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<p><i>Codonopsis</i>, a genus of important medicinal plants in the Campanulaceae family, has its roots listed in the Chinese Pharmacopoeia as a traditional tonic herb. This study conducted a systematic analysis of the chloroplast genome data from eight <i>Codonopsis</i> species, focusing on parameters such as the base composition of codons (GC1/2/3), relative synonymous codon usage (RSCU), and the effective number of codons (ENC), utilizing tools such as Codon W 1.4.2 and CUSP. The underlying causes of codon preference were examined using ENc-plot, PR2-plot, and neutrality plots. Common optimal codons were identified, and the codon usage frequencies of four model organisms, including <i>Arabidopsis thaliana</i> and <i>Nicotiana tabacum</i>, were compared to assess the most suitable heterologous expression hosts. The findings indicated that codon preference within the chloroplast genomes of <i>Codonopsis</i> was relatively weak (average ENC = 51.03, CAI = 0.17), with GC content demonstrating a pattern of GC1 &gt; GC2 &gt; GC3 (all &lt; 50%), and a marked preference for A/U-ending codons (96.55% of high-frequency codons ended with A/U). Codon preference was influenced by both natural selection and mutation, with natural selection identified as the predominant factor (regression slope 0.20–0.43). Eight common optimal codons were identified, all terminating with A/U. The comparison of usage frequencies suggested that <i>Arabidopsis thaliana</i> and <i>Nicotiana tabacum</i> were the most suitable hosts for heterologous expression. This study lays a foundation for molecular breeding, chloroplast genetic engineering, and adaptive evolution research in&#xa0;<i>Codonopsis</i>.</p>

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Natural selection-driven A/U-ending preference in codon usage patterns of Codonopsis chloroplast genomes

  • 期刊论文

  • 发表日期：

    2025年12月16日

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  • Fulin Yan,
  • Songsong Wu,
  • Yongxin Zhou,
  • Shenghua Wei

摘要

Codonopsis, a genus of important medicinal plants in the Campanulaceae family, has its roots listed in the Chinese Pharmacopoeia as a traditional tonic herb. This study conducted a systematic analysis of the chloroplast genome data from eight Codonopsis species, focusing on parameters such as the base composition of codons (GC1/2/3), relative synonymous codon usage (RSCU), and the effective number of codons (ENC), utilizing tools such as Codon W 1.4.2 and CUSP. The underlying causes of codon preference were examined using ENc-plot, PR2-plot, and neutrality plots. Common optimal codons were identified, and the codon usage frequencies of four model organisms, including Arabidopsis thaliana and Nicotiana tabacum, were compared to assess the most suitable heterologous expression hosts. The findings indicated that codon preference within the chloroplast genomes of Codonopsis was relatively weak (average ENC = 51.03, CAI = 0.17), with GC content demonstrating a pattern of GC1 > GC2 > GC3 (all < 50%), and a marked preference for A/U-ending codons (96.55% of high-frequency codons ended with A/U). Codon preference was influenced by both natural selection and mutation, with natural selection identified as the predominant factor (regression slope 0.20–0.43). Eight common optimal codons were identified, all terminating with A/U. The comparison of usage frequencies suggested that Arabidopsis thaliana and Nicotiana tabacum were the most suitable hosts for heterologous expression. This study lays a foundation for molecular breeding, chloroplast genetic engineering, and adaptive evolution research in Codonopsis.