Genomic insights that advance the species definition for prokaryotes
Genomic insights that advance the species definition for prokaryotes
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DOI：
10.1073/pnas.0409727102
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发表时间：
2005-02-15
影响因子：
11.1
通讯作者：
Tiedje, JM
中科院分区：
文献类型：
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作者：
Konstantinidis, KT;Tiedje, JM
为了帮助推进原核生物的物种定义，我们比较了70个密切相关和完全测序的细菌基因组的基因内容，以确定是否存在物种边界，并确定生物体的生态对其共享基因内容的作用。我们发现，两个菌株之间的共享基因的平均核苷酸同一性（ANI）是一个强大的手段来比较菌株之间的遗传相关性，ANI值约为94%，对应于传统的70% DNA-DNA重新关联的标准，目前的物种定义。在94%ANI临界值下，当前物种仅包括中度同质菌株，例如，大多数>4-Mb的基因组仅共享它们基因的65-90%，这显然是菌株在不同生态环境中进化的结果。此外，诊断遗传标记（边界）在相同物种的菌株组之间是明显的，组间遗传相似性可高达98-99% ANI，表明即使在核苷酸水平几乎相同的生物体中也可能发现合理的物种。值得注意的是，大部分，例如，高达65%的物种内基因含量的差异与噬菌体和转座酶元件有关，揭示了这些元件在细菌物种形成过程中的重要作用。我们的研究结果是一致的物种的定义，将包括一个更均匀的一组菌株比目前的定义和一个考虑生态的菌株，除了他们的进化距离。
To help advance the species definition for prokaryotes, we have compared the gene content of 70 closely related and fully sequenced bacterial genomes to identify whether species boundaries exist, and to determine the role of the organism's ecology on its shared gene content. We found the average nucleotide identity (ANI) of the shared genes between two strains to be a robust means to compare genetic relatedness among strains, and that ANI values of approximate to 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition. At the 94% ANI cutoff, current species includes only moderately homogeneous strains, e.g., most of the >4-Mb genomes share only 65-90% of their genes, apparently as a result of the strains having evolved in different ecological settings. Furthermore, diagnostic genetic signatures (boundaries) are evident between groups of strains of the same species, and the intergroup genetic similarity can be as high as 98-99% ANI, indicating that justifiable species might be found even among organisms that are nearly identical at the nucleotide level. Notably, a large fraction, e.g., up to 65%, of the differences in gene content within species is associated with bacteriophage and transposase elements, revealing an important role of these elements during bacterial speciation. Our findings are consistent with a definition for species that would include a more homogeneous set of strains than provided by the current definition and one that considers the ecology of the strains in addition to their evolutionary distance.