Zhou Meng, Tong Chun-Fa, Shi Ji-Sen
The Key Laboratory of Forestry Genetics and Engineering of State Forestry Administration & Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao. 2007 Aug;33(4):285-93.
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 EN(c) (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 GC3(s) 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.
杨树是世界人工林中最重要的落叶树种之一，已被用作树木分子遗传学的重要模型系统。密码子使用情况的分析可能会增进对杨树密码子分布和变异机制的理解，以及对影响密码子使用模式的因素的理解。在此，采用有效密码子数（EN(c)）绘图法和一种称为对应分析（COA）的多元统计方法，来研究杨树314个基因的密码子使用情况。结果表明，主要趋势与通过“密码子适应指数”值评估的基因表达水平高度负相关。此外，轴1坐标与GC3(s)含量和基因长度之间存在两个显著相关性，我们推断基因核苷酸组成和基因长度在塑造杨树密码子使用偏性方面也起着重要作用。相对同义密码子使用（RSCU）分析结果显示，密码子使用对以A或T结尾的密码子存在高度偏性。此外，我们比较了杨树、拟南芥、水稻、人类和大肠杆菌之间的密码子偏好性，发现杨树与拟南芥最相似，与大肠杆菌最不相似。本文通过对杨树中高表达密码子的分析首次定义的10个密码子，可能为杨树基因工程提供一些有用信息。
