Genome-wide identification and profiling of microRNA-like RNAs from Metarhizium anisopliae during development

Metarhizium anisopliae is one of the most common species of entopathogenic fungi. It has economic and social benefits in many countries where used in agriculture as an important biological control agent of insect pests. M. anisopliae can exist as multiple cell types, which suggests that this fungus has a complex way of gene regulation. MicroRNAs (miRNAs) are endogenous small noncoding RNAs. They play a crucial role in the regulation of gene expression and cell function in plants, animals, and in fungi where they were termed miRNA-like RNAs (milRNAs). In this study, we aimed to identify potential milRNAs in M. anisopliae that may regulate the processes of mycelium growth and conidiogenesis (CO). Two small RNA (sRNA) libraries were constructed and submitted to Solexa sequencing. Fifteen milRNAs were identified using deep-sequencing and computational analysis; most of these milRNAs originated from single genes. Database searches revealed that these novel milRNAs had no homologues in other organisms and were, therefore, M. anisopliae-specific. Many of the milRNAs had differential expression profiles for either mycelium growth or CO. The expression of the selected milRNAs was validated by quantitative reverse transcription polymerase chain reaction. Seventy-eight potential target mRNAs for 14 of the milRNAs were identified successfully by computational analysis. These milRNAs may play an important role in the regulation of mycelial growth and conidiation in M. anisopliae. To our knowledge, this study is the first report of milRNA profiles of organisms in the order Hypocreales. This information could be used to study the regulation of genes and their networks in M. anisopliae.