Identification of microRNAs from the stems of three Dendrobium species

We used sRNA-seq to identify the microRNAs (miRNAs) from the stems of three Dendrobium species. Firstly, according to the plant mature miRNAs already registered in miRBase (release 22.1), conserved miRNAs were discovered from the three Dendrobium species. Besides, based on the RNA-seq data and de novo transcriptome assembly from Dendrobium, we performed a transcriptome-wide prediction of the miRNA precursors. In addition to the precursors encoding conserved miRNAs, those producing novel miRNAs were also discovered. Target prediction followed by degradome-seq data-based validation was also reported in this study. Several regulatory networks were constituted by dozens of miRNA--target pairs.