Fig. 4

Expected and observed abundance of different TE families in piRNA clusters. A Histogram showing the expected abundance based on simulations under the trap model (for haploid genomes). B Observed abundance based on short reads aligned to the reference genome and the reference annotations of piRNA clusters. C Observed abundance based on strain-specific assemblies and a lift-over of the reference annotations of piRNA clusters, using unique sequences flanking the clusters. D Observed abundance based on strain-specific assemblies and de novo annotations of piRNA clusters. All counts refer to copy numbers per haploid genomes. For the observed data, we averaged the abundance in the five investigated strains. Only TE families active in the germline were considered. At least 98% of the simulations under the trap model are between the red lines. The x-axis was truncated at 30 insertions