Fig. 1

Abundant piRNAs in T. castaneum embryos originate from discrete, TE-rich clusters. a Size and count distribution of total reads mapping to single or multiple genomic positions from T. castaneum oocyte and embryonic small RNA libraries. The sequence logo for 25–35-nt reads is shown. b Size and count distribution of total reads mapping to consensus TE sequences in sense and antisense orientation. Sequence logos for sense and antisense reads are shown. c Distribution of 25–35-nt reads across the first 2 Mb of chromosome 10. Coloured bars indicate the number of reads starting with A, T, C or G per 10-kb window. Regions defined as piRNA clusters are highlighted. d Cumulative proportion of piRNA reads in clusters. e Positions of piRNA clusters on the assembled chromosomes of T. castaneum. f TE sequence enrichment in piRNA clusters. Bar graphs show the average proportion of RepeatMasker TE annotations per 1-kb windows within piRNA clusters (n = 5774), the whole genome excluding piRNA clusters (n = 155,977) and the mean and standard deviation for randomly sampled 1-kb windows of an equal sample size as piRNAs clusters (n = 5774) 1000 times. g Multi-level Gene Ontology (GO) Biological process pie chart of terms associated with annotated transcripts residing in piRNA clusters. h Numbers of best Censor hits (score cutoff 100) of annotated protein-coding transcripts in piRNA clusters with >10 RPM piRNA coverage