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民族药小白及与近缘种叶绿体基因组密码子偏好性分析

Codon use bias analysis of chloroplast genome of Bletilla Rchb. f.

  • 摘要: 为深入理解白及属植物遗传特性,分析白及属4个物种的密码子使用模式及其主要影响因素,利用CUSP、Codon W 1.4.2及EMBOSS等程序对小白及、白及、华白及和黄白4种植物的叶绿体基因密码子进行有效密码子数分析(ENC-plot)中性绘图、最优密码子等分析。结果表明:这4个物种共有的4个最优密码子均呈现出第3位碱基为A/U的特征,且所有蛋白编码基因的ENC均超越了35的阈值,反映了白及属植物在密码子偏好性方面的相对较弱趋势;进一步通过奇偶偏好性(PR2-Plot)分析,观察到基因在4个区域中的分布并非均衡;而ENC-Plot则表明,大部分基因均位于标准曲线的下方。此外,在中性绘图分析中,所有基因均显著偏离对角线,向上偏移。因此,密码子的使用偏差受到了突变与自然选择的双重影响,但自然选择在此过程中扮演了更为关键的角色,对密码子偏好性产生了更为显著的影响。

     

    Abstract: The analysis of codon usage patterns and their main influencing factors in four species of Bletilla Rchb. lays a solid theoretical foundation for a deeper understanding of the genetic characteristics, environmental adaptability, genetic improvement, and variety cultivation strategies of Bletilla Rchb. plants. The neutrality plot, ENC-plot, and PR2-plot analysis of chloroplast genome codons in 4 Bletilla Rchb. plants of Bletilla striata, Bletilla formosana, Bletilla sinensis, Bletilla ochracea were conducted based on CUSP, Codon W 1.4.2 and EMBOSS software. The study revealed that the four optimal codons shared by these four species all exhibit the characteristic that the third base is A/U, and the effective number of codons (ENC) of all protein-coding genes exceeds the threshold of 35. This phenomenon reflects a relatively weak trend in codon preference in Lepidoptera species. Furthermore, through parity preference (PR2-Plot) analysis, we observed that the distribution of genes in the four regions is not balanced; and effective codon number analysis (ENC-Plot) showed that most genes are located below the standard curve. Furthermore, in the neutral plot analysis, all genes were significantly shifted upward from the diagonal. This series of analyzes collectively shows that codon usage bias is affected by both mutation and natural selection, but natural selection plays a more critical role in this process and has a more significant impact on codon preference. In summary, this study provides a comprehensive and in-depth analysis of the codon usage bias in the chloroplast genomes of four species of the genus Bryoides, and clearly points out that natural selection is the dominant factor in shaping their codon preferences. This discovery not only enriches our understanding of the genetic characteristics of Albus genus plants, but also lays a solid theoretical foundation for subsequent exploration of their environmental adaptability, genetic improvement and variety breeding strategies.

     

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