van Berkum Peter, Terefework Zewdu, Paulin Lars, Suomalainen Sini, Lindström Kristina, Eardly Bertrand D
Soybean Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, Maryland 20705, USA.
J Bacteriol. 2003 May;185(10):2988-98. doi: 10.1128/JB.185.10.2988-2998.2003.
It is evident from complete genome sequencing results that lateral gene transfer and recombination are essential components in the evolutionary process of bacterial genomes. Since this has important implications for bacterial systematics, the primary objective of this study was to compare estimated evolutionary relationships among a representative set of alpha-Proteobacteria by sequencing analysis of three loci within their rrn operons. Tree topologies generated with 16S rRNA gene sequences were significantly different from corresponding trees assembled with 23S rRNA gene and internally transcribed space region sequences. Besides the incongruence in tree topologies, evidence that distinct segments along the 16S rRNA gene sequences of bacteria currently classified within the genera Bradyrhizobium, Mesorhizobium and Sinorhizobium have a reticulate evolutionary history was also obtained. Our data have important implications for bacterial taxonomy, because currently most taxonomic decisions are based on comparative 16S rRNA gene sequence analysis. Since phylogenetic placement based on 16S rRNA gene sequence divergence perhaps is questionable, we suggest that the proposals of bacterial nomenclature or changes in their taxonomy that have been made may not necessarily be warranted. Accordingly, a more conservative approach should be taken in the future, in which taxonomic decisions are based on the analysis of a wider variety of loci and comparative analytical methods are used to estimate phylogenetic relationships among the genomes under consideration.
从全基因组测序结果可以明显看出，横向基因转移和重组是细菌基因组进化过程中的重要组成部分。由于这对细菌系统分类学具有重要意义，本研究的主要目的是通过对rrn操纵子内三个位点进行测序分析，比较一组具有代表性的α-变形菌之间的估计进化关系。用16S rRNA基因序列生成的树形拓扑结构与用23S rRNA基因和内部转录间隔区序列组装的相应树形结构有显著差异。除了树形拓扑结构不一致外，还获得了证据表明，目前归类于慢生根瘤菌属、中生根瘤菌属和中华根瘤菌属的细菌的16S rRNA基因序列的不同片段具有网状进化历史。我们的数据对细菌分类学具有重要意义，因为目前大多数分类学决策都是基于比较16S rRNA基因序列分析。由于基于16S rRNA基因序列差异的系统发育定位可能存在疑问，我们认为已提出的细菌命名法或其分类学变化不一定合理。因此，未来应采取更保守的方法，即分类学决策基于对更广泛位点的分析，并使用比较分析方法来估计所考虑基因组之间的系统发育关系。
