Codon Usage Bias Analysis Of Orthoptera Transcriptome Genes

Codon bias refers to the unique pattern of codon usage that the difference frequency of codons in an organism's genes.Natural selection acts on the codon usage pattern,because codon bias may affect the rate of translation elongation in genes,the rate of protein synthesis,the rate of RNA degradation,and the accuracy of protein folding and etc.Meanwhile,codon usage patterns are affected by non-selective factors such as genome mutation pressure and gene conversion preferences.Investigating the codon usage preferences of a single species or a group provides a window into how different evolutionary factors—natural selection,mutation,and drift—affect the genome of that species or group.The codon bias research of Orthoptera insects mainly focuses on the mitochondrial genome.A large part of the reason is that mitochondria are the type of data collected in previous work.However,the number of mitochondrial genes is small,and there are unique inheritance patterns,and the amount of gene expression is also very different from the overall genome.Therefore,the codon usage pattern of mitochondrial genes doesn't represent the codon usage pattern of the entire genome of nuclear genes.In addition,existing studies are often based on sequence analysis without considering the influence of the gene expression level of the species on its codon bias.In this thesis,we studied the complete transcriptome data of 20 species of Orthoptera insects,and analyzed the codon usage patterns of these insect transcriptome gene sequences and their similarities and differences.Transcriptome data can provide both gene sequence and expression information,making it possible not only to calculate traditional,sequence-based codon preference statistics(such as ENC,RSCU),but also to obtain the number of preferred codons related to expression.The specific research content and main results of the thesis are as follows:First of all,this study completed the assembly of the transcriptome data of 20 Orthoptera insects,including 1 species of T.meditationis and 19 species of 15 genera of Acridoidea,greatly expanding the molecular database of Orthoptera insects.Due to the great controversy in the phylogeny of Orthoptera,especially Acridoidea,the transcriptome data of these insects will greatly help the future phylogenetic analysis to resolve the controversy.Secondly,this thesis separately analyzes the codon bias of T.meditationis.Although the degree of codon bias of a species is affected by many factors,Some researchers found have pointed out that the selection effect related to transcription is relatively weak and can only be reflected in species with large effective populations.T.meditationis is an insect that is widely distributed in China and is commonly found in human habitats.In view of the distribution range of this species and its strong adaptability to the environment,we predict that there should be a larger effective population of T.meditationis insect.Therefore,the transcriptome should have obvious codon bias and should be strongly related to the level of gene expression.But unexpectedly,our analysis found that in the transcriptome gene sequence of T.meditationis,the RSCU of all 61 codons(excluding the stop codon)was less than 1.5,and we didn't find any preferred codon related to the frequency of use and gene expression.Although the overall slight bias towards codons ending with GC,and part of the explanation can be explained by differences in GC content in genes.It shows that the codon usage bias of T.meditationis is relatively weak,which is contrary to prediction.We may need to further analyze the genetic diversity and pedigree structure of T.meditationis to obtain a more accurate effective population size.Finally,In this study we compared 19 species of Acridoidea to search for various gene parameters(GC3 content,gene expression,protein length,hydrophobicity and aromaticity of amino acids)related to codon bias.The study found that the spieces of Acridoidea are different from T.meditationis,preferring codons ending in AU.The content of GC3 in most species is a decisive factor affecting the ENC value and RSCU value of codons,that is,mutation pressure is the primary cause of codon bias.A few species found correlations between other genetic parameters(gene expression,protein length,hydrophobicity and aromaticity of amino acids)and codon usage except GC3 content.It shows that the codon bias caused by selection only appears in a few species.Our research also found that there is a weak correlation between the number of preferred codons related to expression and genome size.In view of the fact that the possibility of direct interaction between codon preference and genome size is very small,it may be a correlation caused by some factors acting on both at the same time.Of course,this correlation has yet to be confirmed by more species data and comparative phylogenetic methods.Conclusion:This study utilizes that although T.meditationis and a variety of Acridoidea species are widely and common species,but the research results are contrary to predictions.The codon bias of these species is weak on the whole and mutation pressure is the main evolutionary driving force.Only in a few species of Acridotidae have codon bias been found to be influenced by coding proteins.On the one hand,we may need to do more population genetic investigations on the pedigree structure and history of these species to obtain more accurate and effective population size data.On the other hand,there may be other factors in Orthoptera that make species with large populations not necessarily able to have obvious codon preference.The further collection of transcriptome data of more species in Orthoptera will help to discover more biological factors related to codon bias and enrich our understanding of the laws of codon usage.