Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight, is a major threat to rice productivity. Here, we performed RNA-Seq based transcriptomic analysis of Xoo transcripts isolated under in planta growth (on both susceptible and resistant hosts) and in vitro culture conditions. Our in planta extraction method resulted in successful enrichment of Xoo cells and provided RNA samples of high quality. A total of 4,619 differentially expressed genes were identified between in planta and in vitro growth conditions. The majority of the differentially expressed genes identified under in planta growth conditions were related to the nutrient transport, protease activity, stress tolerance, and pathogenicity. Among them, over 1,300 differentially expressed genes were determined to be secretory, including 184 putative type III effectors that may be involved in Xoo pathogenicity. Expression pattern of some of these identified genes were further validated by semi-quantitative RT-PCR. Taken together, these results provide a transcriptome overview of Xoo under in planta and in vitro growth conditions with a focus on its pathogenic processes, deepening our understanding of the behavior and pathogenicity of Xoo.

中文翻译：

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Xanthomonas oryzae pv的全球转录组分析。稻在植物生长和体外培养条件下的情况。

Xanthomonas oryzae pv。稻瘟病的病因是稻米（Xoo），对稻米的生产力构成重大威胁。在这里，我们对植物生长（在易感和抗性宿主上）和体外培养条件下分离的Xoo转录本进行了基于RNA-Seq的转录组分析。我们在植物中的提取方法成功地富集了Xoo细胞，并提供了高质量的RNA样品。在植物体内和体外共鉴定出4,619个差异表达基因生长条件。在植物生长条件下鉴定出的大多数差异表达基因均与营养物质转运，蛋白酶活性，胁迫耐受性和致病性有关。其中，有超过1300个差异表达基因被确定为分泌型，包括184个可能与Xoo致病性有关的III型效应子。通过半定量RT-PCR进一步验证了其中一些已鉴定基因的表达模式。两者合计，这些结果提供的转录概况白叶枯病下在植物中和在体外以其致病过程为重点的生长条件，加深了我们对Xoo行为和致病性的了解。