Identification of microRNA-Like RNAs in the Filamentous Fungus <i>Trichoderma reesei</i> by Solexa Sequencing

<div><p>microRNAs (miRNAs) are non-coding small RNAs (sRNAs) capable of negatively regulating gene expression. Recently, microRNA-like small RNAs (milRNAs) were discovered in several filamentous fungi but not yet in <i>Trichoderma reesei</i>, an industrial filamentous fungus that can secrete abundant hydrolases. To explore the presence of milRNA in <i>T. reesei</i> and evaluate their expression under induction of cellulose, two <i>T. reesei</i> sRNA libraries of cellulose induction (IN) and non-induction (CON) were generated and sequenced using Solexa sequencing technology. A total of 726 and 631 sRNAs were obtained from the IN and CON samples, respectively. Global expression analysis showed an extensively differential expression of sRNAs in <i>T. reesei</i> under the two conditions. Thirteen predicted milRNAs were identified in <i>T. reesei</i> based on the short hairpin structure analysis. The milRNA profiles obtained in deep sequencing were further validated by RT-qPCR assay. Computational analysis predicted a number of potential targets relating to many processes including regulation of enzyme expression. The presence and differential expression of <i>T. reesei</i> milRNAs imply that milRNA might play a role in <i>T. reesei</i> growth and cellulase induction. This work lays foundation for further functional study of fungal milRNAs and their industrial application.</p>