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Background  Citrus canker is a disease caused by the phytopathogens  Xanthomonas citri  subsp.  citri ,  Xanthomonas fuscans  subsp.  aurantifolli  and  Xanthomonas alfalfae  subsp.  citrumelonis . The first of the three species, which causes citrus bacterial canker type A, is the most widely spread and severe, attacking all citrus species. In Brazil, this species is the most important, being found in practically all areas where citrus canker has been detected. Like most phytobacterioses, there is no efficient way to control citrus canker. Considering the importance of the disease worldwide, investigation is needed to accurately detect which genes are related to the pathogen-host adaptation process and which are associated with pathogenesis.    Results  Through transposon insertion mutagenesis, 10,000 mutants of  Xanthomonas citri  subsp.  citri  strain 306 (Xcc) were obtained, and 3,300 were inoculated in Rangpur lime ( Citrus limonia ) leaves. Their ability to cause citrus canker was analyzed every 3 days until 21 days after inoculation; a set of 44 mutants showed altered virulence, with 8 presenting a complete loss of causing citrus canker symptoms. Sequencing of the insertion site in all 44 mutants revealed that 35 different ORFs were hit, since some ORFs were hit in more than one mutant, with mutants for the same ORF presenting the same phenotype. An analysis of these ORFs showed that some encoded genes were previously known as related to pathogenicity in phytobacteria and, more interestingly, revealed new genes never implicated with  Xanthomonas  pathogenicity before, including hypothetical ORFs. Among the 8 mutants with no canker symptoms are the  hrpB4  and  hrpX  genes, two genes that belong to type III secretion system (TTSS), two hypothetical ORFS and, surprisingly, the  htrA  gene, a gene reported as involved with the virulence process in animal-pathogenic bacteria but not described as involved in phytobacteria virulence. Nucleic acid hybridization using labeled cDNA probes showed that some of the mutated genes are differentially expressed when the bacterium is grown in citrus leaves. Finally, comparative genomic analysis revealed that 5 mutated ORFs are in new putative pathogenicity islands.    Conclusion  The identification of these new genes related with Xcc infection and virulence is a great step towards the understanding of plant-pathogen interactions and could allow the development of strategies to control citrus canker.

New genes of Xanthomonas citri subsp. citri involved in pathogenesis and adaptation revealed by a transposon-based mutant library