Figure 3.

MicroRNA predictions across Solanaceae support a lineage-specific expansion of miRNAs. Venn diagrams of total microRNAs (miRNAs) predicted by miRPrefer, Shortstack, and both programs for each species (A). Upset plots showing previously unannotated (B) and miRBase annotated (C) miRNAs that are shared across Solanaceae species. For each Upset plot: the bottom left shows the entire size of each set as a horizontal histogram, the bottom right shows the intersection matrix, and the upper right shows the size of each combination as a vertical histogram. The red line marks miRNAs common to all species, the purple line marks miRNAs common to both Petunia species, the orange line marks miRNAs common to both Solanum species, the green line marks miRNAs common to both Nicotiana species, and the blue and yellow lines mark benthi- and pepper-specific miRNAs, respectively.