Fig. 6

Examples of piRNA and RNAseq coverage at specific loci. a piRNA cluster encoding a sequence homologous to a gypsy related reverse transcriptase. b Cluster encoding a sequence homologous to a SARTTc6 element. Upper left panels show the density and normalized counts (RPM) of 25–35-nt small RNAs mapping to the positive (green) and negative (purple) DNA strands throughput the development of T. castaneum. Darker shades indicate uniquely mapping reads, and lighter shades reads mapping to this and other genomic positions. Black lines indicate the positions of the protein-coding genes encoded in the clusters. Zoomed views of these regions are shown on the right, together with sequence logos of reads mapping to each strand. Below are RNA coverage histograms for each DNA strand of two replicates (black and grey lines) from oocytes, 8–16, 16–24 and 24–48-h embryos. Lower left panels show the number of reads with and without a 10-bp overlapping antisense partner at each stage and in a strand-specific manner