sRNA profiling in Aspergillus flavus reveals differentially expressed miRNA-like RNAs response to water activity and temperature

•sRNA sequencing was performed to characterize the sRNA in Aspergillus flavus.•Differentially expressed sRNA loci were identified in A. flavus under different water activity and temperature conditions.•MiRNA-like RNAs were identified and their response to water activity and temperature factors were vilified by RT-qPCR assay.•MiRNA-like RNAs might play important roles in the mycotoxin biosynthesis and mycelium growth in fungi A. flavus. Small non-coding RNA (sRNA) in various organisms remains a mysterious subject. Although microRNAs (miRNAs) have been intensively investigated in plants and animals, the study of miRNAs in fungi has been limited. Only microRNA-like RNAs (milRNAs) have been reported in several filamentous fungi. In this study, Illumina deep sequencing was performed to characterize the sRNA in Aspergillus flavus and to evaluate their responses to water activity and temperature. Global expression analysis showed an extensively differential expression of sRNA loci in A. flavus under different temperature or water activities. In addition, a total of 135 milRNAs were identified in A. flavus. The milRNA profiles obtained in deep sequencing were further validated by RT-qPCR assay. The presence and differential expression of milRNAs under different temperature or water activities in A. flavus imply that milRNAs might play important roles in the mycotoxin biosynthesis and mycelium growth in fungi A. flavus.