Xanthomonas citri subsp. citri (Xac) is the causal agent of citrus canker, a disease that affects citrus crops of economic importance. Sweet orange cultivars “Pera Rio” (Citrus sinensis) are intermediate susceptible to the disease, while acid lime ‘Galego’ (Citrus aurantifolia) are highly susceptible. To understand the molecular mechanism underlying the differences in Xac response when infecting these two citrus genotypes, in vivo transcriptomic profiles of Xac infecting both genotypes were compared using high throughput sequencing of RNA. Bioinformatics analysis detected 839 and 982 differentially expressed genes (DEGs) in Xac during their interaction with sweet orange and acid lime compared to controls, respectively. Moreover, 607 DEG genes were found to be common in both genotypes. In both hosts, the annotation of DEGs showed that Xac induced genes involved with the Type III Secretion System and corresponding effector genes, cell wall degrading enzymes, and xanthan gum synthesis. In addition, higher expression values in Xac genes associated with oxidative stress resistance were found in their interaction with sweet orange, compared to acid lime. The results collectively allow the proposition of the main genetic modulation mechanism used by Xac to develop the disease in the early stages of host infection and reveal different transcriptional responses when the bacteria interact with C. sinensis and C. aurantifolia. Thus, our study provides information about the intercellular environment of Xac and the possible strategies it uses to promote the disease.

柑橘黄单胞菌亚种。柑橘( Xac ) 是柑橘溃疡病的病原体，这种病害会影响具有经济重要性的柑橘作物。甜橙品种“Pera Rio”（Citrus sinensis）对该病具有中等敏感性，而酸性石灰“Galego”（Citrus aurantifolia）高度易感。为了了解感染这两种柑橘基因型时Xac反应差异的分子机制，使用 RNA 的高通量测序比较了感染这两种基因型的Xac的体内转录组谱。生物信息学分析在Xac中检测到 839 和 982 个差异表达基因 (DEG)在它们与甜橙和酸橙的相互作用过程中，分别与对照组相比。此外，发现 607 个 DEG 基因在两种基因型中都很常见。在这两种宿主中，DEGs 的注释表明Xac诱导了与 III 型分泌系统和相应的效应基因、细胞壁降解酶和黄原胶合成有关的基因。此外，与酸橙相比，在与甜橙的相互作用中发现了与抗氧化应激相关的Xac基因的更高表达值。这些结果共同提出了Xac使用的主要遗传调制机制的命题在宿主感染的早期阶段发展该疾病，并在细菌与C. sinensis和C. aurantifolia相互作用时揭示不同的转录反应。因此，我们的研究提供了有关Xac的细胞间环境及其用于促进该疾病的可能策略的信息。