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!

Don't rein on our parade

Reindeer (Rangifer tarandus L. 1758), or caribou, is a prominent semi-domesticated cervid species (family Cervidae, subfamily Capreolinae). Reindeer is one of the few modern hoofed species in which domestic and wild forms coexist on the same territory. It exists in the northern boreal, tundra, and subarctic zone of two continents, Eurasia and North America, and nearby islands. The reindeer in the distant past made it possible for humans to explore the North, and currently remains the most important biological resource for more than twenty nations of Eurasia and North America. Reindeer were domesticated at least 3000 years ago. Reindeer are bred and hunted for meat, skins, and milk and are also used for riding and as pack transport (Corlatti and Zachos, 2022).

IMG_1499. Photo by Hazel Watson, via flickr.com [CC BY-NC 2.0]

It is generally recognized that there are two ecological forms: tundra and taiga; some authors distinguish, in addition, mountain. The intraspecific taxonomy of Rangifer tarandus is highly controversial. Various authors distinguish up to fourteen reindeer subspecies: two extinct and twelve modern (Holand, I Mizin, RB Weladji, 2022).

Today, we share a chromosome-length assembly of the reindeer based on the Zoonomia draft RanTarSib_v1_BIUU (GCA_004026565.1) [Zoonomia Consortium, 2020]. The chromosome-length upgrade was done with Hi-C generated using cultured cells from the primary fibroblast cell line (passages 4-7). Hi-C libraries were constructed by Guzel Davletshina, Natalia Lemskaya, and Polina Perelman.

The primary fibroblast cell line was established from the ear biopsy by Anastasia Proskuryakova. The fibroblast cell line was cultivated by Katerina Ivanova. Biopsy from a three-year-old female was kindly provided by Primorsky Safari-Park (Director Dmitry Mezentsev, https://safaripark25.ru/) and was collected by Vasilina Belik. According to the habitat (Russian Far East), the studied reindeer likely belongs to the R. t. phylarcus subspecies. This subspecies inhabits Siberia, east of the river Lena, including Transbaikalia, the Amur region, the coast of the Sea of Okhotsk, the Kamchatka and Sakhalin (Harding, 2022). The biopsy collection was organized by Olga Uphyrkina (Far East Biodiversity Center). The scaffolding was done using 3D-DNA and Juicebox Assembly Tools.

The assembly (see interactive contact map below) is consistent with the standard cervid karyotype with 2n=70. Interestingly, reindeer have huge sex chromosomes (X and Y) enriched with repetitive sequences (Graphodatsky et al., 2020). A comparative chromosome map of the reindeer with dromedary homologies (Proskuryakova et al., 2022) identified the conservation of chromosomes in the Capreolinae subfamily at large scale. We are excited to see how whether if this conservation is confirmed at a finer scale, the analysis that is now enabled with chromosome-length assemblies across the subfamily.

We thank Dr. A.S. Graphodatsky, N.S. Serdyukova, Yu. Butakova for thelp with this assembly.

Citations:

1. Atlas of mammalian chromosomes (2nd edition). eds. Graphodatsky AS, Perelman PL, O’Brien SJ. Wiley-Blackwell, USA, 2020, 1008 p.

2. Holand O., Mizin I., Weladji R.B. Reindeer Rangifer tarandus (Linnaeus, 1758). Terrestrial Cetartiodactyla, 2022. 248-269

3. Harding, Lee E., 2022. Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies. ZooKeys: 117-151.

4. Proskuryakova A.A., Ivanova E.S., Perelman P.L., Ferguson-Smith M.A., Yang F., Okhlopkov I.M., Graphodatsky A.S. Comparative Studies of Karyotypes in the Cervidae Family. Cytogenic and Genome Research, 2022.

Seals fur reals

Arctocephalus forsteri, a species of fur seal found mainly around southern Australia and New Zealand, is an animal of many a common name. The Māori call it kekeno, the name "New Zealand fur seal" has been commonly used by English speakers in New Zealand, whereas the Australians prefer calling it the long-nosed fur seal. Although the Australian and New Zealand populations show some genetic differences, their morphologies are very similar, and thus they remain (for now at least) classified as a single species.

Photo Description - New Zealand Fur Seal (Arctocephalus forsteri). Photo Credits and acknowledgements – Alexandre Roux (CC BY-NC-SA 2.0), via flickr

The animal is a medium-sized seal with long white whiskers and dark tan ears. Females are metallic on the back and paler underneath with a brown belly. Males have dark grey-brown dorsal fur, a pale muzzle, a pointed snout and a thick mane of long guard hairs. Males are much larger than females and around three times heavier! Pups are dark brown with silvery-grey fur on the head and neck. They feed mainly on fish, cephalopods and seabirds such as penguins.

This eared seal forms breeding colonies in New Zealand and its Subantarctic islands as well as the coasts and islands off southern Australia including Macquarie Island. Non-breeding animals are also known from New South Wales, Queensland and New Caledonia. Mating occurs from mid-November to mid-January and births occur a year later. Females give birth from 4-6 years of age and live for up to 26 years. Males mature at 5-6 years of age, hold territories and mate from 8-9 years, and live up to 15 years in the wild. A small proportion of males defend territories, generally containing around 5-8 females.

In New Zealand, Arctocephalus forsteri was hunted for their fur by Polynesians and Europeans for centuries and nearly to extinction by the 19th century. They are now protected by New Zealand's Marine Mammals Protection Act and are beginning to recover and re-colonize areas in their pre-exploitation range. In Australia, the numbers are now at around 80,000. Known predators include sharks, orcas, leopard seals, New Zealand sea lions, and humans.

Today, we share the chromosome-length genome assembly of a New Zealand fur seal Arctocephalus forsteri. This is a short-read genome assembly from a primary fibroblast cell line. We gratefully acknowledge Dr. Gina Lento for providing a skin sample of the female New Zealand fur seal (ID#: 98VB-05) in 1998 from the School of Biological Sciences, University of Auckland, New Zealand. The primary fibroblast cell line (AFO-5) was established by Mary Thompson at the Laboratory of Genomic Diversity (LGD). We sincerely acknowledge Dr. Stephen J. O’Brien for providing the cell line for this study. The cell line for Hi-C was grown by Polina Perelman and Ruqayya Khan. We are grateful to Drs. Melody Roelke-Parker, Carlos Driscoll, Christina Barr, as well as David Goldman and Stephen Lindell for the preservation of the LGD cell line collection. Passage 4 was used to make the WGS and Hi-C library. We also thank the Pawsey Supercomputing Centre and DNA Zoo Australia team at the University of Western Australia for computational support of this genome assembly.

Check out the contact map below showing the 18 chromosome-length scaffolds, consistent with the previously reported karyotype 2n=36 (Beklemisheva et al., 2020). The karyotypes of seals were formed by one extra fusion of two ancestral carnivoran segments corresponding to three human chromosome segments 1q/7q/16p and one possible inversion or centromere reposition on chromosome 8. Additional heterochromatic blocks are present on several chromosomes of the New Zealand fur seal.

Blog post by Parwinder Kaur, with contributions from Polina Perelman and Gina Lento.

References:

Beklemisheva VR, Perelman PL, Lemskaya NA, Proskuryakova AA, Serdyukova NA, Burkanov VN, Gorshunov MB, Ryder O, Thompson M, Lento G, O'Brien SJ, Graphodatsky AS. Karyotype Evolution in 10 Pinniped Species: Variability of Heterochromatin versus High Conservatism of Euchromatin as Revealed by Comparative Molecular Cytogenetics. Genes (Basel). 2020 Dec 10;11(12):1485. doi: 10.3390/genes11121485.