TY - JOUR

T1 - A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments

AU - Yudin, Nikolay S.

AU - Larkin, Denis M.

AU - Ignatieva, Elena V.

PY - 2017/12/28

Y1 - 2017/12/28

N2 - Background: Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals. Results: After a search for publications containing keywords: "whole genome", "transcriptome or exome sequencing data", and "genome-wide genotyping array data" authors looked for information related to genetic signatures ascribable to positive selection in Arctic or Antarctic mammalian species. Publications related to Human, Arctic fox, Yakut horse, Mammoth, Polar bear, and Minke whale were chosen. The compendium of genes that potentially underwent positive selection in >1 of these six species consisted of 416 genes. Twelve of them showed traces of positive selection in three species. Gene ontology term enrichment analysis of 416 genes from the compendium has revealed 13 terms relevant to the scope of this study. We found that enriched terms were relevant to three major groups: terms associated with collagen proteins and the extracellular matrix; terms associated with the anatomy and physiology of cilium; terms associated with docking. We further revealed that genes from compendium were over-represented in the lists of genes expressed in the lung and liver. Conclusions: A compendium combining mammalian genes involved in adaptation to cold environment was designed, based on the intersection of positively selected genes from six Arctic and Antarctic species. The compendium contained 416 genes that have been positively selected in at least two species. However, we did not reveal any positively selected genes that would be related to cold adaptation in all species from our list. But, our work points to several strong candidate genes involved in mechanisms and biochemical pathways related to cold adaptation response in different species.

AB - Background: Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals. Results: After a search for publications containing keywords: "whole genome", "transcriptome or exome sequencing data", and "genome-wide genotyping array data" authors looked for information related to genetic signatures ascribable to positive selection in Arctic or Antarctic mammalian species. Publications related to Human, Arctic fox, Yakut horse, Mammoth, Polar bear, and Minke whale were chosen. The compendium of genes that potentially underwent positive selection in >1 of these six species consisted of 416 genes. Twelve of them showed traces of positive selection in three species. Gene ontology term enrichment analysis of 416 genes from the compendium has revealed 13 terms relevant to the scope of this study. We found that enriched terms were relevant to three major groups: terms associated with collagen proteins and the extracellular matrix; terms associated with the anatomy and physiology of cilium; terms associated with docking. We further revealed that genes from compendium were over-represented in the lists of genes expressed in the lung and liver. Conclusions: A compendium combining mammalian genes involved in adaptation to cold environment was designed, based on the intersection of positively selected genes from six Arctic and Antarctic species. The compendium contained 416 genes that have been positively selected in at least two species. However, we did not reveal any positively selected genes that would be related to cold adaptation in all species from our list. But, our work points to several strong candidate genes involved in mechanisms and biochemical pathways related to cold adaptation response in different species.

KW - Adaptation

KW - Cold

KW - Database

KW - Gene

KW - Genome

KW - Mammal

KW - Positive selection

KW - Antarctic Regions

KW - Cold Temperature

KW - Gene Expression

KW - Datasets as Topic

KW - Genes

KW - Humans

KW - Selection, Genetic

KW - Mammals/genetics

KW - Animals

KW - Arctic Regions

KW - Acclimatization/genetics

KW - Gene Ontology

KW - ACTIVATION

KW - SUSCEPTIBILITY

KW - BROWN ADIPOSE-TISSUE

KW - TEMPERATURE

KW - SIGNATURES

KW - TRANSCRIPTOME

KW - IDENTIFICATION

KW - GENOMICS

KW - COLD

KW - ASSOCIATION

UR - http://www.scopus.com/inward/record.url?scp=85039697141&partnerID=8YFLogxK

U2 - 10.1186/s12863-017-0580-9

DO - 10.1186/s12863-017-0580-9

M3 - Article

C2 - 29297313

AN - SCOPUS:85039697141

VL - 18

SP - 111

JO - BMC Genetics

JF - BMC Genetics

SN - 1471-2156

IS - Suppl 1

M1 - 111

ER -