Abstract
BackgroundPectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid subspecies, P. carotovorum subsp. brasiliense (Pcb), P. carotovorum subsp. carotovorum (Pcc), and P. carotovorum subsp. odoriferum (Pco).ResultsThirty-two P. carotovorum strains had their whole genomes sequenced, including the first complete genome of Pco and another circular genome of Pcb, as well as the high-coverage genome sequences for 30 additional strains covering Pcc, Pcb, and Pco. In combination with 52 other publicly available genome sequences, the comparative genomics study of P. carotovorum and other four closely related species P. polaris, P. parmentieri, P. atrosepticum, and Candidatus P. maceratum was conducted focusing on CRISPR-Cas defense systems and pathogenicity determinants. Our analysis identified two CRISPR-Cas types (I-F and I-E) in Pectobacterium, as well as another I-C type in Dickeya that is not found in Pectobacterium. The core pathogenicity factors (e.g., plant cell wall-degrading enzymes) were highly conserved, whereas some factors (e.g., flagellin, siderophores, polysaccharides, protein secretion systems, and regulatory factors) were varied among these species and/or subspecies. Notably, a novel type of T6SS as well as the sorbitol metabolizing srl operon was identified to be specific to Pco in Pectobacterium.ConclusionsThis study not only advances the available knowledge about the genetic differentiation of individual subspecies of P. carotovorum, but also delineates the general genetic features of P. carotovorum by comparison with its four closely related species, thereby substantially enriching the extent of information now available for functional genomic investigations about Pectobacterium.
Highlights
Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt
We focus our studies on genome-level variation in known virulence factors such as Plant Cell Wall Degrading Enzymes (PCWDEs), secretion systems, flagellin, siderophores, and polysaccharides, as well as CRISPR-Cas systems, in genus Pectobacterium, and especially in the heterogeneous species P. carotovorum in order to improve our understanding of the genetic basis for pathogenicity in general
We found that several genomic features that distinguish these Chinese P. carotovorum subsp. odoriferum (Pco) strains from others: the genomes of these Pco strains are the largest in size, have the lowest GC content, and have the least number of both tandem repeats and minisatellite DNA sequences compared with these Chinese P. carotovorum subsp. carotovorum (Pcc) and P. carotovorum subsp. brasiliense (Pcb) strains (Fig. 1c, d, and e)
Summary
Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases of important crops and ornamental plants including soft rot, blackleg, and stem wilt. P. carotovorum is a genetically heterogeneous species consisting of three valid subspecies, P. carotovorum subsp. Pectobacterium spp. are necrotrophic bacterial plant pathogens of the family Pectobacteriaceae, responsible for a wide spectrum of diseases (including soft rot, blackleg, and stem wilt) of important crops and ornamental plants worldwide [1]. We focus our studies on genome-level variation in known virulence factors such as Plant Cell Wall Degrading Enzymes (PCWDEs), secretion systems, flagellin, siderophores, and polysaccharides, as well as CRISPR-Cas systems, in genus Pectobacterium, and especially in the heterogeneous species P. carotovorum in order to improve our understanding of the genetic basis for pathogenicity in general
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