LAUSR

Bacterial spot disease, caused by Xanthomonas species, is a significant threat to tomato and pepper production worldwide. This study aims to characterise these pathogens and evaluate their genomic diversity in Thailand. Sixty bacterial strains were isolated from symptomatic tomatoes and peppers across Thailand from 1987 to 2022. Morphological, physiological, biochemical, pathological and species‐specific PCR analyses identified these strains as X. euvesicatoria pv. euvesicatoria (Xee) and X. euvesicatoria pv. perforans (Xep). Genome sequence analysis, including pairwise average nucleotide identity (ANI) and in silico DNA–DNA hybridisation (isDDH), revealed high genetic similarity to Xee‐ and Xep‐type strains, with ANI values above 98.6% and isDDH values higher than 97%. ANI values exceeding 99% supported distinguishing pathovars within X. euvesicatoria. Core genome phylogeny of 60 Thai Xanthomonas genomes and 121 Xanthomonas genomes from GenBank (NCBI) showed that 30 Thai strains clustered with Xee strains, while 29 clustered with Xep strains. The pan‐genome analysis of these Xanthomonas strains further supported the core genome phylogeny. Additionally, individual core genome phylogeny categorised the Thai strains into three groups within Xee and three groups within Xep, some of which correlate to geographical location. The pan‐genome of individual Xee and Xep strains contains 8222 and 8413 predicted genes, respectively, with 61.3% and 61.8% identified as accessory genes, reflecting the genetic diversity within species. These findings offer valuable insights into the genetic diversity of Xee and Xep strains in Thailand, contributing to the development of more effective disease management strategies.