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An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea

文献类型： 外文期刊

作者： Li, Yaqi 1 ; Hu, Xiang 2 ; Xiao, Mingkun 1 ; Huang, Jiaxiong 1 ; Lou, Yuqiang 1 ; Hu, Faguang 1 ; Fu, Xingfei 1 ; Li, Yanan 1 ; He, Hongyan 1 ; Cheng, Jinhuan 1 ;

作者机构： 1.Yunnan Acad Agr Sci, Inst Trop & Subtrop Cash Crops, Baoshan, Yunnan, Peoples R China

2.Yunnan Acad Agr Sci, Inst Trop Ecoagr, Yuanmou, Yunnan, Peoples R China

3.Yunnan Acad Agr Engn, Kunming, Yunnan, Peoples R China

关键词： Coffee; Chloroplast genome; Codon usage bias; Heterologous expression

期刊名称：BMC GENOMIC DATA （ 影响因子：1.9； 五年影响因子：1.9 ）

ISSN：

年卷期： 2023 年 24 卷 1 期

页码：

收录情况： SCI

摘要： BackgroundThe chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation.ResultsAnalysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes.ConclusionThis study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

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