Reprogramming of Fungal mRNA and Small RNA Production in Response to Virus Infection

Sclerotinia sclerotiorum is a damaging and widely distributed fungal plant pathogen that significantly reduces yields of multiple crop species each year. Because mycoviruses have the potential to reduce the impacts of fungal plant pathogens on crop productivity, this study characterized changes in mRNA and small RNA accumulation in S. sclerotiorum in response to infection by Sclerotinia sclerotiorum hypovirus 2L (SsHV2L). Infection by SsHV2L significantly altered the accumulation of 1,150 mRNAs and 835 small RNA-producing loci. The differentially expressed mRNAs included more than 100 mRNAs encoding proteins involved in the metabolism and trafficking of carbohydrates and lipids. Both S. sclerotiorum endogenous and virus-derived small RNAs were of predominantly 22 nt in length. Global analyses of mRNA, small RNA, and degradome data confirmed that small RNAs produced by S. sclerotiorum were capable of directing the cleavage of 44 mRNAs, one of which was predicted to target the mRNA encoding a homologue of Argonaute 2, a microRNA function conserved in many eukaryotes. In addition to sequences resembling microRNAs, S. sclerotiorum produced phased small interfering RNAs from noncoding RNAs that have the potential to regulate mRNA abundance in trans. Finally, a subset of S. sclerotiorum 22-nt small RNAs were shown to be complementary to mRNAs of plant hosts. Hence, the analysis showed that infection of S. sclerotiorum by a hypovirulence-inducing virus produced large-scale reprogramming of mRNA and small RNA production and demonstrated that S. sclerotiorum possesses robust RNA silencing pathways for antiviral defense and endogenous gene regulation.