Molecular Mechanisms Of Adaptation To Cold Environments In Sable (Martes Zibellina)

Cold adaptation has always been a hot issue for biologists.In recent years,with the rapid development of OMICS,the research on the genetic mechanism of cold adaptation has become a hot issue in the field of evolutionary biology.Sable(Martes zibellina)belongs to Martes,Mustelidae,Carnivora,while due to the loss of habitat and human over-hunting,the number of sables has fallen sharply and has been listed as a national first-level protected animal in China.The main habitat of the sable is the sub-frozen coniferous forest zone,which is cold with an annual average temperature below zero and minimum temperature below-30?.Animals living in cold regions will adopt different adaptation strategies to cope with the harsh external environment,such as machine insulation fur,thick fat,and some animals will adopt hibernation strategies to cope with the chilly winter.The current research on cold adaptation is mainly focused on mammals in polar habitats such as humans,polar bears,and arctic foxes.In addition,a large number of cold domestication coping mechanisms have been studied in rodents.Sables are thinner with lower fat content and do not have hibernation,which seems to be a great challenge for sables living in cold regions,while there is still a lack of research on the genetic mechanism of sable's cold adaptation.In recent years,with the rapid development of high-throughput sequencing technology,it has become a common and effective means to study the genetic differences between different species or different populations from the multi-omics level and screen key candidate genes for adaptive evolution of species.In this paper,we comprehensively analyze the genomics,transcriptomics,and population genomics,screening selected genes and differentially expressed genes related to the cold adaptation of sable,and mining candidate genes and metabolic pathways related to the cold adaptation at the gene level and expression level,to reveal the potential genetic mechanism of the cold adaptation of sable.The main research of this paper is as follows:(1)Based on the whole genome data of sable,the adaptive evolution of heat preservation-related genes was analyzed by comparative genomics.The heat preservation mechanism of mammals is of great significance to reveal the genetic mechanism of their adaptation to cold environments.As the first barrier of the body,fur is the main medium for heat exchange between animals and the environment,and the insulation of fur can effectively reduce the heat loss of the body.Sable has high cold-resistant fur,and hair follicle development plays an important role in regulating its fur quality.Constriction of skin blood vessels can increase the insulation of the fur and greatly reduce the heat transfer to the external environment.Therefore,investigating the evolution and expression level of heat preservation-related gene in sable is an important scientific question to solve its cold adaptation characteristics.In our study,123 genes involved in hair follicle development and vascular smooth muscle contraction were screened through the GO and KEGG database,and the genes were retrieved based on the whole genome of sables and the representative animals of the carnivore.As a result,we found that ADORA2B gene was positively selected and MAP2K2,FST,and TP63 gene experienced rapid evolution in sable by PAML analysis,indicating that these four genes have undergone adaptive evolution.We speculated that the adaptive evolution of these genes may have enhanced the heat preservation ability of sable,which is more beneficial to maintaining body temperature in a cold environment In addition,we used the transcriptome data of sable skin samples to analyze the expression levels of hair follicle development genes in different seasons and found that there were 42 genes with significant seasonal differences in the expression levels.It shows that the heat preservation performance of sable fur in winter and summer has significant differences,which is beneficial for meeting the heat preservation requirements in different seasons.(2)Based on the whole genome data of sable,the adaptive evolution of thermogenesis-related genes was analyzed by comparative genomics.Mammalian heat production ability is the key to adapt to the cold environment,and lipid metabolism and glucose metabolism are accompanied by heat production.Thermogenesis is crucial for mammals to adapt to the cold.Both lipid metabolism and carbohydrate metabolism are accompanied by heat generation.Fat tissue not only plays an important role in keeping the body warm,but it is also an important source of carbohydrate metabolism and body heat production.Carbohydrate metabolism can not only provide the energy required for various life activities of the organism but also generate heat to maintain the core temperature of the body.Exploring the evolution of genes related to lipid metabolism is important to clarify the cold adaptation mechanism of sables.In this paper,we screened 238 genes associated with lipid metabolism,carbohydrate metabolism,and thermogenesis from the KEGG database.Based on the genomic data of sables and other carnivores,we screened thermogenesis-related genes of various species by performing sequence screening.Through selective pressure analysis,it was found that the PNLIP,ACSS2,ACACB,NDUFB4,ALDH9A1,GAPDHS,NDUFB1,NDUFA2,and ACSL1 genes have received positive selection in sable,and the GOT2,IDH3G,NDUFB6,NDUFB1,ALDH2,PKM,ACSL6,NDUFA3,RPS6.RPS6KA1,and ZNF516 genes have undergone rapid evolution in sable,indicating that these candidate genes have undergone adaptive evolution in sable,which may be related to the enhanced metabolic thermogenesis of sable in a cold environment.(3)RNA-seq technique was applied to sequence the transcriptome of heart,liver,fat,and muscle of sable in summer and winter of sable,and 31.14G expression data were obtained.By differentially expressed analysis,798,3552,759,and 2535 seasonal differentially expressed genes in heart,liver,fat,and muscle,respectively.Through the enriched analysis of seasonal different expressed genes in these tissues,it was found that these candidate genes were significantly enriched in glucose metabolism,lipid binding,proteolysis,and mitochondrial-related GO terms.Meanwhile,the result of KEGG enriched analysis revealed that differentially expressed genes were significantly enriched in metabolic pathways such as carbon metabolism,fatty acid metabolism,glycolysis/gluconeogenesis,and oxidative phosphorylation.This may be related to the energy demand for sable to keep its body temperature in different seasons,which is beneficial to the energy supply in a cold environment.We revealed the regulation mode of various metabolic tissues in the process of sable cold adaptation,and identified candidate genes and signal pathways related to sable cold adaptation from the expression level.(4)The whole genome of 20 sables from Russia,Mongolia,and China was resequenced,and high-quality data of more than 23Gb were obtained from each sample,and a total of 20869315 SNP loci were identified.Based on the SNP database,we explored the phylogenetic relationship,genetic structure,genetic diversity,and selection of the two populations,and found that there was a certain genetic distance between the two populations,but the difference in genetic diversity was not obvious.Through selective sweep analysis,the positively selected regions of the Russian sable population were identified.Through selection elimination analysis,the selected regions of the Russian sable population were identified,and a large number of selected gene regions were found.The functional enrichment analysis of GO and KEGG based on the candidate genes in the selected region showed that the candidate genes were significantly enriched in metabolism-related biological processes such as oxidoreductase activity,protein kinase C activity,lipid response,proteolysis process,and protein secretion regulation.We hypothesized that this might be related to the extremely cold environment faced by the Russian sable population and that heat production by protein metabolism might be a common strategy for its cold adaptation.In this study,through the evolutionary analysis of candidate genes related to heat preservation and heat production of sable,the difference of gene expression levels in four metabolic tissues in winter and summer,and the molecular mechanism of the difference in environmental adaptation of different sable populations,the genetic mechanism of sable cold adaptation was revealed from the gene level and expression level.