Shifting the genomic gold standard for the prokaryotic species definition
Shifting the genomic gold standard for the prokaryotic species definition
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DOI：
10.1073/pnas.0906412106
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发表时间：
2009-11-10
影响因子：
11.1
通讯作者：
Rossello-Mora, Ramon
中科院分区：
文献类型：
--
作者：
Richter, Michael;Rossello-Mora, Ramon
DNA-DNA杂交（DDH）作为原核生物在基因组水平上的金标准已经使用了近50年。它是唯一一种提供数值和相对稳定的物种边界的分类方法，它的使用对当前分类的构建产生了至关重要的影响。然而，现在，在基因组学时代，DDH似乎是一种过时的分类方法，需要被取代。两个基因组之间的平均核苷酸同一性（ANI）似乎是最有前途的方法，因为它反映了DDH密切。在这里，我们检查工作包JSpecies作为一个用户友好的，面向生物学家的界面来计算ANI和成对基因组比较之间的四核苷酸签名的相关性。结果同意使用ANI替代DDH，其具有可设定为类似于95- 96%的窄边界。此外，JSpecies软件包实现了四核苷酸特征相关性指数，这是一个无干扰的参数，通常与ANI相关，可以帮助决定何时将给定的一对生物体分类为同一物种。此外，出于分类学目的，可以通过简单地随机测序查询菌株的至少20%的基因组而不是获得其全序列来进行分析。
DNA-DNA hybridization (DDH) has been used for nearly 50 years as the gold standard for prokaryotic species circumscriptions at the genomic level. It has been the only taxonomic method that offered a numerical and relatively stable species boundary, and its use has had a paramount influence on how the current classification has been constructed. However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted. The average nucleotide identity (ANI) between two genomes seems the most promising method since it mirrors DDH closely. Here we examine the work package JSpecies as a user-friendly, biologist-oriented interface to calculate ANI and the correlation of the tetranucleotide signatures between pairwise genomic comparisons. The results agreed with the use of ANI to substitute DDH, with a narrowed boundary that could be set at similar to 95-96%. In addition, the JSpecies package implemented the tetranucleotide signature correlation index, an alignment-free parameter that generally correlates with ANI and that can be of help in deciding when a given pair of organisms should be classified in the same species. Moreover, for taxonomic purposes, the analyses can be produced by simply randomly sequencing at least 20% of the genome of the query strains rather than obtaining their full sequence.