Description of Xanthomonas hortorum subsp. lycopersiciseminum
Seed transmission of bacterial plant pathogens is a major concern in the tomato (Solanum lycopersicum) industry. Routine testing of tomato seed at the Naktuinbouw in the Netherlands resulted in the isolation of two bacterial strains from separate seedlots. Whole-genome sequencing revealed that the strains shared 99.9% average nucleotide identity (ANI) with each other and slightly more than 95% with Xanthomonas hortorum type strain CFBP 4925T. Phylogenies based on multi-locus sequence analysis and core-genome comparisons placed the two strains within X. hortorum, though in a clade separate from all other existing pathovars. Both strains induced a typical hypersensitive reaction in tomato but were non-pathogenic when tested on other known hosts of X. hortorum. Interestingly, whole-genome sequence analysis revealed a complete type III secretion system (T3SS) and several type III effectors (T3Es), including xopJ4, which is also present in the tomato pathogen, X. euvesicatoria pv. perforans (Xp). Considering their non-pathogenic phenotype and clear genomic and phylogenetic separation from other X. hortorum strains, we formally propose the designation of these tomato seed-associated strains as a novel subspecies: Xanthomonas hortorum subsp. lycopersiciseminum subsp. nov. (ly.co.per.si.ci. se'mi.num. N.L. n. lycopersici seminum, of tomato seeds), with strain NBC5720T (LMG 33367 = NCPPB 4763) designated as the type strain. In addition, to enhance taxonomic resolution within the species, we propose the creation of two additional subspecies of X. hortorum, X. hortorum subsp. hortorum comb. nov., which contains the type strain of the species-hederae, and X. hortorum subsp. cynarae subsp.  nov., which contains strains belonging to pathovars cynarae, gardneri, taraxaci, and vitians.