Fig. 2

Exemplified graphic outputs of the case study by using PmiRDiscVali. a Secondary structures of the pri-miRNAs (primary microRNAs) predicted by using the sequencing data of the leaf organ of Dendrobium officinale. The mature miRNAs located on the 5′ arms of the pri-miRNAs were marked by green lines, and those located on the 3′ arms were marked by red lines. The processing sites supported by degradome sequencing data were highlighted by blue circles on the pri-miRNAs. b A global view of the small RNA (sRNA) expression levels on the predicted pri-miRNAs. The total counts of the sRNAs mapped onto the pri-miRNAs from different sRNA sequencing (sRNA-seq) data sets (four sequencing data sets, including flowers, leaves, roots and stems, in the case study) are shown together on the histograms. For each histogram, the x axis indicates the nucleotide position on each pri-miRNAs, and the regions predicted to encode the mature miRNAs were in yellow color. The y axis measures the total accumulation levels (in RPM, reads per million) of the sRNAs mapped onto each pri-miRNA. The dot-bracket notation below each histogram show the base pairing status of the secondary structure of the miRNA precursor. The bracket indicates a paired base, while the dot indicates an unpaired base