Affiliation:
1. Chinese Academy of Agricultural Sciences Lanzhou Institute of Husbandry and Pharmaceutical Science, Lanzhou, China
2. Institute of Grassland Science, Chinese Academy of Agricultural Sciences, Hohhot, China
Abstract
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, GC3 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.
Funder
National Natural Science Foundation of China
Central Public-interest Scientific Institution Basal Research Fund
Science and Technology Innovation Program of Lanzhou Institute of Husbandry and Pharmaceutical Science
Chinese Academy of Agricultural Sciences
Innovation Project of Chinese Academy of Agricultural Sciences
Gansu Provincial Science and Technology Major Projects
Subject
General Agricultural and Biological Sciences,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience
Cited by
28 articles.
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