Transcriptome-wide identification of microRNAs and functional insights inferred from microRNA—target pairs in <i>Physalis angulata</i> L

<i>Physalis angulata</i> L., a member of the family Solanaceae, is widely used as the folk medicine in various countries. Continuous research efforts are devoted to the discovery of the effective medicinal ingredients from <i>Physalis angulata</i>. However, due to the limited resources of genome and transcriptome sequencing data, only a few studies have been performed at the gene regulatory level. In this study, the transcriptomes of five organs (roots, stems, leaves, flowers and fruits) of <i>Physalis angulata</i> were reported. Based on the transcriptome assembly containing 196,117 unique transcripts, a total of 17,556 SSRs (simple sequence repeats) were identified, which could be useful RNA-based barcoding for discrimination of the plants closely relative to <i>Physalis angulata</i>. Additionally, 24 transcripts were discovered to be the potential microRNA (miRNA) precursors which encode a total of 31 distinct mature miRNAs. Some of these precursors showed organ-specific expression patterns. Target prediction revealed 116 miRNA–target pairs, involving 31 miRNAs and 83 target transcripts in <i>Physalis angulata</i>. Taken together, our results could serve as the data resource for in-depth studies on the molecular regulatory mechanisms related to the production of medicinal ingredients in <i>Physalis angulata</i>.