Evaluation of small non-coding RNAs as a possible epigenetic mechanism mediating the transition from biotrophy to necrotrophy in the life cycle of Phytophthora infestans

Summary Phytophthora infestans , causal agent of late blight disease of potatoes, causes billion-dollar losses worldwide each year. This plant pathogen is a hemibiotroph, first feeding on the host and later killing it. Even though the transcription dynamics of this transition are characterized, the role that small non-coding RNAs (sRNAs) might have is still unknown. Furthermore, a bioinformatic pipeline to search and analyze sRNAs in P. infestans , is needed. Using our proposed pipeline, 146 sRNAs were found to be significantly differentially expressed between the evaluated stages of the pathogen’s life cycle. One hundred of these sRNAs were successfully annotated and classified into nine functional categories. The expression of the genes associated to ten of these sRNAs was validated via qRT-PCR. Among these, the expression levels of genes encoding for effectors were inversely correlated to that of the sRNAs aligning to them, which is expected if sRNAs are indeed regulating their expression. This correlation was not clear for sRNAs in other functional categories and should not be confused with strict causality. This study works as a starting point for considering sRNAs as role players in the transition from biotrophy to necrotrophy in P. infestans when infecting Solanum tuberosum .