Abstract
Background Rheum 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.
Highlights
Codon degeneracy is a common phenomenon among living beings as the 20 different amino acids are encoded by 64 types of codons
A previous study has found that there was no significant correlation between codon usage bias and gene expression level in mammals, which was inconsistent with our result that the codon bias in R. palmatum genes was influenced by gene expression level (Karlin & Mrázek, 1996)
We carried out the codon usage bias analysis of R. palmatum genes based on the transcriptome data
Summary
Codon degeneracy is a common phenomenon among living beings as the 20 different amino acids are encoded by 64 types of codons. Most amino acids encoded by two to six codons except for Met or Trp (Duret, 2002; Ang et al, 2016), this phenomenon is defined as synonymous codon. It has been reported that the using frequency of synonymous codon in encoding amino acids is non-random for different genes or genomes, which is regarded as codon usage bias (Romero, Zavala & Musto, 2000). The codon usage bias may affect gene. Analysis of synonymous codon usage of transcriptome database in Rheum palmatum. 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. 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
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
