Function and diversity of oomycetous and fungal small RNAs suppressing host plant immunity

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The outcome of the interaction between a pathogen and a host plant largely relies on the immune strength of the plant and on the ability of the pathogen to suppress host immunity. We discovered recently that the plant pathogen Botrytis cinerea produces sRNAs that hijack the plant RNA interference pathway and silence important plant immunity genes. Based on this knowledge, the aim of this project is to investigate the occurrence and nature of host immune-suppressive sRNAs in distinct pathogens that evolved independently. We propose a workflow that aims at identifying novel pathogen sRNAs produced by representative plant pathogens of the fungus and oomycete kingdoms, namely Golovinomyces orontii causing the powdery mildew disease in Arabidopsis, Hyaloperonospora arabidopsidis causing the downy mildew disease in Arabidopsis, and Phytophthora infestans causing the late blight disease in tomato and potato, using high throughput screening approaches. Candidate sRNAs will be narrowed down through plant mRNA degradome analysis. The primary focus will be on candidates with high potential to target host genes related to plant stress response and immunity. Proof of bona-fide silencing of candidate host target genes will be performed by in planta pathogen sRNA expression. Moreover, the functional role of the silenced host target genes in defence and host immunity will be characterized. Finally, we will apply analytical and stochastic evolutionary models to address whether convergent patterns exist among plant genes, gene families, and molecular pathways targeted by pathogen sRNAs. Additionally, we aim to detect signatures of positive selection within host genes targeted by pathogen sRNAs with respect to the co-evolutionary arms race between pathogens and their hosts. This project is therefore designed to answer the following fundamental questions. I) Do distinct filamentous plant pathogens utilize sRNAs to suppress host immunity? II) What are the roles of targeted host genes and pathways in host immunity? III) Do sRNAs produced by distinct pathogens show target gene convergence? IV) Are there signatures of positive selection in host genes and pathways targeted by pathogen sRNAs?