Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Jun 2;10(1):8980.
doi: 10.1038/s41598-020-65487-y.

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Melak Weldenegodguad #  1   2 , Kisun Pokharel #  1 , Yao Ming #  3 , Mervi Honkatukia  1   4 , Jaana Peippo  1 , Tiina Reilas  1 , Knut H Røed  5 , Juha Kantanen  6
Affiliations

Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia

Melak Weldenegodguad et al. Sci Rep. .

Abstract

Reindeer are semi-domesticated ruminants that have adapted to the challenging northern Eurasian environment characterized by long winters and marked annual fluctuations in daylight. We explored the genetic makeup behind their unique characteristics by de novo sequencing the genome of a male reindeer and conducted gene family analyses with nine other mammalian species. We performed a population genomics study of 23 additional reindeer representing both domestic and wild populations and several ecotypes from various geographic locations. We assembled 2.66 Gb (N50 scaffold of 5 Mb) of the estimated 2.92 Gb reindeer genome, comprising 27,332 genes. The results from the demographic history analysis suggested marked changes in the effective population size of reindeer during the Pleistocene period. We detected 160 reindeer-specific and expanded genes, of which zinc finger proteins (n = 42) and olfactory receptors (n = 13) were the most abundant. Comparative genome analyses revealed several genes that may have promoted the adaptation of reindeer, such as those involved in recombination and speciation (PRDM9), vitamin D metabolism (TRPV5, TRPV6), retinal development (PRDM1, OPN4B), circadian rhythm (GRIA1), immunity (CXCR1, CXCR2, CXCR4, IFNW1), tolerance to cold-triggered pain (SCN11A) and antler development (SILT2). The majority of these characteristic reindeer genes have been reported for the first time here. Moreover, our population genomics analysis suggested at least two independent reindeer domestication events with genetic lineages originating from different refugial regions after the Last Glacial Maximum. Taken together, our study has provided new insights into the domestication, evolution and adaptation of reindeer and has promoted novel genomic research of reindeer.

PubMed Disclaimer

Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Gene ontology comparison among genomes of reindeer and nine mammalian species. (a) Distribution of gene clusters among the compared mammalian species. (b) Venn diagram showing unique and shared gene families among five ruminants (cattle, goat, reindeer, sheep and yak). (c) Gene expansion and contraction in the reindeer genome. The numbers of gene families that have expanded (green, +) and contracted (red, -) after splitting are shown on the corresponding branch and pie charts. MRCA, most recent common ancestor. (d) Phylogenetic tree based on 4-fold degenerate sites of 7,951 single-copy orthologous genes. Estimates of divergence time with 95% confidence interval (CI) are shown at each node.
Figure 2
Figure 2
Demographic history of R. tarandus reconstructed from the draft reference genome by using PSMC. The X axis shows the time in thousands of years and the Y axis shows the effective population size. In the figure, the red line describes the fluctuation of effective population size, the pink line the relative sea level (RSL, 10 m sea level equivalent) and the yellow line atmospheric surface air temperature °C (Tsurf).
Figure 3
Figure 3
Principal component analysis (PCA) of 23 resequenced animals and the reference individual. (FI-R-R, Finnish reindeer (i.e. the reference animal); Fe-W-T, Fennoscandian wild tundra reindeer; Fe-D-T, Fennoscandian domestic tundra reindeer; Ru-W-T, Russian wild tundra reindeer; Ru-D-F, Russian domestic forest reindeer; Ru-W-A, Russian wild arctic reindeer (i.e. Novaya Zemlya); Sv-W-A, Svalbard wild arctic reindeer; Al-D-T, Alaska domestic tundra reindeer; Al-W-C, Alaska wild caribou).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Helskog K, Indrelid S. Humans and reindeer. Quat. Int. 2011;238:1–3.
    1. Bjørklund I. Domestication, Reindeer Husbandry and the Development of Sámi Pastoralism. Acta Boreal. 2013;30:174–189.
    1. Flagstad O, Roed KH. Refugial origins of reindeer (Rangifer tarandus L.) inferred from mitochondrial DNA sequences. Evolution. 2003;57:658–670. - PubMed
    1. Lin Z, et al. Biological adaptations in the Arctic cervid, the reindeer (Rangifer tarandus) Science (80-.). 2019;364:eaav6312. - PubMed
    1. Blix AS. Adaptations to polar life in mammals and birds. J. Exp. Biol. 2016;219(1093):LP-1105. - PubMed

Publication types