Fig. 6: Subgenome-parallel retention of TE-derived TFBSs associated with balanced target gene transcription.

a, b Fraction of triads with unbalanced (a) and balanced (b) TF binding embedded in TEs. The TFs (n = 36) with >200 targeted triads are presented. c Fraction of triads with balanced and unbalanced TE-embedded TF binding in one, two, or three subgenomes. TFs (n = 36) targeting >200 triads are presented. Horizontal lines in boxplots show median, hinges show IQR, whiskers show 1.5 × IQR, points beyond 1.5 × IQR past hinge are shown. d Schematic for defining dTE and dTE-derived TFBS. e Fraction of triads with balanced and unbalanced TF binding embedded in TE and corresponding dTE present in one, two, or three subgenomes. TFs (n = 25) targeting >20 triads with TE-embedded TFBSs are presented. Boxplots definition is the same as Fig. 6c. f Left: schematic for identifying triads with similar TE and dTE-TFBS. Right: Fraction of triads with high sequence similarity of TFBS derived from TE and corresponding dTE (n = 25). Boxplots definition is the same as Fig. 6c. g Genome tracks illustrating dTEs contributing to the convergent TF binding to URE promoters. h Multiple sequence alignment of the promoter region in Fig. 6g. i Alignment of the TFBS in Fig. 6h with AP2 motifs highlighted. j Conservation score and epigenetic profiles surrounding dTE-derived TFBSs and non-TE TFBSs. k Correlation between subgenome-biased chromatin openness of TE-embedded DHS and target gene expression. left: ternary plots showing the relative chromatin openness of d TE-embedded DHSs in triad promoters. The dot color represents the Euclidean distance of DHS density to the balanced point; right: triad genes were grouped according to the unbalanced level of promoter DHS, and the two-tailed Wilcoxon signed-rank test was used to compare triads (n = 671) expression distance. l Homoeolog pairs of triads were grouped according to the DH divergence, and the two-tailed Wilcoxon signed-rank test was used to compare expression divergence between subgenomes A and B (n = 604), B and D (n = 489), A and D (n = 611), respectively. Boxplots definition is the same as Fig. 6c. Source data are provided as a Source Data file.