Background: The bacterial species Xanthomonas campestris infects a wide
range of Brassicaceae. Specific pathovars of this species cause black rot
(pv. campestris), bacterial blight of stock (pv. incanae) or bacterial
leaf spot (pv. raphani).
Results: In this study, we extended the genomic coverage of the species by
sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R
and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named
barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome
at the species level, the core type III effectome was limited to only three putative
type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector
proteins are injected inside the plant cells by the type III secretion system and
contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy
was adopted in order to experimentally refine genome annotation for strain CFBP 5828R.
This approach also allowed the experimental definition of novel ORFs and non-coding RNA
transcripts. Using a constitutively active allele of hrpG, a master regulator of
the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with
the type III secretion system was identified. Importantly, all these genes but seven are
positively regulated by HrpG and 56 of those encode components of the Hrp type III
secretion system and putative effector proteins.
Conclusions: This dataset is an important resource to mine for novel type III
effector proteins as well as for bacterial genes which could contribute to pathogenicity
of X. campestris.
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