Identification of novel miRNA--target pairs in rice (Oryza sativa) by a reversed approach

MicroRNAs (miRNAs) are crucial regulators of gene expression in plants. Here, we performed a comprehensive computational search for novel miRNA--target pairs in rice by a reversed approach. First, the potential cleavage sites in all the 67,392 cDNAs of rice were searched by degradome sequencing datasets. Then, the ‘bait’ sequences, which may be acted as the miRNAs binding sites in the targets, were generated by adding 10 nt sequences both upstream and downstream of the cleavage sites. Finally, the potential miRNA candidates were extracted by BLAST of these ‘bait’ sequences against the AGO1-associated sRNA sequencing data and were further validated considering the structure and expression characteristics of miRNA. As a result, 144 previously validated miRNA--target pairs and 7 novel miRNA candidates together with 15 mRNA targets were identified. According to the literature, some of these 15 corresponding targets play very important role in the stress signaling pathways in rice. Other interesting findings were the non-canonical slicing sites and higher accumulation isomiRs were identified in some of the previously validated miRNA--target pairs.