Fig. 3: Expression dynamics of TE-alone transcripts during zebrafish early embryonic development.

a Fraction of transcript abundance of DNA transposons, LINEs and LTR over 11 developmental stages. b Dynamic activation and transcription pattern of seven representative LTR families (top) and six ERV1 subfamilies (bottom). c Heatmap showing the differential activation and expression of 19 loci from BHIKHARI_I subfamily. d Heatmap (right) showing the expression of 695 ZTA TE-alone transcripts, categorized into eight groups with hierarchical clustering. Line plots (left) showing the overall/merged expression trend (with the colored line as mean value and the gray band as standard deviation value) across all transcripts in each group. e Distribution of entropy (which is used to measure the complexity of expression pattern of TE-alone transcripts/loci from the same subfamily) of each TE subfamily based on the number of patterns. Pie charts representing the transcript constitution of three representative TE subfamilies. The color of the pie chart is consistent with the expression clusters shown in (d). Line plots showing the expression pattern of transcripts from corresponding subfamilies during early embryonic development. f Comparison of Kimura divergence between active and silent TE copies among different TE types. Wilcoxon rank sum test, two-sided was applied. The number of silent and active copies is 29,235 and 342 for LTR, 172,202 and 127 for DNA transposon, and 35,795 and 79 for LINE. g Density plot for comparing the LTR insertion years between expressed and not expressed intact copies which are do novo identified. K-S Kolmogorov-Smirnov test, two-sided. Insertion years larger than 0.5 million years are not shown. h Line plot to show expression pattern of evolutionarily young and old TE-alone loci.