Endogenous activated small interfering RNAs in virus‐infected Brassicaceae crops show a common host gene‐silencing pattern affecting photosynthesis and stress response

Viral infections are accompanied by a massive production of small interfering RNAs (siRNAs) of plant origin, such as virus‐activated (va)siRNAs, which drive the widespread silencing of host gene expression, and whose effects in plant pathogen interactions remain unknown. By combining phenotyping and molecular analyses, we characterized vasiRNAs that are associated with typical mosaic symptoms of cauliflower mosaic virus infection in two crops, turnip (Brassica rapa) and oilseed rape (Brassica napus), and the reference plant Arabidopsis thaliana. We identified 15 loci in the three infected plant species, whose transcripts originate vasiRNAs. These loci appear to be generally affected by virus infections in Brassicaceae and encode factors that are centrally involved in photosynthesis and stress response, such as Rubisco activase (RCA), senescence‐associated protein, heat shock protein HSP70, light harvesting complex, and membrane‐related protein CP5. During infection, the expression of these factors is significantly downregulated, suggesting that their silencing is a central component of the plant’s response to virus infections. Further findings indicate an important role for 22 nt long vasiRNAs in the plant’s endogenous RNA silencing response. Our study considerably enhances knowledge about the new class of vasiRNAs that are triggered in virus‐infected plants and will help to advance strategies for the engineering of gene clusters involved in the development of crop diseases.