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).
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:
Atlas of mammalian chromosomes (2nd edition). eds. Graphodatsky AS, Perelman PL, O’Brien SJ. Wiley-Blackwell, USA, 2020, 1008 p.
Holand O., Mizin I., Weladji R.B. Reindeer Rangifer tarandus (Linnaeus, 1758). Terrestrial Cetartiodactyla, 2022. 248-269
Harding, Lee E., 2022. Available names for Rangifer (Mammalia, Artiodactyla, Cervidae) species and subspecies. ZooKeys: 117-151.
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.