Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth
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ORIGINAL ARTICLE
Analysis of codon usage bias and evolution in the chloroplast genome of Mesona chinensis Benth Danfeng Tang 1
&
Fan Wei 1 & Zhongquan Cai 2 & Yanyan Wei 2 & Aziz Khan 2 & Jianhua Miao 1 & Kunhua Wei 1
Received: 25 May 2020 / Accepted: 4 November 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Mesona chinensis Benth (MCB) is one of the main economic crops in tropical and subtropical areas. To understand the codon usage bias (CUB) in M. chinensis Benth, chloroplast genome is essential to study its genetic law, molecular phylogenetic relationships, and exogenous gene expression. Results showed that the GC content of 53 CDS sequences was 37.95%, and GC1, GC2, and GC3 content were 46.02%, 38.26%, and 29.85%, respectively. The general GC content order was GC1>GC2>GC3. Moreover, the majority of genes had an effective number of codon (ENC) value greater than 40, except ndhE, rps8, and rps18. Correlation analysis results revealed that the GC content was significantly correlated with GC1, GC2, GC3, and ENC. Neutrality plot analysis, ENC-plot analysis, and PR2-plot analysis presented that the CUB of M. chinensis Benth chloroplast genome was mainly affected by mutation and selection. In addition, GGG, GCA, and TCC were found to be the optimal codons. Furthermore, results of cluster analysis and evolutionary tree showed that M. chinensis Benth was closely related to Ocimum basilicum, indicating that there was a certain correlation between the CUB of the chloroplast gene and the genetic relationship of plant species. Overall, the study on the CUB of chloroplast genome laid a basis for genetic modification and phylogenetic research of M. chinensis Benth chloroplast genome. Keywords Codon usage bias . Chloroplast genome . Mesona chinensis Benth . Evolution and cluster analysis
Introduction Codon, as a connection between the nucleic acid and protein, plays an important role in the process of genetic information transmission (Zhang 2019). The genetic information carried on DNA is transmitted in the form of triplet codons in the process of transferring from RNA to protein, and each amino acid corresponds to at least one codon and at most six codons (Li et al. 2019). Codons encoding the same amino acid were referred to as synonymous codons (Duret 2002). The Communicated by Yves Deveaux * Danfeng Tang [email protected] * Fan Wei [email protected] 1
Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
2
Guangxi University, Nanning, China
probability of synonymous codon utilization was different during protein synthesis. In the case of natural selection or mutation preference, a species or a gene tended to use one or more specific synonymous codons called synonymous codon usage bias (CUB) (Hershberg and Petrov 2008; Wang et al. 2018; Long et al. 2018). CUB existed widely in different organisms. It was not only affected by environmental factors, base mutation, gene drift in the long-term ev
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