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<p>The chloroplast genome has a high degree of conservation and a slower evolutionary rate. Studying the codon usage bias (CUB) of the chloroplast genome can clarify the efficiency of gene expression, explore the factors that influence the formation of CUB, and determine the process of plant systematic evolution and species evolution. This study analyzed the codon usage bias of chloroplast gene CDS sequences of 27 <i>Ardisia</i> species, including <i>Ardisia japonica</i>, <i>A. mamillata</i>, <i>A. lindleyana</i>, <i>A. pedalis</i>, and <i>A. merrillii</i>, etc. The analysis results show that the condon usage bias of 27 <i>Ardisia</i> species genus is similar, and their genetic sequences are major in A/T bases, with the third base of codon mainly ending in A/T. The average GC content of the CDS sequences of chloroplast gene in 27 species is 37.34%-38.39%, none of which exceeds 50%. The effective number of codon (ENC) for each gene in the leaf chloroplast genomes of 27 species of <i>Ardisia</i> ranges from 37.16 to 57.63, which are all significantly greater than 35, indicating that the codon usage bias in the chloroplast genomes of these 27 species is relatively weak. The ENC-plot, PR2-plot, and neutral plot analysis show that the codon usage bias in 27 <i>Ardisia</i> species is formed by the joint action of natural selection, base mutation, and other factors, with natural selection playing a dominant role. Through the analysis of relative synonymous codon usage (RSCU), 28 high-frequency codons with A/T ending and 28 low-frequency codons with G/C ending were found. Based on the RSCU and △RSCU values, the study finally identified 5 optimal codons, including ACA (threonine), UAU (tyrosine), CAU (histidine), AGA (arginine), and GGA (glycine). The above results may provide reference for the systematic evolution of <i>Ardisia</i> genus plants and subsequent exogenous gene improvement of chloroplast genomes.</p>

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Codon usage biases in the chloroplast genomes of 27 Ardisia species

  • 期刊论文

  • 发表日期：

    2026年1月16日

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  • Shengqun Chen,
  • Dongbo Wu,
  • Ai Rao,
  • Na Hou,
  • Yueyun Wang,
  • Mao Li

摘要

The chloroplast genome has a high degree of conservation and a slower evolutionary rate. Studying the codon usage bias (CUB) of the chloroplast genome can clarify the efficiency of gene expression, explore the factors that influence the formation of CUB, and determine the process of plant systematic evolution and species evolution. This study analyzed the codon usage bias of chloroplast gene CDS sequences of 27 Ardisia species, including Ardisia japonica, A. mamillata, A. lindleyana, A. pedalis, and A. merrillii, etc. The analysis results show that the condon usage bias of 27 Ardisia species genus is similar, and their genetic sequences are major in A/T bases, with the third base of codon mainly ending in A/T. The average GC content of the CDS sequences of chloroplast gene in 27 species is 37.34%-38.39%, none of which exceeds 50%. The effective number of codon (ENC) for each gene in the leaf chloroplast genomes of 27 species of Ardisia ranges from 37.16 to 57.63, which are all significantly greater than 35, indicating that the codon usage bias in the chloroplast genomes of these 27 species is relatively weak. The ENC-plot, PR2-plot, and neutral plot analysis show that the codon usage bias in 27 Ardisia species is formed by the joint action of natural selection, base mutation, and other factors, with natural selection playing a dominant role. Through the analysis of relative synonymous codon usage (RSCU), 28 high-frequency codons with A/T ending and 28 low-frequency codons with G/C ending were found. Based on the RSCU and △RSCU values, the study finally identified 5 optimal codons, including ACA (threonine), UAU (tyrosine), CAU (histidine), AGA (arginine), and GGA (glycine). The above results may provide reference for the systematic evolution of Ardisia genus plants and subsequent exogenous gene improvement of chloroplast genomes.