【作者】 郭玉平； 郭显； 周佳佳； 桂丽娟； 孙觅真； 袁延超； 邢会贤； 伊海法； 王丽媛； 宋宪亮； 孙学振；

【机构】 山东农业大学农学院/作物生物学国家重点实验室；

【摘要】 利用CodonW软件对棉花1 3个A、D基因组二倍体棉种和2个异源四倍体棉种的核基因组蛋白编码序列进行了同义密码子偏爱性分析。结果表明,不同棉种的密码子碱基构成相似,而且使用T结尾的频率高于A,使用C结尾的频率高于G,即密码子第三位碱基上嘧啶出现频率高于嘌呤。RSCU值分析表明不同棉种在密码子选用上存在明显的偏爱性,并且这种偏爱性在不同棉种间存在较高的一致性;确定了在1 5个棉种中通用的20个高频密码子,并通过比较两个高低偏性库密码子的RSCU值,确定出15个棉种的15个最优密码子(Preferred codon)(△RSCU≥0.3)。ENC-plot分析表明密码子偏性用法主要由突变和选择共同作用所致,其中选择起主导作用。与前人研究比较发现,陆地棉核基因组与叶绿体基因组在涉及8种氨基酸的高频密码子上和最优密码子上存在较大差异。15个棉种基于RSCU值的聚类分析的结果与传统分类方法的结果有很好的一致性。更多还原

【Abstract】 Synonymous codon usage bias(SCUB) of coding DNA sequences of proteins in nuclear genome of 13 diploid(A,D genome) and 2 allotetraploid(AD genome) cotton species were analyzed by CodonW program.The results showed that 15 cotton species have similar base composition of codons which possess more pyrimidines(A and C) than purines(T and G) at the third codon position.Relative synonymous codon usage analyses(RSCU) found significant and highly concurrent codon usage bias among the 15 cotton species.Twenty high frequency codons were used universally in 15 cotton species.Inconsistent with such concurrence,quite different preferred codons(ARSCU≧O.3) were determined among the 15 cotton species. Compared with a previous study(Shang et al,2011),the nuclear genome and chloroplast genome showed similar codon composition especially at the third codon position but quite different high-frequency codons of 8 amino acids.ENC-plot analysis indicated that the SCUB is related to mutation and selection,in which selection plays a leading role.The relationship of the 15 cotton species revealed by cluster analysis based on RSCU value was highly consistent with their taxonomic results widely accepted,suggesting the codon usage bias pattern could reflect the relationship of the origin and evolution of different cotton species at a certain degree.更多还原