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13种植物actin基因的密码子使用特性分析
作者: 赵 洋  杨培迪  刘 振  成 杨  杨 阳*  
单位: (湖南省农业科学院 茶叶研究所  长沙 410125)  
关键词: actin基因  密码子用法  密码子偏性  
分类号:Q943.2
出版年,卷(期):页码:2016 ,47 ( 4 ): 页码:519-523
摘要:

【目的】分析13种植物actin基因的密码子组成、密码子偏性及聚类关系,了解其密码子使用模式及影响密码子使用的因素,为深入研究分子进化及物种进化提供参考。【方法】运用CodonW 1.4.4软件分析13种植物的肌动蛋白基因(actin)密码子组成及使用参数,并对影响密码子偏性的因素进行研究。应用MEGA 4.1对13条基因的CDS序列进行聚类分析,采用SPSS 20.0进行密码子偏性的聚类分析。【结果】双子叶植物中actin基因的GC含量为45.0%~51.2%、GC3s含量为36.3%~53.8%,单子叶植物中GC含量为53.0%~58.3%、GC3s含量为60.9%~75.8%;actin基因在单子叶植物中偏爱G/C结尾的密码子,双子叶植物中偏爱A/T结尾的密码子。GC和GC3s与有效密码子数(ENC)呈极显著负相关(P<0.01),相关系数均为-0.906。ENC绘图分析结果表明,actin基因密码子偏性同时受突变和选择压力影响,单子叶植物受选择压力影响的程度大于双子叶植物。基于actin基因密码子偏性的聚类将单子叶植物高粱、玉米聚为一类,水稻、大麦、竹聚为一类,8种双子叶植物聚为一类。【结论】actin基因密码子偏性与碱基组成密切相关,其密码子偏性在单、双子叶植物间存在差异,依据密码子偏性的聚类能在一定程度上反映物种间的亲缘关系。

【Objective】In order to provide a reference for further research on molecular evolution and species evolution, the codon composition, usage bias and clustering of actin genes for 13 species of plants were analyzed to study condon usage patterns and factors affecting codon usage. 【Method】Using CodonW 1.4.4 software, the condon composition and usage of actin genes for 13 species of plants were studied, and the factors that affected the codon bias were analyzed. And then the clustering analysis of codon usage bias was conducted by SPSS 20.0 software, and the CDSs of 13 actin genes were clustered and analyzed using MEGA 4.1 software. 【Result】The results showed that, in the dicots, the GC content of actin gene was 45.0%-51.2%, and GC3s content was 36.3%-53.8%. In monocots, GC content was 53.0%-58.3% and GC3s content was 60.9%-75.8%. The actin genes preferred to codons ending with C/G in monocots, but preferred to codons ending with A/T in dicots. GC and GC3s were extremely significant negative correlation with effective number of codon(ENC)(P<0.01), with correlation coefficient of -0.906. ENC plot results showed that the codon usage bias of actin gene was influenced by mutation and natural selection pressure, and the influence of selective pressure on monocots was greater than that on dicots. Based on clustering analysis of codon usage bias, sorghum and maize were clustered into one cluster, rice, barley and bamboo were clustered into one cluster, the 8 dicots were clustered into another cluster. 【Conclusion】The codon usage bias of actin gene is closely related to base composition. And there were some difference in codon usage bias of actin gene between monocots and dicots. Clustering analysis results based on codon usage bias can reflect phylogenetic relationships among species to a certain extent.

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