(A) Distribution of TEs by their average maternally deposited sense (top, red) and anti-sense (bottom, blue) piRNA coverage. TEs with stage 3 peaks (stage 3 TEs), early stage 4 peaks (stage 4e TEs), and all TEs are in decreasing color intensity. p-values of pairwise comparisons determined by Wilcoxon’s rank sum test are marked beside the legends. (B) Correlation between average H3K9me3 enrichment across a TE at different developmental stages and average piRNA abundance. Pearson’s correlation coefficients (r) are labeled beside the regression lines. (C) Average expression of TEs with stage 3 peaks, early stage 4 peaks, and all TEs across embryonic development. Pairwise significance is determined by Wilcoxon’s rank sum rest: *p value<0.05 and **p value<0.001 after multiple-testing correction with false discovery rate. (D) Zygotic expression of different TE classes is approximated by the fold difference between early embryonic stages. Pairwise significance determined as in (C). (E) For each position of stage 3 nucleating TEs, the H3K9me3 enrichment is plotted against the number of piRNA reads mapped. Linear regression is plotted in dotted line and Pearson's correlation coefficient (r) is labeled. (F) Negative correlation between maternally deposited anti-sense piRNA and expression of all TEs (light blue dots), stage 3 TEs (dark blue diamonds), and early stage 4 TEs (blue boxes). Expression of TEs is scaled by copy number by dividing the RNA-seq read counts with DNA-seq read counts. Dotted line demarcates the linear regression and r represents the Pearsons’ correlation coefficient.