Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method
Analysis of nucleotide distribution in the genome of Streptomyces coelicolor A3(2) using the Z curve method
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DOI：
10.1016/s0014-5793(03)00263-1
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发表时间：
2003-04-10
期刊：
影响因子：
3.5
通讯作者：
Zhang, CT
中科院分区：
文献类型：
--
作者：
Ou, HY;Guo, FB;Zhang, CT
用Z曲线法分析了天蓝色链霉菌A3(2)基因组中全部33527个开放阅读框(ORF)(大于或等于300bp)的核苷酸分布。每个ORF被映射到9维空间中的一个点上。为了可视化映射点的分布，基于主成分分析将映射点投影到主平面上。因此，主平面上的33527个点的分布格局呈花状，其中有7个明显的区域。除了中心区，中心周围还有六个花瓣状区域，其中一个对应于7172个编码序列。中心区和其余5个花瓣状区分别对应于基因间序列和框外非编码ORF。结果表明，选择压力对三个密码子的G+C含量产生了显著的偏向，导致了观察到的有趣现象。G+C含量较高的其他细菌基因组也存在类似现象，如铜绿假单胞菌PA01(G+C=66.6%)。而枯草芽孢杆菌(G+C=43.5%)和产气荚膜梭菌(G+C=28.6%)的基因组则没有观察到类似的现象。这一发现可能有助于改进高G+C含量基因组的基因寻找算法。网站http：//tubi.tju.edu.cn/Highgc/提供了一套补充材料，其中包括显示12种原核生物中ORFs的基本分布模式的曲线图。(C)2003年，埃尔塞维尔科学公司代表欧洲生化学会联合会出版。
The nucleotide distribution of all 33 527 open reading frames (ORFs) (greater than or equal to 300 bp) in the genome of Streptomyces coelicolor A3(2) has been analyzed using the Z curve method. Each ORF is mapped onto a point in a 9-dimensional space. To visualize the distribution of mapping points, the points are projected onto the principal plane based on principal component analysis. Consequently, the distribution pattern of the 33 527 points in the principal plane shows a flower-like shape, in which there are seven distinct regions. In addition to the central region, there are six petal-tike regions around the center, one of which corresponds to 7172 coding sequences. The central region and the remaining five petal-like regions correspond to the intergenic sequences and out-of-frame non-coding ORFs, respectively. It is shown that selective pressure produces a remarkable bias of the G+C content among three codon positions, resulting in the interesting phenomenon observed. A similar phenomenon is also observed for other bacterial genomes with high genomic G+C content, such as Pseudomonas aeruginosa PA01 (G+C = 66.6%). However, for the genomes of Bacillus subtilis (G+C = 43.5%) and Clostridium perfringens (G+C = 28.6%), no similar phenomenon was observed. The finding presented here may be useful to improve the gene-finding algorithms for genomes with high G+C content. A set of supplementary materials including the plots displaying the base distribution patterns of ORFs in 12 prokaryotes is provided on the website http:// tubic.tju.edu.cn/highGC/. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.