Whole genome sequence-based classification of Xanthomonas euvesicatoria pv.

Xanthomonas species infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as Xanthomonas perforans. However, the strains failed to elicit a hypersensitive response (HR) on either tomato or pepper. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves failed to grow to significant levels in comparison to well characterized X. euvesicatoria pv. perforans (Xp) strains. We sequenced the whole genome of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomato and pepper. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effectors, XopD, present in all plant pathogenic Xp and Xeu strains, were absent in the Xee strains. Comparison of the hrp cluster of Xee, Xp and Xeu genomes, revealed that hrpE in Xee strains was very different from that of Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has hypervariable N-terminus in Xanthomonas spp. in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.