Analysis of synonymous codon usage of transcriptome database inRheum palmatum

Abstract

BackgroundRheum palmatumis an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias forR. palmatumCDSs. In this project, codon usage bias was determined based on theR. palmatum2,626 predicted CDSs from R. palmatum transcriptome.MethodsIn this study, all codon usage bias parameters and nucleotide compositions were calculated by Python script, Codon W, DNA Star, CUSP of EMBOSS.ResultsThe average GC and GC3 content are 46.57% and 46.6%, respectively, the results suggested that there exists a little more AT than GC in theR. palmatumgenes, and the codon bias ofR. palmatumgenes preferred to end with A/T. We concluded that the codon bias inR. palmatumwas affect by nucleotide composition, mutation pressure, natural selection, gene expression levels, and the mutation pressure is the prominent factor. In addition, we figured out 28 optimal codons and most of them ended with A or U. The project here can offer important information for further studies on enhancing the gene expression using codon optimization in heterogeneous expression system, predicting the genetic and evolutionary mechanisms inR. palmatum.