Analysis Of Codon Usage Genome And Its Phylogenetic Relationship In Orchidaceae

Codons are the core elements of protein translation in gene coding regions.Analysis of codon usage characteristics in genome coding regions is of great significance to the study of gene function and system evolution.Orchidaceae is one of the largest families of angiosperms,which has the characteristics of complex genome,diverse morphology and wide distribution,and the classification among species is still controversial.Therefore,this study analyzed 3 nuclear genome species and 138 chloroplast genome species with complete annotation of all orchids.This is the first time to systematically analyze codon usage characteristics in coding regions of Orchidaceae genomes,explaining the relationship between codon usage and gene expression in nuclear genomes of Orchidaceae plants,as well as codon preference in chloroplast genomes and phylogenetic relationships among species.The main research results are as follows:1.Analysis of codon usage characteristics of coding sequence in Orchidaceae genome shows that GC contents in nuclear genomes of three orchids are higher than those of 138 chloroplast genomes,and codons of three orchids prefer U/C endings,while codons of 138 orchids prefer A/U endings.Moreover,the codon preference of nuclear genomes of three orchids is lower than that of chloroplast genomes of 138 orchids.2.ENC-plot analysis,PR2-plot analysis and neutral-plot analysis indicates that natural selection is the main reason for codon preference formation in protein coding region of Orchidaceae genome(3 species genome and 138 chloroplast genome).3.The analysis of the relationship between codon usage and gene expression in genomes shows that the gene expression in genomes of Apostasia shenzhenica,Dendrobium catenatum and Phalaenopsis equestris is positively correlated with GC3 content and negatively correlated with ENC,which indicates that the higher the gene expression in the nuclear genome of Orchidaceae plants,the stronger codon preference.4.Phylogenetic trees were constructed based on 138 orchid chloroplast genomes,CDS sequences and codon preference RSCU values respectively.The results show that the evolutionary relationship between species based on codon preference is significantly different from the first two.The evolutionary relationship between chloroplast genomes and CDS sequences is closer to the real classification of species.The results further support that site mutation and non-coding region sequences often play an important role in the evolution of organisms.