The presence of satellite RNA exacerbates symptoms and transcriptomic response of Nicotiana benthamiana during peanut stunt virus infection

Peanut stunt virus (PSV) of Cucumovirus genus is serious vegetables and legume pathogen. Some PSV strains are associated with satellite RNA (satRNA). SatRNAs are dependent on their helper virus and their presence usually attenuates the severity of the disease symptoms induced by the virus. However, the final outcome of satRNA pathogenesis modification depends on the satRNA sequence, virus strain and external conditions. In this study we elucidated the plant response to PSV-G strain which occurs in natural conditions without satRNA. However, it was found that it might easily acquire satRNA which causes exacerbation of pathogenesis in Nicotiana benthamiana. In order to study plant response to PSV infection and to explain mechanisms underlying symptoms exacerbation caused by satRNA we did transcriptome profiling of N. benthamiana challenged by PSV with/ without satRNA using species-specific microarrays. Agilent microarrays in 2x105k format (two microarrays per slide) were used for hybridization of labeled RNA from upper parts of treated N. benthamiana plants (infected PSV-G, PSVG+satRNA or mock-inoculated) labeled with Cy5 versus a common reference (ref): pooled RNA extracted from a mix of tissues and treatments, labeled with Cy3. Three biological replicates were used for each treatment.