The Mitochondrial Genome Codon Preference Of Orthoptera And Its Evolutionary Analysis

13 encoding protein sequences related respiratory in animal mitochondrial genome, were commonly used as molecular markers in animal systematics and evolutionary study currently. With the rapid development of The New Generation of sequencing technology, a large number of animal mitochondrial genome data had been sequenced. In Insecta, codon bias of mitochondrial genome in Lepidoptera, Diptera and Hymenoptera had been carried out continuously, but Orthoptera, as one of the old Insecta groups, sequenced mitochondrial genome species contained 2 suborders,7 superfamilies,77 species. Based on research methods of bioinformatics, using a large number of biology software, combining Orthoptera mitochondrial genome and codon usage bias, the study probed the evolutional information hidded in the Orthoptera mitochondrial genome.In this paper, firstly, codon bias pattern of mitochondrial genome was investigated; secondly, the main causative factors of bias was mainly analyzed; finally,77 Orthoptera species were used for hierarchical cluster analysis based on Relative Synonymous Codon Usage (RSCU) of 13 encoding protein sequences(13CDs), three different phylogenetic trees that used Bayesian method (BI), Maximum-Likelihood (ML) and Maximum-Parsimony (MP) based on 13CDs were built, while, cluster results were compared with phylogenetic trees, to discuss clustering situtation of different methods in each Orthoptera species, meanwhile, to decide the validity of hierarchical cluster analysis in reconstructing Orthoptera internal evolutionary relationship, and to study the relation between codon bias and Orthoptera species relationship.The concrete conclusions were as follows:1. The Effective Number of Codon (ENC) of mitochondrial genome among 77 Orthoptera species in this study fluctuated from 33.10 to 51.25, of which, Caelifera with a mean value of 36.86, close to 35; Ensifera with a mean value of 42.57, which suggested the general codon preference of protein encoding genes in this order, but there was an obvious difference between Caelifera and Ensifera in codon bias; and Caelifera was stronger than Ensifera. RSCU values based 13 CDs in 77 Orthoptera mitochondrial genome revealed the frequency of 62 codons were used disparately in Orthoptera mitochondrial genome, some RSCU values were large, their use frequency was high; other RSCU values were small, their use frequency was low. According to the definition of high-frequency codon and comprehensive analysis of RSCU values based in 77 Orthoptera mitochondrial genome,26 high-frequency codons were identified in coding amino acid, used frequenly, which were ended with A or T, besides,7 codons hardly used, which were ended with G or C. In addition, for different species in different suborders, the RSCU values of same codons also existed distinction. In conclusion, Orthoptera mitochondrial genome existed a general codon bias, prefering to end with A or T, avoiding ending with G or C.2. ENC plot analysis and Neutral plot analysis indicated natural selection dominated the codon preference of Orthoptera mitochondrial genome, while the mutation bias only played a minor role. Base composition including A, T, C and G in three points and amino acid composition analysis revealed base composition bias and amino acid composition bias may also affected codon bias. Principal Component Analysis(PCA) and Correlation Analysis(COA) suggested gene expression level, the hydrophobic and aromaticity of amino acids also played an important role on this taxa codon bias, gene length had little impact on it. The research of interation between codon and anticodon suggested transfer RNA (tRNA) abundance had little effect on codon bias in Orthoptera mitochondrial genome.3. Evolutionary analysis:the combination of hierarchical cluster analysis based on RSCU values of 13CDs and three different phylogenetic trees that used BI, ML and MP methods based on 13CDs indicated hierarchical cluster analysis results could effect Orthoptera species evolution relationship in some degree, and furthermore, species that codon bias was the more similar, its relationship was closer. Thus, clustering analysis based on the codon RSCU value could be used as a reference of evolutionary analysis.This research could help us better understand the codon bias in Orthoptera, could provide a new perspective for Orthoptera evolution, meanwhile, provide certain reference value for the comparative study of codon bias in different orders of Insecta.