miRNA analysis

Sequences mapped to reference genome were used for known and novel miRNA identification using miRDeep2 software. The effective reads mapped to reference genomes were aligned against precursor and mature sequences of known wheat miRNA in miRBase. If precursor sequence, mature sequence, and hairpin structure were consistent, the effective reads were regarded as known miRNAs. Novel miRNA prediction was done using miRDeep2 software, which can identify novel miRNA by predicting hairpin structure, analyzing Dicer enzyme splice sites, and calculating free energy. Moreover, length distribution statistics and base preference analysis of identified miRNAs were performed.