Analysis of codon usage bias of chloroplast genomes in Gynostemma species

• Published in: Physiology and molecular biology of plants 2021-12, Vol.27 (12), p.2727-2737
• Main Authors: Zhang, Peipei, Xu, Wenbo, Lu, Xu, Wang, Long
• Format: Article
• Language: English
• Subjects: Base composition; Bias; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Cell Biology; Chloroplasts; Codons; Composition; Economic analysis; Evolution; Gene expression; Genes; Genomes; Interferon; Life Sciences; Medicinal plants; Multivariate analysis; Multivariate statistical analysis; Mutation; Natural selection; Optimization; Phylogeny; Plant Physiology; Plant Sciences; Plant species; Research Article; Species; Statistical analysis; Use statistics
• ISSN: 0971-5894; 0974-0430
• DOI: 10.1007/s12298-021-01105-z

Gynostemma plants are important Chinese medicinal material and economic crops. Codon usage analysis is a good way to understand organism evolution and phylogeny. There is no report yet about analysis of codon usage bias of chloroplast genomes in Gynostemma species. In this study, the chloroplast genomes in nine Gynostemma species were analyzed systematically to explore the factors affecting the formation of codon usage bias. The codon usage indicators were analyzed. Multivariate statistical analysis including analysis of neutrality plot, effective number of codons plot, parity rule 2 plot and correspondence were performed. Composition analysis of codons showed that the frequency of GC in chloroplast genes of all nine Gynostemma species was less than 50%, and the protein-coding sequences of chloroplast genes preferred to end with A/T at the third codon position. The chloroplast genes had an overall weak codon usage bias. A total of 29 high frequency codons and 12 optimal codons were identified. These could provide useful information in optimizing and modifying codons thus improving the gene expression of Gynostemma species. The results of multivariate analysis showed that the codon usage patterns were not only affected by single one factor but multiple factors. Mutation pressure, natural selection and base composition might have an influence on the codon usage patterns while natural selection might be the main determinant. The study could provide a reference for organism evolution and phylogeny of Gynostemma species and help to understand the patterns of codons in chloroplast genomes in other plant species.