Fig. 3

Small RNA mapping to transposable elements. a Schematic view of the transposable element Jordan. Location of miRNAs targeting Jordan are marked with black bars. TIR, terminal inverted repeat; nt, nucleotide. b RNA blot validation of the expression two miRNAs encoded by a Jordan element. The hairpin structure of the respective putative precursor is shown to the right. The mature (detected) miRNA strand is depicted in red, the star strand in blue. c Small RNA coverage of the repetitive elements Jordan (upper panel), Gypsy5-I (middle panel) and Gypsy4-I (lowest panel). Diagrams show small RNA coverage over the length of the element for the plus (red) and the minus (blue) strand (consensus sequence from Repbase19.02 was used). The left column shows the reads measured in the VcAGO3 library, the middle column shows reads from the library of somatic cells during vegetative growth and the column on the right shows the reads from the library of reproductive cells during vegetative growth. For Gypsy5-I, black arrows indicate miRNA binding sites which are detailed in the panel below. Grey arrows indicate miRNA binding sites where the miRNA expression itself is rather low