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.

Oncillary function

The oncilla (Leopardus tigrinus), aka the “small jaguar”, graciously walks the neotropical rainforests from Costa Rica in Central America down south to Northern Argentina. It is also commonly called tigrillo, tigrina, or tiger cat. Highly adaptive, this small cat also lives in savannas (pushed there by deforestation) and in mountains up to the snow-line. Unlike many other felids, oncillas enjoy swimming. Previously hunted for beautiful pelt with rosettes and ringed tail, now this species is listed as vulnerable, with a population of about 10,000.

Profile of an oncilla, photo by Tambako The Jaguar, [CC BY-ND 2.0], via Flickr.com

Oncilla is a bit bigger than a house cat with a small muzzle and slender body. It scouts the ground for small rodents and lizards and likes to rest safely on trees. Birds and eggs are also on the menu, including farm birds that make oncillas a target for farmers intruding into the oncilla’s habitat. Otherwise, these secretive solitaire hunters are rarely seen by humans.

The genus Leopardus is a distinct phylogenetic lineage (so-called - Ocelot lineage) that split off about 10 million years ago from other felids (Johnson et al., 2006) and 6 million later started to form different species. Oncilla still hybridizes with its cousins in the genus Leopardus such as the Pampas cat and Geoffroy's cat.

In general, we know very little about these mostly nocturnal cats. The oncilla phylo-geography is still poorly studied due to a lack of sampling across the species range. Recent comparative molecular studies of small cats from the Leopardus genus revealed a fascinating picture of multiple ancient and modern interspecific hybridizations. Genetic distances indicate that many current subspecies are eligible for the species rank. In fact, the whole species of oncilla is paraphyletic, with the Costa-Rican cat (L.t. oncillus) possibly being a separate species. Interestingly, North-eastern L. tigrinus possesses a mitochondrial genome of an entirely different species - that of a pampas cat! (Li et al., 2016; Trindade et al., 2021). The southern subspecies of oncilla already earned the species rank, L. guttulus. Oncillas vary in fur coloring patterns throughout the range, with differences in background color and spots indicating at least three distinct groups (Nascimento and Feijo, 2017). Many oncillas are melanistic (black cats with black spots).

Oncilla, photo by Tambako The Jaguar, [CC BY-ND 2.0], via Flickr.com

To help study the species today we release the chromosome-length assembly for the oncilla (Leopardus tigrinus)! The skin biopsy used for this assembly was collected from a captive female tiger cat at the zoo on April 21, 1982. The primary fibroblast cell line (LTI-3) was established by Mary Thompson at the Laboratory of Genomic Diversity (LGD), led by Dr. Stephen O’Brien. We sincerely acknowledge Dr. Stephen J. O’Brien for providing the cell line for this study. 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.

The assembly suggests a karyotype, 2n=36, that is rather unusual for cats that are typically very conservative with a 2n=38. This is consistent with prior studies that showed that Leopardus is the only genus with a lower diploid number of chromosomes (2n=36) in the entire felid family. The 2n is lower because the fusion of felid chromosomes F1 and F2 forms unique metacentric chromosome C3 - ancestral for the whole genus. Browse the chromosomes of the oncilla in the interactive Juicebox.js session below!

References

1. Graphodatsky AS, Perelman PL, O’Brien SJ. Atlas of mammalian chromosomes. 2nd ed. Wiley-Blackwell; 2020. pp. 727-732

2. Li G, Davis BW, Eizirik E, Murphy WJ. Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae). Genome Res. 2016 Jan;26(1):1-11. doi: 10.1101/gr.186668.114.

3. Nascimento, FO, Feijo, A. Taxonomic revision of the tigrina Leopardus tigrinus (Schreber, 1775) species group (Carnivora, Felidae). Pap. Avulsos Zool. 57 (19), 2017, https://doi.org/10.11606/0031-1049.2017.57.19

4. Trindade FJ, Rodrigues MR, Figueiró HV, Li G, Murphy WJ, Eizirik E. Genome-Wide SNPs Clarify a Complex Radiation and Support Recognition of an Additional Cat Species. Mol Biol Evol. 2021 Oct 27;38(11):4987-4991. doi: 10.1093/molbev/msab222.