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Background   Xanthomonas oryzae  pv.  oryzae  ( Xoo ) and  X. oryzae  pv.  oryzicola  ( Xoc ) are bacterial pathogens of the worldwide staple and grass model, rice.  Xoo  and  Xoc  are closely related but  Xoo  invades rice vascular tissue to cause bacterial leaf blight, a serious disease of rice in many parts of the world, and  Xoc  colonizes the mesophyll parenchyma to cause bacterial leaf streak, a disease of emerging importance. Both pathogens depend on  hrp  genes for type III secretion to infect their host. We constructed a 50–70 mer oligonucleotide microarray based on available genome data for  Xoo  and  Xoc  and compared gene expression in  Xoo  strains PXO99 A  and  Xoc  strain BLS256 grown in the rich medium PSB vs. XOM2, a minimal medium previously reported to induce  hrp  genes in  Xoo  strain T7174.    Results  Three biological replicates of the microarray experiment to compare global gene expression in representative strains of  Xoo  and  Xoc  grown in PSB vs. XOM2 were carried out. The non-specific error rate and the correlation coefficients across biological replicates and among duplicate spots revealed that the microarray data were robust. 247 genes of  Xoo  and 39 genes of  Xoc  were differentially expressed in the two media with a false discovery rate of 5% and with a minimum fold-change of 1.75. Semi-quantitative-RT-PCR assays confirmed differential expression of each of 16 genes each for  Xoo  and  Xoc  selected for validation. The differentially expressed genes represent 17 functional categories.    Conclusion  We describe here the construction and validation of a two-genome microarray for the two pathovars of  X. oryzae . Microarray analysis revealed that using representative strains, a greater number of  Xoo  genes than  Xoc  genes are differentially expressed in XOM2 relative to PSB, and that these include  hrp  genes and other genes important in interactions with rice. An exception was the  rax  genes, which are required for production of the host resistance elicitor AvrXa21, and which were expressed constitutively in both pathovars.

bmc microbiology

A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes