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Pokharel K, Weldenegodguad M, Dudeck S, Honkatukia M, Lindeberg H, Mazzullo N, Paasivaara A, Peippo J, Soppela P, Stammler F, Kantanen J. Whole-genome sequencing provides novel insights into the evolutionary history and genetic adaptation of reindeer populations in northern Eurasia. Sci Rep 2023; 13:23019. [PMID: 38155192 PMCID: PMC10754820 DOI: 10.1038/s41598-023-50253-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023] Open
Abstract
Domestic reindeer (Rangifer tarandus) play a vital role in the culture and livelihoods of indigenous people across northern Eurasia. These animals are well adapted to harsh environmental conditions, such as extreme cold, limited feed availability and long migration distances. Therefore, understanding the genomics of reindeer is crucial for improving their management, conservation and utilisation. In this study, we have generated a new genome assembly for the Fennoscandian domestic reindeer with high contiguity, making it the most complete reference genome for reindeer to date. The new genome assembly was utilised to explore genetic diversity, population structure and selective sweeps in Eurasian Rangifer tarandus populations which was based on the largest population genomic dataset for reindeer, encompassing 58 individuals from diverse populations. Phylogenetic analyses revealed distinct genetic clusters, with the Finnish wild forest reindeer (Rangifer tarandus fennicus) standing out as a unique subspecies. Divergence time estimates suggested a separation of ~ 52 thousand years ago (Kya) between the northern European Rangifer tarandus fennicus and Rangifer tarandus tarandus. Our study identified four main genetic clusters: Fennoscandian, the eastern/northern Russian and Alaskan group, the Finnish forest reindeer, and the Svalbard reindeer. Furthermore, two independent reindeer domestication processes were inferred, suggesting separate origins for the domestic Fennoscandian and eastern/northern Russian reindeer. Notably, shared genes under selection, including retroviral genes, point towards molecular domestication processes that aided adaptation of this species to diverse environments.
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Affiliation(s)
- Kisun Pokharel
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Melak Weldenegodguad
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Stephan Dudeck
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Heli Lindeberg
- Natural Resources Institute Finland (Luke), 71750, Maaninka, Finland
| | - Nuccio Mazzullo
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | - Antti Paasivaara
- Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, 90570, Oulu, Finland
| | - Jaana Peippo
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
- NordGen-Nordic Genetic Resource Center, 1432, Ås, Norway
| | - Päivi Soppela
- Arctic Centre, University of Lapland, 96100, Rovaniemi, Finland
| | | | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland.
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Güere ME, Våge J, Tharaldsen H, Kvie KS, Bårdsen BJ, Benestad SL, Vikøren T, Madslien K, Rolandsen CM, Tranulis MA, Røed KH. Chronic wasting disease in Norway-A survey of prion protein gene variation among cervids. Transbound Emerg Dis 2021; 69:e20-e31. [PMID: 34346562 DOI: 10.1111/tbed.14258] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 11/29/2022]
Abstract
Susceptibility of cervids to Chronic Wasting Disease (CWD), a prion disease, can be modulated by variations in the prion protein gene (PRNP), encoding the cellular prion protein (PrPC ). In prion diseases, PrPC is conformationally converted to pathogenic conformers (PrPSc ), aggregates of which comprise infectious prions. CWD has recently been observed in its contagious form in Norwegian reindeer (Rangifer tarandus) and in novel, potentially sporadic forms, here called 'atypical CWD', in moose (Alces alces) and red deer (Cervus elaphus). To estimate relative susceptibility of different Norwegian cervid species to CWD, their non-synonymous PRNP variants were analyzed. In reindeer, seven PRNP alleles were observed and in red deer and moose two alleles were present, whereas roe deer (Capreolus capreolus) PRNP was monomorphic. One 'archetypal' PRNP allele associated with susceptibility was common to all four cervid species. The distribution of PRNP alleles differed between wild and semi-domesticated reindeer, with alleles associated with a high susceptibility occurring, on average, above 55% in wild reindeer and below 20% in semi-domesticated reindeer. This difference may reflect the diverse origins of the populations and/or selection processes during domestication and breeding. Overall, PRNP genetic data indicate considerable susceptibility to CWD among Norwegian cervids and suggest that PRNP homozygosity may be a risk factor for the atypical CWD observed in moose. The CWD isolates found in the Norwegian cervid species differ from those previously found in Canada and USA. Our study provides an overview of the PRNP genetics in populations exposed to these emerging strains that will provide a basis for understanding these strains' dynamics in relation to PRNP variability.
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Affiliation(s)
- Mariella Evelyn Güere
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Jørn Våge
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Helene Tharaldsen
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Kjersti Sternang Kvie
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Bård-Jørgen Bårdsen
- Arctic Ecology Department, Fram Centre, Norwegian Institute for Nature Research, Tromsø, Norway
| | | | - Turid Vikøren
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Knut Madslien
- Norwegian Veterinary Institute, OIE Reference Laboratory for CWD, Ås, Norway
| | - Christer Moe Rolandsen
- Terrestrial Ecology Department, Norwegian Institute for Nature Research, Trondheim, Norway
| | - Michael Andreas Tranulis
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Knut Håkon Røed
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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