Analysis of synonymous codon usage patterns in seven different citrus species.
Analysis of synonymous codon usage patterns in seven different citrus species.
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七种不同柑橘属植物的同义密码子使用模式分析
DOI：
10.4137/ebo.s11930
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发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Zhuge Q
中科院分区：
文献类型：
--
作者：
Xu C;Dong J;Tong C;Gong X;Wen Q;Zhuge Q
我们使用大样本的表达序列标签来描述7个不同柑橘物种的密码子使用偏向(CUB)模式，并分析它们对选择和碱基组成的进化影响。我们发现A和T结尾的密码子在柑橘类物种中占主导地位。接下来，我们确定了18种不同氨基酸的21个密码子，这些密码子在所有七个物种中都被认为是首选密码子。然后，我们进行了对应分析，并构建了有效密码子数量的曲线图，以分析同义密码子的使用情况。多元回归分析表明，每个物种的基因表达对可选密码子(FOP)的频率有恒定的影响。各比例之间的碱基组成差异很大。最后，在柑橘不同物种的进化过程中检测到了正向选择。总体而言，我们的结果表明密码子的使用是积极选择的结果。柑橘基因间密码子使用的差异受翻译选择、突变偏向和基因长度的影响。在翻译水平上，幼崽受选择压力的影响较大，基因长度的影响较小。一种可能的解释是，选择介导的密码子偏向在柑橘中一直很强，柑橘是种植最广泛的果树之一。
We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus, which is one of the most widely cultivated fruit trees.