A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera
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DOI：
10.1128/jb.01202-08
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发表时间：
2009-01-01
影响因子：
3.2
通讯作者：
Petit, Marie-Agnes
中科院分区：
文献类型：
--
作者：
Deloger, Marc;El Karoui, Meriem;Petit, Marie-Agnes
生物多样性的基本单位是物种。然而，基因组测序发现了细菌种内多样性的显着程度，它揭示了需要制定明确的标准来对一个物种内的菌株进行分组。用于在基因组水平上量化种内变异的两种主要分析类型是平均核苷酸同一性（ANI），其检测核心基因组的DNA保守性，以及DNA含量，其计算两个基因组共享的DNA比例。这两种估计都是基于BLAST比对，用于定义基因组对共有的DNA序列。然而，有趣的是，使用这些方法对种内配对的结果并不相关。这促使我们开发了一个基因组距离指数，同时考虑到两个多样性标准，这是基于两个基因组共享的DNA最大唯一匹配（MUM）。MUM指数的值称为MUMi，与ANI的相关性优于与DNA含量的相关性。此外，MUMi以与常规使用的多位点序列分型树以及基于ANI的树一致的方式对菌株进行分组。我们使用MUMi来确定物种和属水平上所有可用基因组对的相关性。我们的分析揭示了当前细菌物种概念的某种一致性，因为大部分种内和属内值是明确可分离的。它还证实了一些物种比大多数物种更加多样化。由于MUMi计算速度快，它提供了在整个可用基因组数据库上测量基因组距离的可能性。
The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.