Whole-Genome Sequences of Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors.

Multiple species of cause bacterial spot of tomato (BST) and pepper. We sequenced five strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing . We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating from , both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of . Sequence analysis of all the publicly available and strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and strains and >99.6% among the LMG strains and a subset of strains. These results suggest that and should be considered a single species. ANI values between strains of subsp. citrumelonis, , and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as . Analysis of the newly sequenced strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional -specific T3 effectors among the causal agents of BST, orthologs of and , and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from this study supports the finding that T3 effector repertoire and host range are fundamental for the study of host-microbe interaction but of little relevance to bacterial speciation.