Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia
Weldenegodguad, Melak; Pokharel, Kisun; Ming, Yao; Honkatukia, Mervi; Peippo, Jaana; Reilas, Tiina; Røed, Knut H.; Kantanen, Juha (2020)
Weldenegodguad, Melak
Pokharel, Kisun
Ming, Yao
Honkatukia, Mervi
Peippo, Jaana
Reilas, Tiina
Røed, Knut H.
Kantanen, Juha
Julkaisusarja
Scientific reports
Volyymi
10
Nature Publishing Group
2020
Julkaisun pysyvä osoite on
http://urn.fi/URN:NBN:fi-fe2020061042641
http://urn.fi/URN:NBN:fi-fe2020061042641
Tiivistelmä
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.
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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