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An inducible RNA-silencing pathway, involving a single Dicer protein, DCL2, and a single Argonaute protein, AGL2, was recently shown to serve as an effective antiviral defense response in the chestnut blight fungus  Cryphonectria parasitica . Eukaryotic RNA-dependent RNA polymerases (RdRPs) are frequently involved in transcriptional and posttranscriptional gene silencing and antiviral defense. We report here the identification and characterization of four RdRP genes ( rdr1–4 ) in the  C. parasitica  genome. Sequence relationships with other eukaryotic RdRPs indicated that RDR1 and RDR2 were closely related to QDE-1, an RdRP involved in RNA silencing (“quelling”) in  Neurospora crassa , whereas RDR3 was more closely related to the meiotic silencing gene SAD-1 in  N. crassa . The RdRP domain of RDR4, related to  N. crassa  RRP-3 of unknown function, was truncated and showed evidence of alternative splicing. Similar to reports for  dcl2  and  agl2 , the expression levels for  rdr3  and  rdr4  increased after hypovirus CHV-1/EP713 infection, while expression levels of  rdr1  and  rdr2  were unchanged. The virus-responsive induction patterns for  rdr3  and  rdr4  were altered in the Δ dcl2  and Δ agl2  strains, suggesting some level of interaction between  rdr3  and  rdr4  and the  dcl2 / agl2  silencing pathway. Single  rdr  gene knockouts Δ rdr1–4 , double knockouts Δ rdr1/2 , Δ rdr2/3 , Δ rdr1/3 , and a triple knockout, Δ rdr1/2/3 , were generated and evaluated for effects on fungal phenotype, the antiviral defense response, viral RNA recombination activity and transposon expression. None of the single or multiple  rdr  knockout strains displayed any phenotypic differences from the parental strains with or without viral infection or any significant changes in viral RNA accumulation or recombination activity or transposon RNA accumulation, indicating no detectable contribution by the  C. parasitica rdr  genes to these processes.

plos one

Characterizing the Roles of Cryphonectria parasitica RNA-Dependent RNA Polymerase-Like Genes in Antiviral Defense, Viral Recombination and Transposon Transcript Accumulation