Coenye Tom, Vandamme Peter
Laboratorium voor Microbiologie, Ghent University, Gent, Belgium.
Syst Appl Microbiol. 2004 Mar;27(2):175-85. doi: 10.1078/072320204322881790.
In this study we investigated the correlation between dinucleotide relative abundance values (the genomic signature) obtained from bacterial whole-genome sequences and two parameters widely used for bacterial classification, 16S rDNA sequence similarity and DNA-DNA hybridisation values. Twenty-eight completely sequenced bacterial genomes were included in the study. The correlation between the genomic signature and DNA-DNA hybridisation values was high and taxa that showed less than 30% DNA-DNA binding will in general not have dinucleotide relative abundance dissimilarity (delta*) values below 40. On the other hand, taxa showing more than 50% DNA-DNA binding will not have delta* values higher than 17. Our data indicate that the overall correlation between genomic signature and 16S rDNA sequence similarity is low, except for closely related organisms (16S rDNA similarity >94%). Statistical analysis of delta* values between different subgroups of the Proteobacteria indicate that the beta- and gamma-Proteobacteria are more closely related to each other than to the other subgroups of the Proteobacteria and that the alpha- and epsilon-Proteobacteria form clearly separate subgroups. Using the genomic signature we have also predicted DNA-DNA binding values for fastidious or unculturable endosymbionts belonging to the genera Rickettsia, Wigglesworthia and Buchnera.
在本研究中，我们调查了从细菌全基因组序列获得的二核苷酸相对丰度值（基因组特征）与广泛用于细菌分类的两个参数之间的相关性，这两个参数分别是16S rDNA序列相似性和DNA-DNA杂交值。本研究纳入了28个已完成全测序的细菌基因组。基因组特征与DNA-DNA杂交值之间的相关性很高，DNA-DNA结合率低于30%的分类单元，其二核苷酸相对丰度差异（δ*）值通常不会低于40。另一方面，DNA-DNA结合率高于50%的分类单元，其δ值不会高于17。我们的数据表明，除了亲缘关系密切的生物（16S rDNA相似性>94%）外，基因组特征与16S rDNA序列相似性之间的总体相关性较低。对变形菌门不同亚群之间的δ值进行统计分析表明，β-变形菌和γ-变形菌彼此之间的关系比它们与变形菌门的其他亚群更为密切，而α-变形菌和ε-变形菌形成了明显独立的亚群。利用基因组特征，我们还预测了属于立克次氏体属、维氏菌属和布赫纳氏菌属的苛求或不可培养内共生菌的DNA-DNA结合值。
