Abstract
The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.
Highlights
Numerous definitions of prokaryotic species and methods to divide prokaryotes into distinct, discrete groups have been proposed (Cohan, 2002)
To further study the observed separation of the plus- and minus-groups, we considered a joint pangenome of P. marinus and a monophyletic clade of eight Synechococcus strains as an outgroup (Figures 2B,C, Supplementary Table S1)
To further test our approach, we considered three known cases where some strains in a species traditionally had been grouped into a different species or even a genus due to their medical importance: Yersinia pestis/pseudotuberculosis, Burkholderia mallei/pseudomallei and Shigella spp./E. coli (Supplementary Tables S4, S6, S7) (Liguori et al, 2011; Gordienko et al, 2013; Zimbler et al, 2015)
Summary
Numerous definitions of prokaryotic species and methods to divide prokaryotes into distinct, discrete groups have been proposed (Cohan, 2002). Approaches were based on phenotypic features of prokaryotes, and various phenotypic databases were compiled, e.g., the Bergey’s Manual of Systematic Bacteriology (Krieg and Holt, 1984) so that each new strain could be characterized based on its phenotype and assigned to a taxonomic group, with a species name assigned after publication in a specialized journal (Funke et al, 1997; Ramasamy et al, 2014; Mohr et al, 2018; Sun et al, 2018). The first formal criterion based on the percentage of DNA–DNA hybridization was proposed by Wayne et al in 1987 (Wayne et al, 1987). By this definition, organisms with 70% DNA hybridization belong to the same species. It became possible to consider phylogenetic trees based on 16S rRNA sequence alignments (Wang et al, 2007), pioneered by Woese et al (Woese et al, 1985; Woese, 1987)
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