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

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.

Post-Translational Protein Deimination Signatures in Plasma and Plasma EVs of Reindeer (Rangifer tarandus)

“…Furthermore, PADs and deimination have been linked to autoimmune thyroid disease and thyroid cancer [ 81 , 82 ]. Deimination enrichment in the vitamin digestion and absorption pathway may furthermore contribute to diverse roles of vitamin processing, which in reindeer is critical as they have undergone adaptions for vitamin D metabolism [ 1 ], and indeed vitamin D-binding protein was identified as a deimination candidate in whole plasma. Interestingly, vitamin D-binding protein has also been identified as a deimination candidate in camelids [ 19 ], which are also metabolically adapted to extreme environments.…”

“…Reindeer play an important role in economy, society, culture and ecological values among populations of Eurasia and were fundamental for the colonization of the northern part of Eurasia. They have been a source of food among indigenous culture and were sporadically used for transportation, and therefore can be considered as a semi-domesticated species [ 1 ]. Reindeer are adapted to extreme environments throughout their evolution, exhibiting distinctive and unique biological characteristics relating to fat metabolism processes, changes to their internal biological clock, limited heat loss and low resting metabolic rate.…”

“…Reindeer are adapted to extreme environments throughout their evolution, exhibiting distinctive and unique biological characteristics relating to fat metabolism processes, changes to their internal biological clock, limited heat loss and low resting metabolic rate. However, the underlying molecular and genetic basis for these traits remains largely unknown [ 1 , 2 ]. The IUCN Red List of Threatened Species (2016) has classified reindeer as a vulnerable species due to a decline of individuals, possibly attributed to habitat shift and/or their susceptibility to chronic wasting disease (CWD), a fatal neurodegenerative disorder [ 3 , 4 ].…”

Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

“…The discovery and genotyping of hundreds of thousands of SNPs in a single assay are enabled by the use of SNP high-throughput arrays, which are available for the majority of the livestock species, thus targeting wide genetic variants that are spread along the entire genome [ 23 , 24 ]. In distinction from the other model species, a genomic era in the study of both the reindeer and the North American caribou has been established recently, and several versions of the Rangifer tarandus genome have occurred [ 25 , 26 , 27 ]. The first genome assembly was announced in 2017 by Li et al [ 25 ] and the latest update was in 2020 by a group of Scandinavian scholars ( Rangifer tarandus —assembly RanTarSib_v1_BIUU) [ 27 ].…”

“…In distinction from the other model species, a genomic era in the study of both the reindeer and the North American caribou has been established recently, and several versions of the Rangifer tarandus genome have occurred [ 25 , 26 , 27 ]. The first genome assembly was announced in 2017 by Li et al [ 25 ] and the latest update was in 2020 by a group of Scandinavian scholars ( Rangifer tarandus —assembly RanTarSib_v1_BIUU) [ 27 ]. Meanwhile, the assignment of reindeer genome scaffolds to their specific chromosomes, as well as the array-based methods in which panels of predetermined polymorphisms are hybridized onto chips by companies such as Affymetrix or Illumina, for the species are still inaccessible.…”