Soft-rot Enterobacteriaceae (SRE), typified by Pectobacterium and Dickeya genera, are phytopathogenic bacteria inflicting soft-rot disease in crops worldwide. By combining genomic information from 100 SRE with whole-transcriptome data sets, we identified novel genomic and transcriptional associations among key pathogenicity themes in this group. Comparative genomics revealed solid linkage between the type I secretion system (T1SS) and the carotovoricin bacteriophage (Ctv) conserved in 96.7% of Pectobacterium genomes. Moreover, their coactivation during infection indicates a novel functional association involving T1SS and Ctv. Another bacteriophage-borne genomic region, mostly confined to less than 10% of Pectobacterium strains, was found, presumably comprising a novel lineage-specific prophage in the genus. We also detected the transcriptional coregulation of a previously predicted toxin/immunity pair (WHH and SMI1_KNR4 families), along with the type VI secretion system (T6SS), which includes hcp and/or vgrG genes, suggesting a role in disease development as T6SS-dependent effectors. Further, we showed that another predicted T6SS-dependent endonuclease (AHH family) exhibited toxicity in ectopic expression assays, indicating antibacterial activity. Additionally, we report the striking conservation of the group 4 capsule (GFC) cluster in 100 SRE strains which consistently features adjacently conserved serotype-specific gene arrays comprising a previously unknown organization in GFC clusters. Also, extensive sequence variations found in gfcA orthologs suggest a serotype-specific role in the GfcABCD machinery.
Supplemental file 1: Overall synteny among strains (Fig. S1); gene conservation (Fig. S2); representativeness of serotype-specific block sizes within GFC region in SRE genomes (Fig. S3); sequence alignment (Fig. S4).
Supplemental file 2: Differential expression summaries of Pcb1692 and D. dadantii during in planta infection (Table S1).
Supplemental file 3: Gene neighborhood screenings and differential expression summary of T6SS elements in Pcb1692 (Table S2).
Supplemental file 4: Identification, gene neighborhood screening, and differential expression of carotovoricin in SRE (Table S3).
Supplemental file 5: Conservation and differential expression of PcbPr1 bacteriophage in Pcb1692 (Table S4).
Supplemental file 6: Differential expression of R. solanacearum Rasop1 and -2 prophages during infection (Table S5).
Supplemental file 7: Conservation, annotation, and gene-neighborhood screenings of GFC regions in SRE (Table S6).
Supplemental file 8 : Species abbreviations and genome build accessions (Table S7).