Nakashima H, Ota M, Nishikawa K, Ooi T
School of Health Sciences, Faculty of Medicine, Kanazawa University, Japan.
DNA Res. 1998 Oct 30;5(5):251-9. doi: 10.1093/dnares/5.5.251.
A set of 16 kinds of dinucleotide compositions was used to analyze the protein-encoding nucleotide sequences in nine complete genomes: Escherichia coli, Haemophilus influenzae, Helicobacter pylori, Mycoplasma genitalium, Mycoplasma pneumoniae, Synechocystis sp., Methanococcus jannaschii, Archaeoglobus fulgidus, and Saccharomyces cerevisiae. The dinucleotide composition was significantly different between the organisms. The distribution of genes from an organism was clustered around its center in the dinucleotide composition space. The genes from closely related organisms such as Gram-negative bacteria, mycoplasma species and eukaryotes showed some overlap in the space. The genes from nine complete genomes together with those from human were discriminated into respective clusters with 80% accuracy using the dinucleotide composition alone. The composition data estimated from a whole genome was close to that obtained from genes, indicating that the characteristic feature of dinucleotides holds not only for protein coding regions but also noncoding regions. When a dendrogram was constructed from the disposition of the clusters in the dinucleotide space, it resembled the real phylogenetic tree. Thus, the distinct feature observed in the dinucleotide composition may reflect the phylogenetic relationship of organisms.
使用一组16种二核苷酸组成来分析9个完整基因组中的蛋白质编码核苷酸序列，这些基因组包括：大肠杆菌、流感嗜血杆菌、幽门螺杆菌、生殖支原体、肺炎支原体、聚球藻属、詹氏甲烷球菌、嗜热栖热菌和酿酒酵母。不同生物体之间的二核苷酸组成存在显著差异。生物体的基因分布在二核苷酸组成空间中围绕其中心聚集。来自亲缘关系较近的生物体（如革兰氏阴性菌、支原体物种和真核生物）的基因在该空间中显示出一些重叠。仅使用二核苷酸组成，就能以80%的准确率将来自9个完整基因组以及人类的基因区分到各自的簇中。从整个基因组估计的组成数据与从基因获得的数据相近，这表明二核苷酸的特征不仅适用于蛋白质编码区域，也适用于非编码区域。当根据二核苷酸空间中簇的分布构建树形图时，它类似于真实的系统发育树。因此，在二核苷酸组成中观察到的独特特征可能反映了生物体的系统发育关系。
