Taxonomic use of DNA G plus C content and DNA-DNA hybridization in the genomic age
Taxonomic use of DNA G plus C content and DNA-DNA hybridization in the genomic age
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DOI：
10.1099/ijs.0.056994-0
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发表时间：
2014-02-01
影响因子：
2.8
通讯作者：
Goeker, Markus
中科院分区：
文献类型：
--
作者：
Meier-Kolthoff, Jan P.;Klenk, Hans-Peter;Goeker, Markus
基因组的G+C含量经常用于物种和属的分类描述。在过去，它是用传统的间接方法测定的，但现在直接根据日益可用和负担得起的基因组序列计算DNA G+C含量是合理的。然而，预期准确度的提高可能会改变G+C含量用于得出分类结论的方式。我们在这里使用基因组数据集重新估计了文献假设，即G+C含量在物种内可以变化高达3-5%。将得到的G+C含量差异与使用GGDC网络服务器在Silico中计算的DNA DNA杂交(DDH)相似性进行比较，以70%的相似性作为物种边界的金标准阈值。结果表明，如果根据基因组序列计算，G+C含量在物种内的差异不超过1%。仅基于较大差异的统计模型就可以否定两个菌株属于同一物种的假设。由于两个非类型菌株之间的DDH相似性出现在基因组数据集中，我们还检查了在什么程度和什么条件下，这种相似性可能=70%。然而，结果表明，使用50%的边界不会影响关于DNA G+C含量的结论。因此，我们认为，物种描述中提供的G+C含量数据与基因组测序后重新计算的G+C含量数据之间的差异>；=1%是由于应用的传统方法的显著不准确，因此需要对物种描述进行校正。
The G+C content of a genome is frequently used in taxonomic descriptions of species and genera. In the past it has been determined using conventional, indirect methods, but it is nowadays reasonable to calculate the DNA G+C content directly from the increasingly available and affordable genome sequences. The expected increase in accuracy, however, might alter the way in which the G+C content is used for drawing taxonomic conclusions. We here re-estimate the literature assumption that the G+C content can vary up to 3-5% within species using genomic datasets. The resulting G+C content differences are compared with DNA DNA hybridization (DDH) similarities calculated in silico using the GGDC web server, with 70% similarity as the gold standard threshold for species boundaries. The results indicate that the G+C content, if computed from genome sequences, varies no more than 1 % within species. Statistical models based on larger differences alone can reject the hypothesis that two strains belong to the same species. Because DDH similarities between two non-type strains occur in the genomic datasets, we also examine to what extent and under which conditions such a similarity could be = 70%. However, it is shown that using a 50% boundary would not affect the conclusions regarding the DNA G+C content. Hence, we suggest that discrepancies between G+C content data provided in species descriptions on the one hand and those recalculated after genome sequencing on the other hand >= 1 % are due to significant inaccuracies of the applied conventional methods and accordingly call for emendations of species descriptions.