Fig. 7: Ancestral expansion of RLC_famc1.4 dominates TE-derived subgenome-convergent TFBSs.

a Enrichment of TE (left) and dTE (right) families that contributed to the balanced TF binding across triad promoters, with the fraction of TE in the genome as the background. b Dendrogram presenting the sequence similarity of the full-length RLC_famc1.4 members. c Sequence distance of full-length RLC_famc1.4, RLG_famc13, and RLG_famc7.3 members among three wheat subgenomes as well as between wheat and rye and wheat and barley. For each TE subfamily, 500 copies from subgenome A were randomly selected. The copy numbers for the B and D subgenomes as well as rye and barley were selected according to the total copy numbers in the B and D subgenomes as well as in rye and barley relative to the total copy number in subgenome A. For each TE copy, the sequences of the LTR at the 5′ end and 3′ ends were merged and aligned to other merged LTRs. The copy numbers of the full-length RLC_famc1.4 and RLG_famc7.3 members in barley were <25. Thus, these sequences were not considered in this analysis. d Enrichment of TE families contributing to the balanced chromatin openness across triad promoters. The fraction of TE in the genome was used as background. e Enrichment of dTE families contributing to the balanced chromatin openness across triad promoters. The fraction of TE in the genome were used as background. f Enrichment of TE subfamilies in the TAD boundaries with and without TFBSs, with the fraction of TAD boundaries in the genome as the background. g Enrichment of TE subfamilies in the subgenome-common and -unique TAD boundaries, with the fraction of subgenome-syntenic and -unique TADs as the background, respectively. Source data are provided as a Source Data file.