| Summary: | <p>Abstract</p> <p>Background</p> <p>Bacterial leaf blight causes significant yield losses in rice crops throughout Asia and Africa. Although both the Asian and African strains of the pathogen, <it>Xanthomonas oryzae </it>pv. <it>oryzae </it>(<it>Xoo</it>), induce similar symptoms, they are nevertheless genetically different, with the African strains being more closely related to the Asian <it>X. oryzae </it>pv. <it>oryzicola </it>(<it>Xoc</it>).</p> <p>Results</p> <p>Changes in gene expression of the African <it>Xoo </it>strain MAI1 in the susceptible rice cultivar Nipponbare were profiled, using an SSH <it>Xoo </it>DNA microarray. Microarray hybridization was performed comparing bacteria recovered from plant tissues at 1, 3, and 6 days after inoculation (dai) with bacteria grown <it>in vitro</it>. A total of 710 bacterial genes were found to be differentially expressed, with 407 up-regulated and 303 down-regulated. Expression profiling indicated that less than 20% of the 710 bacterial transcripts were induced in the first 24 h after inoculation, whereas 63% were differentially expressed at 6 dai. The 710 differentially expressed genes were one-end sequenced. 535 sequences were obtained from which 147 non-redundant sequences were identified. Differentially expressed genes were related to metabolism, secretion and transport, pathogen adherence to plant tissues, plant cell-wall degradation, IS elements, and virulence. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. The <it>Xoo </it>MAI1 non-redundant set of sequences was compared against several <it>X. oryzae </it>genomes, revealing a specific group of genes that was present only in MAI1. Numerous IS elements were also found to be differentially expressed. Quantitative real-time PCR confirmed 86% of the identified profile on a set of 14 genes selected according to the microarray analysis.</p> <p>Conclusions</p> <p>This is the first report to compare the expression of <it>Xoo </it>genes <it>in planta </it>across different time points during infection. This work shows that as-yet-unidentified and potentially new virulence factors are appearing in an emerging African pathogen. It also confirms that African <it>Xoo </it>strains do differ from their Asian counterparts, even at the transcriptional level.</p>
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