The Caribou (Rangifer tarandus) Genome

Taylor, Rebecca S.; Horn, Rebekah L.; Zhang, Xi; Golding, G. Brian; Manseau, Micheline; Wilson, Paul J.

doi:10.3390/genes10070540

Cited by 29 publications

(54 citation statements)

References 22 publications

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“…The genetic basis of specific R. tarandus characteristics, such as adaptation to marked annual regulation in daylight, exceptional vitamin D metabolism and behavioural traits, was identified. In the present study, we provide an alternative draft reference genome for reindeer studies and particularly those representing arctic and sub-arctic regions which show phylogenetic distinctiveness compared to existing reference assemblies [21][22][23] . Here, we deep-sequenced and de novo assembled the genome of a male reindeer originating from Sodankylä, northern Finland by using the Illumina HiSeq platform.…”

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confidence: 99%

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

Weldenegodguad

Pokharel

Yao

et al. 2020

Sci Rep

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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.

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confidence: 99%

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

Weldenegodguad

Pokharel

Yao

et al. 2020

Sci Rep

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“…We used Trimmomatic version 0.38 (Bolger, Lohse, & Usadel, 2014) to trim adaptors and other Illumina sequences from the reads using the sliding window approach (4 base pairs at a time) to trim reads once the phred score dropped below 15. We aligned the filtered reads to the reference genome (Taylor et al, 2019) using Bowtie2 version 2.3.0 (Langmead & Salzberg, 2012). The resulting SAM files were then converted to BAM files and sorted using Samtools version 1.5 (Li et al, 2009).…”

Section: Genome Filtering and Variant Callingmentioning

confidence: 99%

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

Taylor

Manseau

Klütsch

et al. 2020

Preprint

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Pleistocene glacial cycles influenced the diversification of high-latitude wildlife species through recurrent periods of range contraction, isolation, divergence, and expansion from refugia and subsequent admixture of refugial populations. For many taxa, research has focused on genetic patterns since the Last Glacial Maximum (LGM), however glacial cycles before the LGM likely impacted genomic variation which may influence contemporary genetic patterns. We investigate diversification and the introgressive history of caribou (Rangifer tarandus) in western Canada using 33 high-coverage whole genomes coupled with larger-scale mitochondrial data. Contrary to the well-established paradigm that caribou ecotypes and contemporary genetic diversity arose from two major lineages in separate refugia during the LGM, a Beringian-Eurasian (BEL) and a North American (NAL) lineage, we found that the major diversifications of caribou occurred much earlier at around 110 kya, the start of the last glacial period. Additionally, we found effective population sizes of some caribou reaching ~700,000 to 1,000,000 individuals, one of the highest recorded historical effective population sizes for any mammal species thus far. Mitochondrial analyses dated introgression events prior to the LGM dating to 20-30 kya and even more ancient at 60 kya, coinciding with colder periods with extensive ice coverage, further demonstrating the importance of glacial cycles and events prior to the LGM in shaping demographic history. Reconstructing the origins and differential introgressive history has implications for predictions on species responses under climate change. Our results highlight the need to investigate pre-LGM demographic patterns to fully reconstruct the origin of species diversity, especially for high-latitude species.

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“…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 ].…”

Section: Introductionmentioning

confidence: 99%

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

Харзинова

Dotsev

Solovieva

et al. 2020

Animals

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To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.

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The Caribou (Rangifer tarandus) Genome

Cited by 29 publications

References 22 publications

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

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

Major diversification of caribou shaped by glacial cycles before the Last Glacial Maximum

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

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