Analysis of codon usage patterns of the chloroplast genome in Delphinium grandiflorum L. reveals a preference for AT-ending codons as a result major selection constraints

文献类型： 外文期刊

第一作者： Duan, Huirong

作者： Duan, Huirong;Zhang, Qian;Wang, Chunmei;Tian, Fuping;Lu, Yuan;Hu, Yu;Yang, Hongshan;Cui, Guangxin;Li, Fang

作者机构：

关键词： Delphinium grandiflorum L.; Chloroplast genome; Synonymous codon usage bias; Evolutionary forces

期刊名称：PEERJ （ 影响因子：2.984； 五年影响因子：3.369 ）

ISSN： 2167-8359

年卷期： 2021 年 9 卷

页码：

收录情况： SCI

摘要： Background. Codon usage bias analysis is a suitable strategy for identifying the principal evolutionary driving forces in different organisms. Delphinium grandiflorum L. is a perennial herb with high economic value and typical biological characteristics. Evolutionary analysis of D. grandiflorum can provide a rich resource of genetic information for developing hybridization resources of the genus Delphinium. Methods. Synonymous codon usage (SCU) and related indices of 51 coding sequences from the D. grandiflorum chloroplast (cp) genome were calculated using Codon W, Cups of EMBOSS, SPSS and Microsoft Excel. Multivariate statistical analysis combined by principal component analysis (PCA), correspondence analysis (COA), PR2-plot mapping analysis and ENC plot analysis was then conducted to explore the factors affecting the usage of synonymous codons. Results. The SCU bias of D. grandiflorum was weak and codons preferred A/T ending. A SCU imbalance between A/T and G/C at the third base position was revealed by PR2-plot mapping analysis. A total of eight codons were identified as the optimal codons. The PCA and COA results indicated that base composition (GC content, GC(3) content) and gene expression were important for SCU bias. A majority of genes were distributed below the expected curve from the ENC plot analysis and up the standard curve by neutrality plot analysis. Our results showed that with the exception of notable mutation pressure effects, the majority of genetic evolution in the D. grandiflorum cp genome might be driven by natural selection. Discussions. Our results provide a theoretical foundation for elucidating the genetic architecture and mechanisms of D. grandiflorum, and contribute to enriching D. grandiflorum genetic resources.

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