A re-evaluation of the taxonomy of phytopathogenic genera Dickeya and Pectobacterium using whole-genome sequencing data

The genera Dickeya and Pectobacterium contain important plant pathogens. However, species from these genera are often poorly defined and some new isolates could not be assigned to any of the existing species. Due to their wide geographic distribution and lethality, a reliable and easy classification scheme for these pathogens is urgently needed. The low cost of next-generation sequencing has generated an upsurge of microbial genome sequences. Here, we present a phylogenomic and systematic analysis of the genera Dickeya and Pectobacterium. Eighty-three genomes from these two genera as well as two Brenneria genomes were included in this study. We estimated average nucleotide identity (ANI) and in silico DNA–DNA hybridization (isDDH) values in combination with the whole-genome-based phylogeny from 895 single-copy orthologous genes using these 85 genomes. Strains with ANI values of ≥96% and isDDH values of ≥70% were consistently grouped together in the phylogenetic tree. ANI, isDDH, and whole-genome-based phylogeny all support the elevation of Pectobacterium carotovorum's four subspecies (actinidiae, odoriferum, carotovorum, and brasiliense) to the species level. We also found some strains could not be assigned to any of the existing species, indicating these strains represent novel species. Furthermore, our study revealed at least ten tested genomes from these genera were misnamed in GenBank. This work highlights the potential of using whole genome sequences to re-evaluate current prokaryotic species definition and establish a unified prokaryotic species definition frame for taxonomically challenging genera.