Multi-dimensional interplay between Xanthomonas oryzae TALEs and the rice genome

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This proposal aims at studying the interaction between plant-pathogenic Xanthomonas oryzae bacteria and the host plant rice (Oryza sativa) in multiple dimensions by a interdisciplinary approach between biology and bioinformatics. The project will focus on TALEs (transcription activator-like effectors) which are key virulence factors of X. oryzae. TALEs function as transcription factors inside plant cells to induce expression of target genes. First, specific TALE targets in rice will be studied for their role in bacterial virulence. Second, genome-wide predictions of TAL-boxes will be combined with total RNA-seq data to detect novel TALE targets not only in protein-coding genes, but also in non-coding RNAs. Third, TALE-mediated gene activation will be studied in a time-dependent manner. While primary TALE targets are activated within the first 24-48 hours after infection, the number of differentially expressed genes increases dramatically between 24 h and 48 h. Defined sets of secondary TALE targets should be attributable to the activity of regulatory TALE targets, e.g., those that function as transcription factors. Unravelling these networks will deepen our understanding of TALEs on the whole infection process. Finally, the evolutionary dimension of TALEs in the pathogen - host interaction will be analyzed by challenging X. oryzae strains with resistant plants that have been generated by genome editing. Selection and analysis of bacteria that overcome these resistances will give insights into the adaptive changes that are possible in TALE genes. This will help to develop strategies for breeding plants with durable resistances. The project will further explore very long-read sequencing technologies to assemble the highly repetitive X. oryzae genomes and extend the successful AnnoTALE bioinformatics toolbox for studying TALEs.