| Adaptation is a process in which organisms adapt to their environment to survive and reproduce in terms of morphological structures and physiological functions.The genus of fox(Vulpes)which contains 12 species is classified under the order Carnivora,family Canidae.They distribute widely and the population remain stable around the world duo to remarkable adaptability.In addition,silver fox and blue fox(the fur color varieties of red fox and arctic fox,respectively)are widely raised due to their higher quality of fur all over the world.There are few studies on adaptation mechanism of fox at present.In this study,comparative transcriptome technique was used to analyze red fox,corsac fox,arctic fox,blue fox and silver fox.We screened the genes and pathways that related to adaptive evolution character like cold acclimatization by screening the orthologous genes and positive selection genes and made further discussion about difference and relative genes of physiology,size,immunity in blue fox and silver fox under long-term human interference.We also screened the genes that may be related to domestication and provided references for the domestication and feeding.Based on the comparative transcriptome technique,we sequenced the transcriptome of 3 tissues(Brain,Liver and Kidney)from 6 individuals of corsac fox,silver fox and blue fox firstly.We analysised the expression level and orthologous gene combining with the transcriptome data of arctic fox and red fox from the NCBI after assembly,annotation and splicing.The analysis results were as follows.1)There were many high expression genes related to the absorption and release of hemoglobin and iron in red fox,corsac fox and arctic fox.Three mitochondrial genes(ATP6,ND2 and ND4)and two genes of(HBA and HBB)related to haemoglobin were highly expressed in arctic fox among the top 100 genes of arctic fox and blue fox.In addition,there were MHC class I genes,GSTPI,CRP and other immune-related genes.Three mitochondrial genes(COX3,ND3 and ND4)were high expressed only in red fox,not silver fox,suggested that wild animals had better athletic ability,higher activity level and needed more energy required for predation than domestic.2)Orthologous gene screening showed that 393 single-copy genes were obtained from red fox,corsac fox and arctic fox.Many of these homologous genes were associated with hypoxic adaptation,stress response,immunity and fat metabolism.Further analysis showed that 17 genes underwent positive selection,55 genes were neutral selection and 369 genes underwent purified selection among the orthologous genes.The protein that encoded by LRP11 played an important role in cold response,and the genes of ARRDC4,NDUFA5,OLIG2,ELP2 and CHAF1A were involved in innate immune response,respiration,neuron development and DNA damage repair among the positive selection genes respectively.In addition,the zinc finger protein genes(KRAB,ZNF311 and ZNF212)could induce gene silencing and maintain the stability of the genome,which played an important role in determining the evolution of species.3)A total of 812 single-copy genes were obtained between arctic fox and blue fox.Enrichment analysis showed that eight homologous genes,F9,SERP1NE2,C1GALT1C1,RHOA,BIN3,APOH,FGB and AQP1 were associated with behaviour and the study of this pathway and genes might contribute to the study of foxes as pets.Selective stress analysis showed that a total of 421 neutral selection genes,11 positive selection genes and 265 purified selection genes were identified in the two samples.GOLGA4,SLC35A2,FGFBP1,ACO1 and CFI genes were correlated with animal mitosis,blood pressure and vascular tension,intracellular iron physiological levels and natural immunity among the positive selection genes respectively.4)Orthologous gene screening showed that 710 single-copy genes were obtained from red fox and silver fox and six homologous genes,APOH,FGA,FGB,SERPINC1,SERPINE1 and SERPINE2,were associated with behaviour.Selective stress analysis showed that a total of 14 positive selection genes,243 neutral selection genes and 383 purified selection genes were identified in the two samples.In the positive selection genes,LRRFIP1 and TMEM41B genes were related to immunity.The protein coded by MDC1 gene was a DNA damage repair can repair DNA damage that caused by ionizing radiation.The protein that encoded by CEP 19 was located in centrosomes and primary cilia.This gene was expressed in a variety of tissues,and its absence could lead to traits such as obesity in animals.We speculated that the rapid evolution of this gene may be related to the differences in body size between domestic species and wild animals.There were differences between the gene tree and species tree of 20 genes in the 27 homologous genes of 5 species,which was speculated to be caused by hybridization and convergent evolution,and could be an important factor in promoting species regional differentiation.The sequence analysis results showed that RRBP1.IGBP1 and LEMD2 genes might be related to the adaptive evolution of red fox and arctic fox as well as the breeding species,that is,the changes of these genes may make them better adapted to their respective environments.In the analysis of 27 homologous genes of five species,there were differences between gene trees and species trees of 20 genes,which were speculated to be caused by hybridization or convergent evolution among species,and this difference may be an important factor promoting the regional differentiation of species.Sequence analysis results showed that RRBP1,IGBP1 and LEMD2 genes might be related to the adaptive evolution of red fox and arctic fox as well as the breeding species,that is,the changes of these genes may make them better adapted to their respective environments.In this study,the molecular mechanism of adaptive evolution of fox,red fox and arctic fox was preliminarily discussed with the help of comparative transcriptome technology,and screened out one positive selection genes related to cold adaptation(LRP11).The possible changes of silver fox and blue fox in captivity were also analyzed,and obtained some positive selection genes and passway related to behaviour and habitus.Three genes related to their adaptation to wild and breeding environments were screened out from wild and breeding species based on the analysis of common homologous genes.Transcriptome data was obtained from fox and blue fox for the first time,and provided molecular basis for the study of survival strategies of fox species in cold and human feeding environment and domestication as pets... |
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