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本研究利用软件Codon W、CUSP和SPSS对甜荞43条叶绿体基因序列进行密码子偏爱性分析和对应性分析,获得CG、ENC、RSCU等参数,并把甜荞和马铃薯、陆地棉、水稻、小麦等植物进行聚类分析。碱基组成结果显示,CG3明显低于CG_1和CG_2,说明甜荞叶绿体基因密码子偏爱A或T结尾。中性绘图分析、ENC与CG_(3s)相关性分析以及对应性分析表明,密码子偏爱性主要受选择作用的影响,但存在部分功能基因(如光合系统基因)主要受突变作用调控。基于RSCU的聚类分析表明,甜荞既不属于单子叶植物,又异于其他双子叶植物,其叶绿体基因密码子用法比较特殊。以上述为基础,我们确定了甜荞叶绿体的14个最优密码子。该研究成果可为进一步确定甜荞在植物分类学中的位置奠定基础,从而对现有的系统发育树进行重要补充。此外,该结果对甜荞叶绿体中某些未知功能基因的预测、发现新基因、提高以甜荞为目的宿主的外源基因的表达量都具有重要意义。
In this study, Codon W, CUSP and SPSS were used to analyze the codon preference of 43 chloroplast genes in buckwheat and their correspondence analysis. The parameters such as CG, ENC and RSCU were obtained, Wheat and other plants for cluster analysis. The results of base composition showed that CG3 was significantly lower than that of CG_1 and CG_2, indicating that the codon usage of chloroplast genes in sweet buckwheat was a-favor for the end of A or T. Neutral mapping analysis, correlation analysis between ENC and CG_ (3s) and correspondence analysis showed that codon preference was mainly affected by the selection effect, but some functional genes (such as photosynthetic system genes) were mainly regulated by mutation. Cluster analysis based on RSCU showed that buckwheat is neither monocotyledonous nor dicotyledonous, and its chloroplast gene codon usage is rather special. Based on the above, we identified 14 optimal codons for sweet buckwheat chloroplast. The results of this study can lay a foundation for further determining the position of sweet buckwheat in plant taxonomy, and thus make an important complement to the existing phylogenetic tree. In addition, the results of the prediction of some unknown genes in sweet buckwheat chloroplast, the discovery of new genes, enhance the expression of exogenous genes expressed in sweet buckwheat host are of great significance.