Abstract: Isolated nucleic acid molecules which are characteristic of pathogenic strains of Xanthomonas are described, as are variants. The variants demonstrate modified virulence as compared to reference sequences, and permit one to connect virulence with specific portions of the genome of Xanthomonas. Proteins encoded by these sequences, as well as other aspects of the invention including recombinant cells, expression vectors, and diagnostic assays, are also disclosed.