Bioinformatics Analysis Of Integrative And Conjugative Element SXT/R391

Integrative and conjugative elements(ICE)is a kind of self-transmissible mobile genetic elements(MGE).Integrative and conjugative elements often endow host bacteria with new traits,such as drug resistance and pathogenicity.At present,SXT/R391 ICE is the largest integrated binding element listed in the ICE database.In recent years,the frequency of bacteria carrying SXT/R391 elements has gradually increased in clinic and environment.They have become important vectors for the transmission of many antibiotic resistance genes.With the increase of SXT/R391 elements,many related studies have been accumulated,but these studies mainly focus on the genomic structure,gene function and fixed molecular mechanism of SXT/R391 elements.There are few systematic studies on the evolution of SXT/R391 elements.Therefore,in order to more effectively deal with the potential threat brought by the evolution and spread of SXT/R391 elements,we have carried out a systematic study on the law of genome evolution,spread and diffusion of SXT/R391 elements.In the first part of work,we first conducted effective screening of the existing data,collected and sorted 83 SXT/R391 elements that obtained the whole genome sequence.Through the developed method for predicting SXT/R391 elements,29 SXT/R391 elements were predicted.Afterwards,the GC content,codon adaptation index and effective number of codon of 29 new elements and their genomes were analyzed.It was found that the SXT/R391 elements carried in marine bacterial strains are relatively close to the host in the above nucleic acid composition indicators,indicating that the marine bacterial elements may be relatively old,supporting the existing marine environment is likely to be SXT/R391 elements The point of origin,and the component sources of Vibrio cholerae,Vibrio alginolyticus and Vibrio parahaemolyticus may have been obtained by recent gene horizontal transfer events.In the second part of this article,we consider the SXT/R391 elements family as a "species" to comprehensively analyze the genetic diversity within the SXT/R391 elements from the genomic level.Through the analysis of the pan-genome model,it was found that there may be a closed pan-genome of the SXT/R391 elements,and the number of core genes of the SXT/R391 elements was determined.After analysis and comparison of the core gene tree and gene content tree,it was found that the gene gain /gene loss events of SXT/R391 elements are very frequent,and hybrid elements may be formed by recombination between elements.Through the evolution of the core genes,the evolution of the core region of the SXT/R391 elements is very complicated.Frequent reorganization may occur between different functional modules.The core genes will undergo evolutionary events such as gene replication,gene fusion / cleavage.In the third part,we explored the adaptive evolution of the core genes of SXT/R391 elements.The core genes of 83 elements were recombined and positive selection analysis.It was found that many core genes have recombination and positive selection.SXT/R391 elements plays an important role in the evolution of the core gene.The reorganization and positive selection mutation of SXT / R391 components are all for the improvement of the suitability of SXT/ R391 components,so as to adapt to the changes of the ecological environment.In the fourth part,a systematic geogenetic analysis was performed on the representative genes of the SXT/R391 elements modules,and it was found that the evolution characteristics and propagation patterns between different modules were completely different,which also confirmed the conservative skeleton region of SXT/R391 elements reported in the literature.May have the characteristics of frequent reorganization and evolution.In the last chapter,we analyzed the distribution and evolution of the three pairs of toxin antitoxin systems that maintain the stability of SXT/R391 elements.It was found that the evolutionary history of the two genes of toxin and antitoxin are not consistent.It is inconsistent with the related reports that there is a co-evolution characteristic between the bacterial toxin antitoxin system.No positive signal was found in the positive selection and recombination detection of the toxin antitoxin,and the adaptive evolution characteristics of the toxin antitoxin system genes were not significant.This project collects and makes full use of the existing SXT/R391 ICEs genome data,creatively introduces the pan-genome model,and uses a variety of bioinformatics techniques,such as phylogenetic geography,phylogeny,molecular evolution and so on,to explore the evolutionary relationship between SXT/R391 elements from the point of view of the whole genome,and combined with adaptive evolution analysis to reveal the micro-evolutionary characteristics of SXT/R391 elements in the process of diffusion.In order to restore the dynamic process of the SXT/R391 elements genome,we can reconstruct the whole evolution process of the origin and spread of this mobile genetic factor family.