The Preference And Evolution Of Insect Mitochondrial Gene Codons

Insect is the largest group of animals in the Earth.Mitochondrial DNA(mtDNA)of Insect is covalently closed double-stranded circular molecule with a small molecular weight.It generally comprises 37 compact arranged genes and 13 of them were protein-coding genes(PCGs).Mitochondrial DNA has been widely used as a neutral molecular marker in phylogenetic studies due to its matrilineal inheritance,conserved gene contents and less recombination,faster mutation rate(compared with nuclear DNA),and nearly constant across different lineages.However,purified or adaptive evolutionary forces are found present in some birds.Since the uneven use of synonymous codons(codon usage bias,CUB)are the indicator of complex evolutionary forces,we had a comprehensive analysis of the codon usage in Insect mitogenomes with the aim to estimate their evolutionary characteristics.Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects.Based on the bioinformatics method,this paper studied the complete mitochondrial genome of 29 orders,372 families and 2,842 species.This study analyzed the codon usage bias patterns of mtDNA in different evolutionary status insects and their similarities and differences.Secondly,combined with the relevant evolutionary index analysis,the main causative factors along with the evolutionary forces were analysed in the present study.A detailed and modified analysis based on mtDNA bias might offer a better understanding into the evolutionary relationships among the different groups of insects.The specific findings and conclusions were as follows:1.Phylogenetic analysis of insect mitochondrial genomeThe topology of phylogenetic tree of the insect relationship constructed based on the mitochondrial genome is consistent with previous morphological and molecular classification studies.Based on the insect phylogenetic tree,exploring the insect mitochondrial genome codon preference pattern and its formation reasons and further analysising of the codon preference patterns of different evolutionary status insects and their similarities and differences.2.The analysis of mitochondrial genome codon bias patterns in insectsAmong the 62 synonymous codons of the insect mitochondrial genome CDS(2 stop codons were excluded),30 were more frequently represented with an RSCU>1 and they ended with A/U bases.The total number and type of codons of RSCU>1 in different evolutionary status insects are basically the same.However,from Apterygota to Pterygota,the RSCU value is generally on the rise.These RSCU>1 codons are used more and more frequently as insects evolve from primitive to evolutionary groups.The ENC values of the 2,842 insects mitochondrial genome ranged from 26.81-56.08 with an average ENC of 37.0.The CAI value fluctuates from 0.200 to 0.868 with an average of 0.579.With the evolution of insects,the ENC value decreases slowly from Apterygota to Pterygota,and the range of variation of ENC values of insects between different species of the same order is reduced.And the CAI value showed a slow upward trend,and the range of CAI values of insects between different species for the same order also decreased.By analyzing the protein coding codons RSCU,ENC and CAI values of insect mtDNA,we found that in insect there is a preference for AU-ending codons,avoiding using codons CG-ending codons.As insects evolve from primitive to evolutionary groups,the insect mitochondrial genome CDS codon preference becomes stronger and stronger.Codons ending with C or G are increasingly avoided,and codons ending with A or U are used more and more frequently.And the closer the species phylogenetic relationship is,the more similar the pattern of use of codons is.3.The analysis of the primary contributing force of insect mitochondrial genome codon bias patternThe concluded that the primary contributing force to this preference of insect mitochondrial genome codon usage bias pattern is selection rather than mutation.And with the evolution of insects,the role of selection plays an increasingly important role.The base composition in the mutational stress is a major factor affecting the insect mtDNA codon usage pattern.In the selection,gene expression levels have an important influence on codon usage preferences,and the effects are similar in different evolutionary insects.The formation of codon preference patterns by protein components and amino acid properties is less affected by different groups of insects.Insect mitochondrial genomes have the same protein lengths,all of which are around 3,000 bp,and the protein lengths have no effect on the codon usage bias of the insect mtDNA genome.This paper analyzes the mitochondrial genome data of most species of hexapoda.Using the combined dataset of these sequences,adequate genetic information can be retrieved to address the nature of mtDNA in insects.This study not only analyzed the mitochondrial genome codon usage bias patterns and the primary contributing force of it in the whole,but also analyzed the codon usage bias patterns of mtDNA in different evolutionary status insects and their similarities and differences by dividing the 29 orders insect studied into five groups.These conclusions will provide new insights for us to better understand the evolution among various groups of insects.