Comparative genomic analysis of Pectobacterium carotovorum subsp. brasiliense SX309 provides novel insights into its genetic and phenotypic features

Abstract

Background: Pectobacterium carotovorum subsp. brasiliense is a broad host range bacterial pathogen, which causes blackleg of potatoes and bacterial soft rot of vegetables worldwide. Production of plant cell wall degrading enzymes is usually critical for Pectobacterium infection. However, other virulence factors and the mechanisms of genetic adaptation still need to be studied in detail.

Results: In this study, the complete genome of P. carotovorum subsp. brasiliense strain SX309 isolated from cucumber was compared with eight other pathogenic bacteria belonging to the Pectobacterium genus, which were isolated from various host plants. Genome comparison revealed that most virulence genes are highly conserved in the Pectobacterium strains, especially for the key virulence determinants involved in the biosynthesis of extracellular enzymes and others including the type II and III secretion systems, quorum sensing system, flagellar and chemotactic genes. Nevertheless, some variable regions of the T6SS and the CRISP-Cas immune system are unique for P. carotovorum subsp. brasiliense.

Conclusions: The extensive comparative genomics analysis revealed highly conserved virulence genes in the Pectobacterium strains. However, several variable regions of type VI secretion system and two subtype Cas mechanism-Cas immune systems possibly contribute to the process of Pectobacterium infection and adaptive immunity.

Keywords: Comparative genomic analysis; Host genetic adaptation; Pathogenicity; Pectobacterium carotovorum subsp. brasiliense.

Fig. 1

Graphical circular map of the P. carotovorum subsp. brasiliense SX309 genome performed with CGview Server. From outside to center, ring 1 and 4 show protein-coding genes oriented in the forward (colored by COG categories) and reverse (colored by COG categories) directions, respectively. Ring 2 and 3 denote genes on forward and reverse strand. Ring 5 shows G+C% content plot (black) and the inner most ring shows GC skews, where green indicates positive values and purple indicates negative values

Fig. 2

Comparison of P. carotovorum subsp. brasiliense SX309 genome sequences against other eight Pectobacterium genome sequences. a Mauve progressive alignment of SX309 genome, BC1 genome, BZA12 genome. b At subspecies level, mauve progressive alignment of SX309 genome, PCC21 genome, BC S7 genome. c At species level, mauve progressive alignment of SX309 genome, SCRI1043 genome, SCC3193 genome, CFBP 3304 genome and RNS08.42.1A genome. SX309 genome as the reference genome. Boxes with same color indicate syntenic regions. Boxes below the horizontal strain line indicate inverted regions. Rearrangements are shown by colored lines. Scale is in nucleotides. d, e and f Venn diagram showing the number of clusters of orthologous genes shared and unique at subspecies and species level

Fig. 3

Physical map of type II secretion system in Pectobacterium spp. Arrows denote putative transcriptional units. The dashed line indicates long distance in the genome

Fig. 4

Genetic organization of the T6SS major structural gene cluster in Pectobacterium spp. Colored ORF indicates the genes with known function, and the same color represents the same or similar biological function. The gene encoding uncharacterized protein is indicated by gray ORF

Fig. 5

Diagram of the clustered regularly interspaced short palindromic repeats (CRISPR) with CRISPR associated proteins (Cas) system in Pectobacterium species. Blue indicates the subtype I-F CRISPR-associated protein, orange indicates the subtype I-E CRISPR-associated protein, yellow represents CRISPR repeats