Deep transcriptome profile analysis reveals different expression patterns of Xanthomonas oryzae pv. oryzae strains
An attempt has been made to investigate gene expression patterns of three Xoo strains in XOM2, PXO99 (P6) and PXO86 (P2) from Phillipines, and GD1358 (C5) from China, which exhibited different virulence in 30 rice varieties, with putative virulence factors using deep sequencing. In total, 4759 transcripts were identified in this study, and 1151 and 3076 genes were differentially expressed when P6 compared with P2 and P6 compared with C5, respectively. Our results indicated that Xoo strains from different regions exhibited distinctly different expression patterns of putative virulence-revelent genes. Interestingly, all genes involved in chemotaxis and motility exhibited higher transcript alteration in C5 compared with P6 and P2, while the most other genes associated with the virulence, including expolysaccharide (EPS) synthesis, Hrp genes and type III effectors, including Xop effectors and transcription activator-like (TAL) effectors, down-regulation differentially expressed in C5 compared with P6 and P2. The data were confirmed by real-time quantitative RT-PCR and test experiment of bacterial motility and enzyme activity analysis of EPS and xylanase. These results highlight the complexity of the Xoo and offer new avenues for improving our understanding of Xoo-rice interactions and evolutionary of Xoo virulence. Overall design: Analyzing the transcriptome profile of 3 Xanthomonas oryzae pv. oryzae strains cultured in XOM2