Biotic stress trigger plant endogenous short non-coding RNAs that regulate components of photosynthetic machinery

A massive and diverse population of short non-coding (s)RNAs accumulates in plant tissues. sRNAs drive RNA silencing-based gene repression. Besides their role in tissue and organ development, differentiation and in the maintenance of genome integrity, sRNA play crucial roles in host response to a wide range of environmental conditions, including biotic stresses. By image data augmentation technique, we have selected Brassica rapa (turnip) and B. napus (canola) plant tissues infected by cauliflower mosaic virus (CaMV) showing mosaic and yellowing symptoms. sRNA populations associated to CaMV-infected tissues of the two crops were characterized by sequencing and bioinformatics and compared with those from the model pathosystem CaMV-Arabidopsis. We revealed orthologues genes producing endogenous sRNAs shared out among turnip, canola and Arabidopsis. In the three plant species, the majority of these siRNAs were from protein coding genes encoding components of the photosynthetic machinery, such as LHCB1.3, LHCB1.4, LHCA1, and FBA1. By quantitative real time PCR we revealed a significant down-regulation of transcripts generating the endogenous RNA in the two crops. Moreover, by in vitro assays we have proved the functionality of selected sRNAs in cleaving the corresponding RNA targets upon incorporation into specific core proteins of the class of "Argonautes". The results herein suggested that the generation of sRNA regulators from specific gene clusters of the photosynthetic machinery is an unifying qualitative feature among plant species of the Brassicaceae family under biotic stress.