Analysis on codon usage of chloroplast genome of gossypium hirsutum | 陆地棉叶绿体基因组密码子使用偏性的分析

Chinese. 【目的】通过分析陆地棉叶绿体基因组密码子使用偏性,探讨影响密码子偏性形成的主要因素。【方法】以陆地棉叶绿体基因组为研究对象,利用Mobyle及其它软件,分析叶绿体50个基因密码子的使用模式。【结果】陆地棉叶绿体基因组密码子GC1与GC2之间的相关系数达到极显著水平,GC3含量最低,与GC12的相关系数为0.14,双尾检验未达到显著水平;单个基因ENC比值多分布在-0.05―0.05;对应性分析,第一轴上显示了10.27%的差异,与GC3、ENC的相关系数分别为0.223和-0.147,均未达到显著水平。【结论】陆地棉叶绿体密码子第三位偏好使用嘧啶,而最优密码子多以A或T结尾;密码子使用模式可能是由选择和突变及其它因素共同作用形成的。

English. 【Objective】The codon usage bias in Gossypium hirsutum chloroplast genome was analyzed to find the factors affecting the formation of codon bias. 【Method】 Codon of fifty genes which were selected from the chloroplast genome sequence of Gossypium hirsutum were studied. Mobyle and other softwares were used to calculate different parameters for the codon usage.【Result】G+C content of the third position in the codons is the lowest among the three positions. The GC3 has a low correlation coefficient (0.14) to the GC12 which is insignificant, whereas GC1 and GC2 have a significant correlation coefficient. ENC ratio of most genes ranged from -0.05 to 0.05. In the corresponding analysis, the first axis shows 10.27% variation. The correlation coefficients for axis1 with GC3 and ENC are 0.223 and -0.147, respectively, and both are insignificant. 【Conclusion】The codon usage bias is formed under effect of mutation and selection, as well as other factors. Genes in function group possibly have the similar factor for the codon formation. The third positions for all codon are preferred to pyrimidine and the most preferred codons end with A and T.