In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas.
In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas.
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DOI：
10.3389/fmicb.2017.01296
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发表时间：
2017
影响因子：
5.2
通讯作者：
Gan HM
中科院分区：
文献类型：
--
作者：
Tran PN;Savka MA;Gan HM
假单胞菌属是细菌王国中物种多样性最大的一种。到目前为止，它的分类仍在修订和更新中。由于在物种水平上的程序不标准化和阈值不明确，主要基于16S rRNA基因或传统的生化分析，公开获得的假单胞菌基因组的物种鉴定仍然存在问题。在这项研究中，我们对所有带有物种标识的假单胞菌基因组（不包括定义明确的铜绿假单胞菌）进行了大规模分析，并通过计算机基因组-基因组杂交和/或与有效型种的遗传比较重新评估了它们的分类。对373个假单胞菌基因组进行了分析，并随后聚类为145个不同的基因种。根据与型菌株的平均核苷酸身份多位点序列分型（MLST）序列相似性，共检测出207个错误标记，并将43个纠正为正确的种。令人惊讶的是，超过一半的最初被指定为丁香假单胞菌和荧光假单胞菌的基因组应该被归类为以前描述的物种或新的基因物种。值得注意的是，在synxantha-P之间观察到较高的成对平均核苷酸一致性（bbb95 %），表明物种水平的相似性。libanensis， P.耐寒性。oryzihabitans和P. kilonensis- P. brassicacearum，以前是基于常规生化测试和/或基因组-基因组杂交技术进行区分的。
The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans–P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.