A Comprehensive Analysis Of Codon Usage Patterns In Morus Notabilis And Development Of Codon Analysis Tool

Codon is the three consecutive bases on m RNA,and stands for one amino acid in protein synthesis.The deciphering of the genetic code is a milestone in the molecular biology,which links the information of protein and nucleic acid.Some amino acids are encoded by several different types of synonymous codons,which makes the genes encoding the same protein may have different codon usage patterns.And the usage of synonymous codon affects the expression level of gene.In the process of cotranslational protein folding,the bias usage of codon changes the conformation of protein,which leads to the differentiation of protein function.Moreover,the stability of m RNA,occurrence of cancer and some diseases are also associated with the usage pattern of codons.In the post genome era,a large number of genome and transcriptome data can be obtained from public databases.How to use these data to provide reference for experimental research is one of the most important research topics in bioinformatics.The genome sequencing of Morus notabilis provides a wealth of gene data for the study of other plants in order Rosales.Mulberry tree has strong adaptability and is widely distributed in the world.In addition,mulberry tree has high edible and medicinal values.In the present study,a comprehensive bioinformatics analysis was carried out on codon usage in M.notabilis.The main results of the study are as follows: 1.Analysis of the chloroplast genome codon of M.notabilisThe study of chloroplast genome of M.notabilis revealed that selective pressure affects the codon usage of genes.Studies on the chloroplasts of fifteen species of order Rosaceae showed that the nucleic acid compositions of these chloroplast genes were similar to each other.The similarity of codon usage patterns in order Rosaceae plant is not entirely consistent with genetic relationship,suggesting that the selection of some genes makes the patterns of codon usage in similar species different.The codon usage of the chloroplast genes in the Rosacea species is generally under selection,and in comparison,M.notabilis has been subjected to the weakest natural selection.2.Analysis of the codon of the nuclear genome of M.notabilisBased on the analysis of the codon usage patterns of the genes in the nuclear genome of M.notabilis,the high frequency codons and optimal codons were identified.Combined with the analysis of transcriptome data showed that the proportion of optimal codons of M.notabilis increases with the level of gene expression,and this phenomenon is more pronounced in housekeeping genes.Based on the analysis of the potential factors affecting codon usage,we found that the nucleotide composition,length,expression,and the molecular weight of the encoded amino acids of genes affect the usage of synonymous codons.In the multiple correlation analysis,we found that the high expression gene in M.notabilis was shorter,had stronger codon preference,higher GC content,and preferred to use lower molecular weight and lower metabolic cost amino acids.Genetic analysis of codon bias and prediction in M.notabilis showed that the genes involved in nucleotide metabolism,energy metabolism,transcription and translation were under stronger selective stress and thus showed stronger codon bias,which means that gene function and codon usage patterns seem to have certain connections.It was found that there were a large number of codon usage patterns in genes involved in pyrimidine metabolism,purine metabolism and RNA polymerase,and other functional genes did not have a very unique codon usage pattern.It was also found that there was a better correspondence between codon bias and gene expression level in housekeeping genes.A similar phenomenon was found in human genes in recent years,and selection on codon usage was suggested to be more pronounced in housekeeping genes.In this study,we found that the expression level of gene affects the codon bias of gene,and the expression level of the housekeeping genes in M.notabilis was significantly higher than that of the tissue expression specific genes and other genes.Same results were obtained when the similar expression levels of housekeeping genes and other genes were compared.This result indicated that the selection pressure of codons was more pronounced in housekeeping genes.Codon context bias was also observed in M.notabilis,and interestingly,it was influenced by gene expression level.Not only codon usage affects adjacent codons,codon position in the gene also affects the bias of synonymous codon usage.The gene start region prefers to use a codon with degenerate site C,while avoids the use of a codon with a degenerate site U.The codons with degenerate site C showed a consistent trend in the use of different genes,while the other codons based on position-based bias were not very consistent.Despite the presence of position-based codon bias in M.notabilis,the bias did not seem to make a significant difference between the folding energy of the M.notabilis gene and the synonymous codon Null model.3.Development of codon analysis software Codons Box with user interfaceCollation of the functions used in this study,Java was used to develop a codon analysis tool Codons Box with user-friendly interface.This makes it possible to avoid some repetitive work,so that the researchers can focus on the more in-depth and personalized codon research.Codons Box's web address is https://github.com/cqwenyan/Codons Box,and the software will help with the research in related fields.Our study provides the basic data not only for the study of codons in other plants,but also for the study of mulberry transgenic and breeding.A simple and efficient method for codon analysis will facilitate future the personalized study of codons in other species.