Synonymous codon usage and gene function are strongly related in Oryza sativa

文献类型： 外文期刊

第一作者： Liu, QP

作者： Liu, QP;Dou, SJ;Ji, ZJ;Xue, QZ

作者机构：

关键词： rice;codon usage;gene function

期刊名称：BIOSYSTEMS （ 影响因子：1.973； 五年影响因子：2.063 ）

ISSN： 0303-2647

年卷期： 2005 年 80 卷 2 期

页码：

收录情况： SCI

摘要： The relationship between codon usage and gene function was investigated while considering a dataset of 2106 nuclear genes of Oryza sativa. The results of standard X 2 test and F-statistic showed that for every 59 synonymous codons, a strongly significant association with gene functional categories existed in rice, indicating that codon usage was generally coordinated with gene function whether it was at the level of individual amino acids or at the level of nucleotides. However, it could not be directly said that the use of every codons differed significantly between any two functional categories. Notably, there existed large difference both in selection for biased codons or selection intensity among functional categories. Therefore, we identified at least two classes of genes: one group of genes, mainly belonging to the "METABOLISM" category, was tended to use G- and/or C-ending codons while the other was more biased to choose codons ending with A and/or U. The latter group contained genes of various functions, especially those genes classified into the "Nuclear Structure" category. These observations will be more important for molecular genetic engineering and genome functional annotation. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

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