杨树同义密码子用法的初步分析

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。

A Preliminary Analysis of Synonymous Codon Usage in Poplar Species

Poplar is among the most important decidu- ous 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 im- prove the understanding of the mechanism of codon dis- tribution and variation in poplar and the understanding of factors shaping the codon usage patterns. Here, an ENC (effective number of codons)-plot method and mul- tivariate statistical method called correspondence analy- sis (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 be- tween 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 syn- onymous 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 sapi- ens 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 pop- lar may provide some useful information for genetic en- gineering of poplar.