Transcriptome-wide identification of microRNAs and functional insights inferred from microRNA-target pairs in Physalis angulata L

Abstract

Physalis angulata 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 Physalis angulata. 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 Physalis angulata 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 Physalis angulata. 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 Physalis angulata. 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 Physalis angulata.

Keywords: Organ-specific transcriptome; SSRs (simple sequence repeats); microRNA (miRNA); targets.

Figure 1.

Statistical results of the assembled unique transcripts of Physalis angulata. (a) Length distribution. (b) GC content distribution.

Figure 2.

Examples of the predicted microRNA (miRNA) precursors identified from the transcriptome assembly of Physalis angulata. Secondary structures of the miRNA precursors were predicted by RNAfold. The mature miRNAs were marked by red lines. The transcript IDs are shown on the top, and the mature miRNA IDs are shown near the red lines.

Figure 3.

Organ-specific expression patterns of the microRNA (miRNA) precursors. The expression levels of the precursors were measured by RPKM (reads per kilobase of exon model per million mapped reads; shown in y axes). The RNA-seq data sets of five organs (roots, stems, leaves, flowers and fruits; three biological replicates for each) were used for calculation.