Fig. 3

Generation of de novo piRNAs in the flanking regions of novel TE insertions. a A schematic diagram illustrating the two hypotheses of how novel piRNAs are induced from TE insertions. The first mechanism is that a TE jumps into a pre-existing piRNA locus so that novel piRNAs are generated by co-transcription of the established piRNA precursor. The second mechanism is that de novo piRNAs are generated in the flanking region of novel TE insertions. b Barplots showing the RPKMs of de novo piRNAs generated in the flanking region (upstream and downstream 2 Kb) of novel TE insertions. The de novo piRNAs are generated with strong strand-asymmetric distributions. KS tests were performed to test the differences in the RPKM values. c Barplots of the fractions of the first nucleotide of de novo piRNAs generated in the flanking region (upstream and downstream 2 Kb) of novel TE insertions. d The ping-pong signature of de novo piRNAs generated in the flanking region (upstream and downstream 2 Kb) of novel TE insertions in 10 GDL strains. The color key for the strains is the same as shown in Fig. 2a. e Examples of de novo piRNAs and siRNAs generated from the flanking region of P-element insertion in 10 GDL strains. The sense-strand small RNAs are plotted in red, and the anti-sense small RNAs are plotted in blue. f Frequencies of novel TE insertions and SNPs. The x-axis is the number of strains that carry the particular category of TE insertions or SNPs, and the y-axis is the percentage of TE insertions or SNPs in each class that is segregating at that particular frequency. The TE insertions in piRNA clusters or with de novo piRNAs are segregating at higher frequencies. Fisher’s exact tests were performed to test the differences in the RPKM values