Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), E-07190 Esporles, Spain.
Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):19126-31. doi: 10.1073/pnas.0906412106. Epub 2009 Oct 23.
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 However, now, in the era of genomics, DDH appears to be an outdated method for classification that needs to be substituted.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 approximately 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.
DNA-DNA 杂交（DDH）作为基因组水平上原核生物种界定的金标准，已经使用了近 50 年。它是唯一提供数字和相对稳定种界的分类方法，其使用对当前分类的构建产生了至关重要的影响。然而，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，因为它与 DDH 非常相似。在这里，我们检查了作为用户友好、面向生物学家的接口的 JSpecies 工作包，用于计算 ANI 和两两基因组比较之间四核苷酸特征的相关性。结果与使用 ANI 取代 DDH 一致，界限缩小到大约 95-96%。此外，JSpecies 包实现了四核苷酸特征相关指数，这是一个无需比对的参数，通常与 ANI 相关，并且可以帮助确定何时应将给定的一对生物体分类为同一物种。此外，对于分类目的，可以通过简单地随机测序查询菌株的基因组的至少 20%来进行分析，而不需要获得它们的完整序列。
