Analysis of synonymous codon usage of transcriptome database in Rheum palmatum

PeerJ

article

Xiaowei Huo¹  Sisi Liu²  Yimin Li³  Hao Wei³  Jing Gao³  Yonggang Yan³  Gang Zhang³  Mengmeng Liu⁴ 

[1]College of Pharmaceutical Science, Institute of Life Science and Green Development, Hebei University

[2]Hunan Academy of Forestry

[3]College of Pharmacy and Shaanxi Provincial Key Laboratory for Chinese Medicine Basis & New Drugs Research, Shaanxi University of Chinese Medicine

[4]College of Traditional Chinese Medicine, Hebei University

关键词: Codon usage bias;    Nucleotide composition;    Transcriptome analysis;    Gene expression level;    Rheum palmatum;   

DOI  :  10.7717/peerj.10450

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundRheum palmatum is an endangered and important medicinal plant in Asian countries, especially in China. However, there is little knowledge about the codon usage bias for R. palmatum CDSs. In this project, codon usage bias was determined based on the R. palmatum 2,626 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 the R. palmatum genes, and the codon bias of R. palmatum genes preferred to end with A/T. We concluded that the codon bias in R. palmatum was 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 in R. palmatum.

【 授权许可】

CC BY