杨树同义密码子用法的初步分析(英文)  

A Preliminary Analysis of Synonymous Codon Usage in Poplar Species

作　　者：周猛[1] 童春发[1] 施季森[1] 

机构地区：[1]南京林业大学国家林业局和江苏省林木遗传和基因工程重点实验室,南京210037

出　　处：《植物生理与分子生物学学报》2007年第4期285-293,共9页Journal Of Plant Physiology and Molecular Biology

基　　金：国家重点基础研究发展项目(No.TG1999016004);江苏省自然科学基金项目(No.BK2003213)资助~~

摘　　要：杨树是世界上广泛栽培的重要造林树种之一,已经成为林木基因工程研究的模式植物。用杨树的314个蛋白编码基因,通过对应分析和ENC-plot分析探讨了若干重要因子对杨树密码子用法的效应。从分析结果中可以看出,在影响最大的第一条向量轴上,基因的坐标位置与该基因的表达水平(CAI)极显著负相关(r=-0.94**),其次是与GC3S和基因长度极显著相关(r=0.86**和r=-0.57**),说明基因表达水平高低是影响密码子发挥作用的主要因素,基因编码区碱基组成和基因长度次之。ENC-plot分析结果也证明了这一点。相对密码子使用值(RSCU)的计算结果表明,高表达基因强烈偏好以A或T结尾的密码子,并确定了TTA和ATA等10个密码子为杨树的主要偏爱密码子。将杨树的密码子使用频率与拟南芥、水稻、大肠杆菌和人等不同模式生物种比较后发现,杨树密码子的偏爱性与同为双子叶植物的拟南芥最为相似,与人和大肠杆菌之间的差异较大。Poplar is among the most important deciduous tree species in plantations over the world and has been used as an important model system for molecular genetics of trees. The analysis of codon usage may improve the understanding of the mechanism of codon distribution and variation in poplar and the understanding of factors shaping the codon usage patterns. Here, an ENc （effective number of codons）-plot method and multivariate statistical method called correspondence analysis （COA） were used to examine the codon usage of 314 genes of poplar. The results show that the main trend was highly negative correlated with the gene expression level assessed by the ＂Codon Adaptation Index＂ value. Moreover, there were two significant correlations between axis 1 coordinates and GC3s content and gene length, we infer that gene nucleotide composition and gene length also play an important role in shaping the codon usage bias in poplar. The result of relative synonymous codon usage （RSCU） analysis shows a high bias of codon usage toward the codon with A or T ending. In addition, we compared the codon preferences among poplar, Arabidopsis thaliana, Oryza sative, Homo sapiens and Escherichia coli, and poplar was found to be most similar to A.thaliana and least similar to E.coli. In this paper, 10 codons defined firstly as optimal codons through an analysis of the high-expression codon in poplar may provide some useful information for genetic engineering of poplar.

关 键 词：密码子用法 对应分析 GC35含量 基因长度 基因表达水平 优越密码子 杨树 

分 类 号：Q943[生物学—植物学]