré

Waterbuck (Kobus ellipsiprymnus) are a species of antelope distributed across central and southern Africa. The name waterbuck derives from their greater dependence on water compared to other antelopes. They are currently classified into two different subspecies, the common (K. e. ellipsiprymnus) and the defassa (K. e. defassa), with striking variation in rump colouration and chromosome number between subspecies. The common waterbuck has a white elliptical ring around its rump and a variable karyotype between 2n = 50 and 2n = 52, whilst the defassa has a completely white rump and a karyotype of either 2n = 53 or 2n = 54 (Kingswood et al. 1998). Differences in chromosome numbers are due to the Robertsonian fusion of chromosomes 6 and 18 and/or chromosomes 7 and 11. Whilst the two subspecies share predominantly different ranges across the African continent, genetic (Lorenzen et al. 2006) and genomic (Wang et al. 2022) studies have found both genetic differentiation between the subspecies but also hybridisation in zones where the two subspecies range overlap.

Waterbuck by Pieter van Noorden via Unsplash

The species is currently listed as Least Concern by the IUCN, with the defassa subspecies listed as Near Threatened. Population numbers have declined across the species range and in some areas have been lost completely. The main threats to the species include habitat loss and hunting, with the majority of the species now residing in protected areas.

Today we share the chromosome-length genome assembly of the defassa waterbuck, created using a combination of PacBio HiFi and Hi-C sequencing. PacBio HiFi sequencing was carried out at Edinburgh Genomics (UK) using DNA extracted from a captive-born female waterbuck fibroblast cell line established by Marta Farré’s research group at the University of Kent (UK). The animal was born at Howletts Wild Animal Park (Aspinall Foundation, UK) and the sample was kindly donated by Tony King (Conservation and Reintroduction Coordinator). PacBio HiFi reads were assembled using HiFiasm at the University of Kent.

The followup Hi-C scaffolding was done by DNA Zoo using data from a female common waterbuck sample obtained from SeaWorld (2n=52). Hi-C data from the original defassa waterbuck was used to help resolve, together with cell line karyotyping results, the assembly karyotype to match the defassa subspecies (2n=54). Another waterbuck from SeaWorld (2n=51) was included in the analyses to help explore the polymorphic waterbuck chromosomes.

Check out the interactive contact maps highlighting the plastic waterbuck karyotype below, and visit the assembly page for more details on the samples and the assembly!

It's all Grevy

Grévy’s zebras (Equus grevyi) are distinguished from the other two zebra species by their large size and elegant, slender stripes. Grévy’s are also unique among zebras for their mating system. Plains and mountain zebra stallions preside over harems of several females, and multiple harems merge into large herds that range over the land together while grazing. In contrast, Grévy’s males hold resource rich territories. Females visit male territories to access food and water, and in the process, may mate with the territorial male. Those with very young foals often take up residence in male territories that are close to water, thus in essence creating short term harem-like associations.

Grevy's Zebra (Equus grevyi) by Bernard DUPONT, [CC BY-SA 2.0], via flickr.com

Grévy’s zebras are currently listed as endangered (IUCN Red List) with a global population of between 2-3000. The bulk of the population resides in central Kenya, with some small populations existing in northern Kenya and Ethiopia. Threats include competition for resources from humans and their livestock, habitat fragmentation, and increased frequency and intensity of drought due to climate change.

Today we release a genomic assembly of Grévy’s zebra (Equus grevyi). The sample for the assembly was provided by a Grevy’s zebra named Zoatira and obtained by Greg Barsh (Hudson Alpha/ Stanford University) and Ren Larison (UCLA) during a visit to the Hearts and Hands Animal Rescue in Ramona, CA, owned by animal lover and zebra whisperer Nancy Nunke. We expect this genome will be a valuable resource for research focused on the evolution and conservation of Grévy’s zebras.

This is the third zebra species we've released here on the DNA Zoo website! Please check out our chromosome length assemblies for the mountain zebra (Equus zebra) and the plains zebra (Equus quagga). Check out the 23 chromosomes of the Grévy's zebra in the interactive JuiceBox.js session below:

We gratefully acknowledge Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational support of this genome assembly.