Fig. 2: Sex-specific transcriptional regime of transposable elements across early embryogenesis.
From: Epigenetic conflict on a degenerating Y chromosome increases mutational burden in Drosophila males
a Heatmap showing the normalized read counts mapping to TEs from developmentally staged and sexed embryos (average of three embryos) from D. pseudoobscura and D. miranda. The list of TE names can be found in Supplementary Fig. 1. For heatmap in FPKM, see Supplementary Fig. 2. b Heatmap depicting the correlation of TE transcript abundance between species, sex, and developmental stages. Samples were ordered by hierarchical clustering. c, d TE transcript abundance across developmental stages, and sexes in D. pseudoobscura and D. miranda. Light lines depict TE transcript abundance for individual TEs, and dark lines depict the median with 95% confidence intervals demarcated by vertical lines. *, **, and *** denote significant differences between males and females with p values of <0.01, <0.0001, and <0.000001, respectively (two-tailed Wilcoxon rank-sum test, n = 303 consensus TEs from the repeat index, no multiple testing correction). e, f Distribution of the fold differences in TE transcript abundance (purple) between sexes in log2 scale. RNA-seq read counts at TEs are further normalized by their DNA-seq read counts to account for copy number, and the fold differences between sexes are depicted (orange); n = 303 consensus TEs from the repeat index. In the boxplots, whiskers delineate the minima and maxima of the distributions, the boxes demarcate the 25th and 75th percentiles, and the centers mark the medians. Source data are provided as a Source data file.
