Functional analysis of the RNA silencing machinery is technically fairly progressed in plants, but a biologically complex process that operates through many rather distinct specific mechanisms. The perhaps most central functional aspect of RNA silencing is how it eventually contributes to regulated protein production. So far, most studies have focused on the small RNAs that provide sequence specificity to the silencing machinery and also, to some extent, on the degradation of target RNAs. At the same time, non-catabolic translation repression, for example, has remained relatively unknown at genome-wide levels during cellular reprogramming toward stress and disease tolerance. Interestingly, pathogenic viruses have evolved effector proteins that suppress the RNA-silencing machinery in different ways and possibly quite selectively. We hypothesize that both the plant and the virus will try to control these processes for their own benefits, and the outcome of these interactions will majorly influence the outcome of plant disease. This project will take an ambitious beginning by a comparative virology approach (parallel analysis of at least four distinct model viruses) in plants capable and incapable of RNA silencing. Genome-wide analyses of small RNA populations, transcriptomes, the RNA degradomes and translatomes creates a bioinformatics cradle for a global understanding of RNA silencing in regulating plant protein production and mRNA metabolism. The PhD student will be the main person driving this project. Emerging concepts will be experimentally challenged and studied more in depth by individually tailored approaches that are hard to foresee at this stage.