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Background  Citrus canker is a disease that has severe economic impact on the citrus industry worldwide. There are three types of canker, called A, B, and C. The three types have different phenotypes and affect different citrus species. The causative agent for type A is  Xanthomonas citri  subsp.  citri , whose genome sequence was made available in 2002.  Xanthomonas fuscans  subsp.  aurantifolii  strain B causes canker B and  Xanthomonas fuscans  subsp.  aurantifolii  strain C causes canker C.    Results  We have sequenced the genomes of strains B and C to draft status. We have compared their genomic content to  X. citri  subsp.  citri  and to other  Xanthomonas  genomes, with special emphasis on type III secreted effector repertoires. In addition to  pthA , already known to be present in all three citrus canker strains, two additional effector genes,  xopE3  and  xopAI , are also present in all three strains and are both located on the same putative genomic island. These two effector genes, along with one other effector-like gene in the same region, are thus good candidates for being pathogenicity factors on citrus. Numerous gene content differences also exist between the three cankers strains, which can be correlated with their different virulence and host range. Particular attention was placed on the analysis of genes involved in biofilm formation and quorum sensing, type IV secretion, flagellum synthesis and motility, lipopolysacharide synthesis, and on the gene  xacPNP , which codes for a natriuretic protein.    Conclusion  We have uncovered numerous commonalities and differences in gene content between the genomes of the pathogenic agents causing citrus canker A, B, and C and other  Xanthomonas  genomes. Molecular genetics can now be employed to determine the role of these genes in plant-microbe interactions. The gained knowledge will be instrumental for improving citrus canker control.

Novel insights into the genomic basis of citrus canker based on the genome sequences of two strains of Xanthomonas fuscans subsp. aurantifolii