• 中文核心期刊
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镰翅羊耳蒜叶绿体基因组密码子偏好性分析

Codon Usage Bias of Chloroplast Genome in Liparis bootanensis

    摘要
  • 摘要:
      目的  分析镰翅羊耳蒜叶绿体基因组密码子偏好性，并探讨影响密码子偏好性形成的主要因素。
      方法  从镰翅羊耳蒜叶绿体基因组中筛选出47条编码序列，通过CodonW和CUSP软件计算不同基因的GC含量，分析密码子使用模式。
      结果  GC3含量为27.99%，低于GC1（47.00%）和GC2（39.41%）；ENC取值范围为40.85～56.80，平均值为47.27；ENC与GC1、GC2之间均无显著相关，与GC3呈极显著正相关；GC12与GC3的相关性不显著，相关系数为0.05；47%基因的ENC比值频数分布在−0.05～0.05区间，53%基因的ENC比值频数分布在−0.05～0.05区间之外；碱基的使用频率为A＞T、G＞C；17个密码子被确定为最优密码子。
      结论  镰翅羊耳蒜叶绿体基因组密码子对A或T碱基结尾有偏好性；密码子偏好性较弱；密码子偏好性主要受选择和突变作用共同影响，同时还受其他因素影响，是多因素综合影响的结果。

     

    Abstract:
      Objective  The coden usage bias and its infulence factor in the chloroplast genome of Liparis bootanensis were analyzed in this study.
      Method  CodonW and CUSP software were used to analyze the codon usage bias based on 47 codon DNA sequences of the chloroplast genome of L. bootanensis.
      Result  The GC content in the 3rd position of the codons was 27.99%, which was lower than those in the 1st and the 2nd. The effective number of codons ranged from 40.85 to 56.80, averaging 47.27. The ENC showed no significant correlation to GC1 and GC2 but a significant positive correlation to GC3. The correlation between GC12 and GC3 was not significant with a coefficient of 0.05. The frequency of ENC ratio of 47% genes was distributed between −0.05 and 0.05, while that of 53% genes outside -0.05 and 0.05 range. A PR2-plot analysis indicated the base usage frequencies to be A＞T and G＞C. There were 17 codons selected after screening.
      Conclusion  The 3rd position of codons was rich in A or T. The codon usage bias was weak, complex, and affected by mutation and selection besides other factors.

     

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