小丛红景天叶绿体基因组密码子使用偏性及其进化驱动因素分析

Codon Usage Bias and Evolutionary Drivers in the Chloroplast Genome of Rhodiola dumulosa

  • 摘要: 通过二代测序技术成功获得了小丛红景天的完整叶绿体基因组序列,分析了52个蛋白质编码序列(CDS)的密码子使用模式及进化驱动因素,阐明影响该物种密码子使用偏好性的主要因素。结果表明:叶绿体总体基因组GC含量为38%;52 条 CDS 的有效密码子数(ENC)的平均值为42.86,偏性水平居中;相对同义密码子使用度(RSCU)>1的密码子有29个,以 A/U 结尾有28个,表明其更偏向于使用以 A/U 结尾的密码子; ENC与GC3、Nc呈极显著正相关,Nc与ENC、GC3呈显著正相关,GC1与GCall和GC2呈极显著正相关,GC3与Nc呈显著正相关,GCall与GC1、GC2、GC3呈极显著正相关,表明它对密码子的使用偏性存在影响;通过中性绘图、ENC−plot、PR2−plot、等价偏倚分析发现小丛红景天叶绿体基因组密码子偏好性受到了突变和选择的共同影响,而这种影响可能与相应基因的功能相关。经过筛选得到18个最优密码子,其中17个以A/U结尾。

     

    Abstract: The study successfully obtained the complete chloroplast genome sequence of Rhodiola dumulosa using second-generation sequencing technology, analyzed the codon usage patterns and evolutionary driving factors of its 52 protein-coding sequences (CDS), thereby elucidating the main factors influencing codon usage bias in this species. The results showed that the overall GC content of the chloroplast genome is 38%. The average values of adequate codon numbers (ENC) values of the 52 CDS were 42.86, and the bias was middle level; 29 of the codons with RSCU > 1, 28 were all ending with A/U, indicating that it is more biased towards the use of codons ending with A/U; ENC exhibited a highly significant positive correlation with GC3 and Nc; Nc displayed a significant positive correlation with ENC and GC3; GC1 was highly significantly positively correlated with GCall and GC2; GC3 showed a significant positive correlation with Nc; GCall was highly significantly positively correlated with GC1, GC2, and GC3, indicates that it has some effect on codon usage bias; through neutral drawing ENC-plot, PR2-plot, Equivalent bias analysis found that the codon preference of the chloroplast genome of R. dumulosa was influenced by both mutation and selection, and this influence may be related to the function of the corresponding genes; after filtering, 18 optimal codons and 17 of which end with A/U.

     

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