Towards a genome-based taxonomy for prokaryotes
Towards a genome-based taxonomy for prokaryotes
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DOI：
10.1128/jb.187.18.6258-6264.2005
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发表时间：
2005-09-01
影响因子：
3.2
通讯作者：
Tiedje, JM
中科院分区：
文献类型：
--
作者：
Konstantinidis, KT;Tiedje, JM
在原核生物分类学中，高于物种的等级主要是基于16 S rRNA基因序列的系统发育分析来指定的，但等级之间的绝对相关性（通过16 S rRNA或其他方法测量）没有明确的标准。因此，仍然不知道不同生物之间的排名有多大可比性。为了深入了解这个问题，我们研究了175个完全测序的菌株的共享基因含量和遗传相关性之间的关系，使用共享基因的平均氨基酸同一性（AAI）作为相关性的可靠指标。我们的研究结果表明，相邻的等级（例如，门与纲）在分组生物的遗传和基因内容相关性方面经常显示出广泛的重叠，因此，当前系统在这方面的预测能力有限。非相邻列之间的重叠（例如，门与科）通常是有限的，并归因于分类学的明显不一致。除了提供标准化分类的手段，我们的AAI为基础的方法提供了一种手段来评估的鲁棒性的替代遗传标记系统发育的目的。例如，23 S rRNA基因被发现是与16 S rRNA基因一样好的标记，而几个广泛分布的蛋白质编码基因，如RNA聚合酶和促旋酶亚基，显示出强烈的系统发育信号，尽管不如rRNA基因强（蛋白质编码基因为0.78 > R-2 > 0.69，rRNA基因为R-2 = 0.84）。这里概述的AAI方法可以为所有微生物的基于基因组的分类做出重大贡献。
The ranks higher, than the species in the prokaryotic taxonomy are primarily designated based on phylogenetic analysis of the 16S rRNA gene sequences, but no definite standards exist for the absolute relatedness (measured by 16S rRNA or other means) between the ranks. Accordingly, it remains unknown how comparable the ranks are between different organisms. To gain insights into this question, we studied the relationship between shared gene content and genetic relatedness for 175 fully sequenced strains, using as a robust measure of relatedness the average amino acid identity (AAI) of the shared genes. Our results reveal that adjacent ranks (e.g., phylum versus class) frequently show extensive overlap in terms of genetic and gene content relatedness of the grouped organisms, and hence, the current system is of limited predictive power in this respect. The overlap between nonadjacent ranks (e.g., phylum versus family) is generally limited and attributable to clear inconsistencies of the taxonomy. In addition to providing means for standardizing taxonomy, our AAI-based approach provides a means to evaluate the robustness of alternative genetic markers for phylogenetic purposes. For instance, the 23S rRNA gene was found to be as good a marker as the 16S rRNA gene, while several of the widely distributed protein-coding genes, such as the RNA polymerase and gyrase subunits, show a strong phylogenetic signal, albeit less strong than the rRNA genes (0.78 > R-2 > 0.69 for the protein-coding genes versus R-2 = 0.84 for the rRNA genes). The AAI approach outlined here could contribute significantly to a genome-based taxonomy for all microbial organisms.