Extended Data Fig. 7: Association of gene expression with hypo-DMRs between sA subgenome of A. suecica and A. arenosa (Aar, A) and between sT subgenome and A. thaliana Ler4 (Ath, T).
From: Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids
a, Upset diagram of hypo-DMRs in CG, CHG and CHH context between sA and A. Numbers and percentages specific to each context were shown in red. b, Upset diagram of hypo-DMR-overlapping genes in CG, CHG and CHH context between sA and A. An asterisk indicates the fraction of the unique CHG or CHH DMRs (unique number / total number of DMRs) compared to that of their unique overlapping genes (unique number / total number of associated genes) was significantly reduced (P < 0.05, Fisher’s exact test). c, Heatmap of CG, CHG, and CHH DMRs (sT-T or sA-A) in Aar/Ath, F1, 733, 738, and Asu. Boxed regions show maintenance of DMRs from F1 to Allo733, Allo738, and A. suecica. d, Expression ratio (Log2[TPM(Asu/Aar)] of the genes as shown in (b). Colours (from left to right) indicate all genes (pale blue) and the genes flanked (2 kb) with hypo-DMRs in CG only (yellow), CHG only (purple), CHH only (red), all three (dark blue), both CG and CHG (orange), both CHG and CHH (green), and both CHH and CG (pink). One and three asterisks indicate statistical significance levels of P < 0.05 and P < 0.001, respectively (Mann–Whitney U-test). e, f, Number of CHG (e) and CHH (f) differentially methylated regions (DMRs) (sT-T or sA-A) in F1, 733, 738, and Asu, respectively.
