Systematic identification of miRNAs and miRNA targets in Oryza sativa

miRNAs play essential roles in plant development and environmental adaption. Here, based on 49 Oryza sativa (rice) small RNA-seq datasets, we systematically analyzed the expressions of known miRNAs and identified novel miRNAs in rice. We showed that only 39% of annotated miRNAs on miRBase have detectable expressions. Additionally, analysis of rice degradome datasets identified a few new miRNA targets including two miR444 targets that encode a WD40 protein and a HSF (heat shock factor)-type DNA-binding protein, respectively.