Whole-Genome-Sequence-Based Classification of pv. and Computational Analysis of the Type III Secretion System.

spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of spp. in Indonesia was originally identified as . However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized pv. () strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with and pv. () strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all strains with pv. . They formed separate clades, which included pv. , pv. , and pv. . Based on ANI, phylogenetic relationships, and pathogenicity, we designated these strains as pv. (). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic and strains, was absent in the strains. Comparison of the hrp clusters of , , and genomes revealed that HrpE in strains was very different from that in and . To determine if it was functional, we deleted the gene and complemented with the , confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in spp., in which the N-terminus of strains differs significantly from those of and strains.