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.

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