杨树种同义密码子使用的初步分析。

植物生理与分子生物学学报 Pub Date : 2007-08-01
Meng Zhou, Chun-Fa Tong, Ji-Sen Shi
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引用次数: 0

摘要

杨树是世界上最重要的落叶乔木树种之一,已被用作研究树木分子遗传学的重要模型系统。对密码子使用规律的分析有助于进一步认识杨树密码子分布和变异的机制以及影响密码子使用规律的因素。本文采用EN(c)图法和对应分析(COA)多元统计方法对杨树314个基因的密码子使用情况进行了分析。结果表明,主要趋势与“密码子适应指数”评价的基因表达水平呈高度负相关。此外,1轴坐标与GC3(s)含量和基因长度存在2个显著相关,推测基因核苷酸组成和基因长度对杨树密码子使用偏好也有重要影响。相对同义密码子使用(RSCU)分析结果表明,密码子的使用倾向于以a或T结尾的密码子。此外,我们比较了杨树、拟南芥、稻谷、智人和大肠杆菌的密码子偏好,发现杨树与拟南芥最相似,与大肠杆菌最不相似。本文通过对杨树高表达密码子的分析,首次确定了10个最优密码子,为杨树基因工程提供了一些有用的信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A preliminary analysis of synonymous codon usage in poplar species.

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.

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