罗秦欢, 段炼, 赵月梅. “红阳”猕猴桃叶绿体基因组密码子使用偏性分析[J]. 西南林业大学学报(自然科学), 2024, 44(6): 1–9. DOI: 10.11929/j.swfu.202312045
引用本文: 罗秦欢, 段炼, 赵月梅. “红阳”猕猴桃叶绿体基因组密码子使用偏性分析[J]. 西南林业大学学报(自然科学), 2024, 44(6): 1–9. DOI: 10.11929/j.swfu.202312045
Luo Qinhuan, Duan Lian, Zhao Yuemei. Codon Usage Bias of Chloroplast Genome in Actinidia chinensis‘Hongyang’[J]. Journal of Southwest Forestry University. DOI: 10.11929/j.swfu.202312045
Citation: Luo Qinhuan, Duan Lian, Zhao Yuemei. Codon Usage Bias of Chloroplast Genome in Actinidia chinensis‘Hongyang’[J]. Journal of Southwest Forestry University. DOI: 10.11929/j.swfu.202312045

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“红阳”猕猴桃叶绿体基因组密码子使用偏性分析

Codon Usage Bias of Chloroplast Genome in Actinidia chinensis‘Hongyang’

  • 摘要: 为了解中华猕猴桃优良品种“红阳”猕猴桃的叶绿体基因组密码子的偏好性,利用Codon W和在线CUSP软件对“红阳”猕猴桃叶绿体基因组中的 51 条编码序列的密码子进行中性绘图、ENC-plot和PR2-plot分析。结果表明:“红阳”猕猴桃密码子不同位置上的GC 碱基含量有明显差异,即GC1>GC2>GC3,表明该植物密码子偏好以 A/U 结尾;ENC值为35.70~56.79,表明该品种的猕猴桃叶绿体基因组密码子使用偏性整体较弱。综合分析表明,“红阳”猕猴桃叶绿体密码子偏性主要受自然选择的影响。最终筛选出 17 个密码子为最优密码子,这些密码子均以 A/U 结尾。

     

    Abstract: ‘Hongyang’ was an excellent cultivar selected from Actinidia chinensis, Studying its codon usage pattern can help to understand the evolutionary mechanism of this species and improve the expression level of exogenous genes. In this study, the 51 coding Sequences(CDS) of Actinidia chinensis ‘Hongyang’ were analyzed to obtain to the results of Neutrality plot, ENC-plot and PR2-plot using Codon W and online software CUSP. The results showed that the GC content varied at different positions of the codons in the chloroplast genome of Actinidia chinensis ‘Hongyang’: Namely: GC1 > GC2 > GC3, indicating that the third base of codons preferred to end with A/U. The ENC value ranges from 35.70 to 56.79, indicating that codon usage bias in the chloroplast genome of A. chinensis ‘Hongyang’ was generally weak. Neutrality plot, ENC plot and PR2 plot indicate that natural selection was the major factors on codon usage patterns in the chloroplast genome of A. chinensis ‘Hongyang’. In addition, 17 codons were selected as the optimal codons and all of them ends with A/U. The results of this research lay the foundation for further chloroplast engineering study, resource conservation and utilization A. chinensis ‘Hongyang’ .

     

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