Supplementary information for: The rice ILI2 locus is a bidirectional target of the African Xanthomonas oryzae pv. oryzae major Transcription Activator-Like Effector TalC but does not contribute to disease susceptibility

This dataset contains additional supporting information related to the discovery of an alternative transcriptional target locus of the Xanthomonas oryzae pv. oryzae (Xoo) TalC effector in the rice genome as described in a manuscript submitted for publication. Xoo strains that cause Bacterial Leaf Blight (BLB), limit rice (Oryza sativa) production and require breeding more resistant varieties. Transcription Activator-Like Effectors (TALE) activate transcription to promote leaf colonization by binding to specific plant host DNA sequences termed Effector Binding Elements (EBE). Xoo major TALEs universally target susceptibility genes of the SWEET transporter family. TALE-unresponsive alleles of clade III OsSWEET susceptibility gene promoter created with genome editing confer broad resistance to Asian Xoo strains. African Xoo strains rely primarily on the major TALE TalC which targets OsSWEET14. Although the virulence of a talC mutant strain is severely impaired, abrogating OsSWEET14 induction with genome editing does not confer equivalent resistance to African Xoo. To address this contradiction, we postulated the existence of a TalC target susceptibility gene redundant with OsSWEET14. Bioinformatics analysis identified a rice locus named ATAC composed of the INCREASED LEAF INCLINATION 2 (ILI2) gene and a putative lncRNA that are shown to be bidirectionally upregulated in a TalC-dependant fashion. Gain of function approaches with designer TALEs inducing ATAC sequences did not complement the virulence of a Xoo strain incapable of activating a SWEET gene. While editing the TalC EBE at the ATAC loci compromised TalC-mediated induction, multiplex edited lines with mutations at the OsSWEET14 and the ATAC loci remained essentially susceptible to African Xoo strains. Overall, this work indicates that ATAC is a probable TalC off-target loci but nonetheless documents a first example of divergent transcription activation by a native TALE during infection. This dataset is composed of two pieces of information related to the trancriptome of the Nipponbare rice leaf undergoing infection with Xoo: - The inferred experimental transcriptome following bacterial inoculation. - The gene-level expression analysis output in response to bacterial treatments.

本数据集包含了与水稻基因组中Xanthomonas oryzae pv. oryzae (Xoo) TalC效应子替代转录靶位点发现相关的额外支持信息，该信息已在投稿的论文中进行描述。Xoo菌株可引起细菌性条斑病（BLB），限制水稻（Oryza sativa）的生产，并要求培育更具抗性的品种。转录激活因子样效应子（TALE）通过结合特定的植物宿主DNA序列，即效应子结合元件（EBE），来激活转录，从而促进叶片的定殖。Xoo的主要TALE普遍靶向SWEET转运蛋白家族的易感基因。使用基因组编辑创建的III类OsSWEET易感基因启动子中的TALE非响应等位基因赋予了对亚洲Xoo菌株的广泛抗性。非洲Xoo菌株主要依赖主要TALE TalC，该TALE靶向OsSWEET14。尽管talC突变菌株的致病性严重受损，但使用基因组编辑消除OsSWEET14的诱导并不赋予对非洲Xoo菌株的同等抗性。为了解决这一矛盾，我们假设存在一个与OsSWEET14冗余的TalC靶位点易感基因。生物信息学分析鉴定出一个名为ATAC的水稻位点，该位点由INCREASED LEAF INCLINATION 2 (ILI2)基因和一个假定的长链非编码RNA组成，这些基因在TalC依赖性方式下双向上调。利用设计型TALE诱导ATAC序列的功能获得性方法并不能弥补无法激活SWEET基因的Xoo菌株的致病性。在ATAC位点上编辑TalC EBE会损害TalC介导的诱导，而具有OsSWEET14和ATAC位点上突变的多重编辑线仍然基本易感于非洲Xoo菌株。总体而言，这项工作表明ATAC可能是TalC的非靶位点，但同时也记录了在感染过程中原生TALE诱导转录差异性的第一个例子。本数据集包括与Xoo感染Nipponbare水稻叶片转录组相关的两份数据信息：- 细菌接种后的推定实验转录组。- 对细菌处理反应的基因水平表达分析输出。