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

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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.