Pathovar-Specific Genomic Features and Effector Diversity of Thai Xanthomonas Strains Causing Bacterial Spot Disease

Abstract
Xanthomonas euvesicatoria pv. euvesicatoria (Xee) and pv. perforans (Xep) are important bacterial pathogens causing bacterial spot disease in tomato and pepper. In this study, we analysed a total of 47 genomes, including 25 Thai Xee, 20 Thai Xep, and the reference strains Xee 85-10 and Xep 91-118, to investigate pathovar differentiation using core genome SNP phylogeny, homologous recombination analysis, effector profiles, and prophage content. The core SNP-based phylogeny and recombination-corrected maximum likelihood tree clearly separated Xee and Xep strains into distinct clades. Homologous recombination analysis revealed that Xee strains exhibited a higher frequency and broader distribution of recombination events compared to Xep. Most strains showed consistency between effector profiles and core SNP phylogeny, supporting their shared evolutionary background. However, strain DOA1686 was genetically distinct from other Xee strains and carried XopC2 and XopAV1, which are typically found in Xep, as well as a unique effector, XopBB, not previously reported in strains causing bacterial spot. Moreover, prophage analysis indicated limited diversity and no association with phylogenetic structure, suggesting a minimal role in lineage differentiation. In addition, the absence of AvrBsT in two Xep strains isolated from pepper may be associated with host range expansion. These findings provide insight into the genomic variation and evolutionary relationships among Thai Xanthomonas, supporting future applications in resistance breeding and regional disease management strategies.