Small RNA processing in the plant pathogenic fungus Sclerotinia sclerotiorum

RNA-based gene silencing serves as a regulatory mechanism for eukaryotic gene expression during development and in response to stress that is mediated by small non-coding RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs). RNA silencing also functions to suppress highly repeated mobile genetic elements, serves as an antiviral defense and has been used with mixed results to develop resistance in plants to bacteria, fungi, insects, nematodes and viruses. However, RNA silencing mechanisms in plant pathogenic fungi are under-studied. Once identified, they can be utilized to improve plant health by more effectively silencing fungal genes from host plants or viral vectors. In this study, we characterized changes in gene expression and small RNA accumulation in Sclerotinia sclerotiorum, a damaging and widely distributed fungal plant pathogen, in response to hypovirus infection. Unlike plants which produce primarily 21 nt small RNAs, high-throughput sequence analysis showed that the fungus produced small RNAs of predominantly 22 nt. The S. sclerotiorum genome was predicted to contain multiple families of miRNA-encoding genes, none of which were conserved with miRNAs produced by other eukaryotes. Similar to other systems, siRNA sequences were primarily derived from retrotransposons. Small RNA sequences derived from the hypovirus genome were predominantly 22 nt in size, and non-randomly derived from both RNA strands. These findings suggest that there is a lack of conservation in small RNA pathways among plant pathogenic fungi that will need to be considered for RNA-based pathogen resistance strategies.