Deletion mutants for Dicer-like genes were obtained for the fungus Clonostachys rosea, and the mRNAs and sRNAs of the mutants were sequenced during interaction with plant pathogens Botrytis cinerea and Fusarium graminearum.

Clonostachys rosea is a mycoparasite of several important plant pathogens. This fungus undergoes extensive transcriptional changes upon contact with the pathogens, but it is not known how much this changes rely on regulation through Dicer-dependant gene silencing. For this reason, the mRNAs and sRNAs of deletion mutants for two Dicer-like genes, interacting with either the pathogen Botrytis cinerea or Fusarium graminearum, were sequenced. To determine genes directly or indirectly regulated through Dicer-dependant gene silencing, a differential expression analysis was conducted, using as reference wild type Clonostachys rosea interacting with Botrytis cinerea or Fusarium graminearum. Furthermore, miRNA-like sequences (milRNAs) were detected and putative targets were predicted for milRNAs underexpressed by the deletion mutants, identifying genes putatively directly regulated by RNA silencing in C. rosea.