Research On Molecular Evolution Of Some TRIM Genes In Carnivores

The immune system is a very important physiological system in the evolution of animals,which can help the body to recognize and resist the invasion of foreign pathogens.It has an important impact on the species to adapt to the environment and broaden the ecological niche,and to some extent reflects the survival ability of species.Many immune gene families play an important role in the immune system,such as pattern recognition receptor TLRs,major histocompatibility complex MHC,and TRIM protein family.TRIM5,TRIM6,TRIM22 and TRIM34 are TRIM genes that appear in placental mammals.They are relatively fixed in the genome and form a gene cluster,whose protein products play an important role in host resistance to virus invasion.In order to explore the expansion and contraction patterns and molecular evolution mechanisms ofTRIM6/34/5/22 gene clusters in carnivores,it is necessary to select important groups from the whole mammal to study in order to understand the evolution of TRIM6/34/5/22 gene clusters in the whole mammalian group.We selected 63 species from mammalia to investigate the evolution of TRIM gene in mammalia.Subsequently,we selected 26 species from the carnivora order as research objects,focusing on the evolution pattern of this gene cluster in carnivora order.Based on genomic data of species,we used Blast to identify 270 sequences in 79 species genomes,including 253 functional genes and 17 pseudogenes.Functional genes included 68 TRIM5 genes,78 TRIM6 genes,42 TRIM22 genes and 65 TRIM34 genes.According to homology analysis and phylogenetic tree construction of mammal TRIM gene,it was found that all carnivores lacked a complete TRIM5 gene.In addition,pseudogenation of TRIM22 gene occurred in cats and hyenas,while TRIM22 gene in mongoose was lost,while TRIM22 gene in Mongoose was lost.The TRIM5 and TRIM22 genes shrink only in cetaceans and carnivores throughout the mammalian population.Among other mammalian groups,TRIM5 and TRIM22 genes are the most active in evolution,with multiple expansions and deletions,reflecting higher species-specific evolution patterns.TRIM6 gene was the most conservative and did not expand or shrink in all the species involved in this study,indicating that it had the most basic function.Meanwhile,selective pressure analysis also indicated that it was strongly selected for purification.The expansion and contraction events of TRIM34 genes were less than those of TRIM5 and TRIM22 genes,but showed more species-specific.In this study,we identified several genes clustered in a single branch in The order Oddioecy,which was called TRIM22-like gene and had high homology with TRIM5 and TRIM22,possibly due to the recombination of early TRIM5 and TRIM22 genes.The selective pressure analysis of the point model in PAML and the FEL and REL methods based on maximum likelihood method in DataMonkey in carnivores and mammalia showed that although TRIM6/34/5/22 gene clusters were purified and selected as a whole,positive selection sites were detected.Through statistical analysis of the distribution of and positive selection sites in different domains,the positive selection sites of TRIM5 and TRIM22 genes were significantly concentrated in the B30.2 domain related to virus recognition,while the selection pressures of TRIM6 and TRIM34 genes were not significantly different in each domain.This may be due to the fact that TRIM5 and TRIM22 genes are in a "arms race" with viruses for a long time,while the functions of TRIM6 and TRIM34 genes are more fundamental.There was no significant difference in the distribution of positive selection sites in the different domains of each TRIM gene in the order carnivora,and the positive selection sites were not significantly distributed in the Domain B30.1,which was related to virus recognition,indicating that the selection pressure of the carnivora was different from that of other mammal groups.The results of branch model analysis of various mammalian groups show that ?of TRIM gene is no significant difference between carnivora and other mammal groups,that is,TRIM gene is not subject to significantly different selection pressure in the order carnivora and other mammal groups.Branch model analysis showed that?of TRIM gene is no significant difference between different family,indicating that there was no significant difference in the selection pressure of TRIM gene.Among them,TRIM6'? is least,indicating that it is subject to strong selection pressure.Compared with other TRIM genes,TRIM22 experienced a certain amount of selective pressure relaxation,the ? and the number of positive selection sites were largest among the carnivora.The TRIM34 gene weresuffer purify selection.In this study,the expansion and contraction mechanism and molecular evolution pattern of TRIM6/34/5/22 gene cluster in mammals,especially in carnivore,were identified,which is helpful to further study the role of TRIM gene in the adaptive evolution of carnivore and provide molecular basis.