Fig. 4: Characteristics of ACRs between two maize subgenomes.

a The number of constrained ACR on m1 and m2 when compared to sorghum and when mutually compared. b A schematic of reciprocal subgenome sequence loss happened on ACRs. Straight lines represent genome sequences; gray dashed boxes represent regions of collinearity between genomes; and triangles represent ACRs on genomes. c ACR length density normalized by the lengths of m1 (red) and m2 (blue) across 15 samples. d ACR length density of highly conserved region normalized by the lengths of highly conserved regions of m1 (red) and m2 (blue) across 15 samples. e The proportion of enriched TFBSs that shared between two subgenomes and specifically existed in m1 or m2 subgenome (n = 15). Except for the TFBSs that annotated across the two subgenomes, we also independently annotated TFBSs in promoter and distal ACRs, respectively. The box denotes the maxima, 25th, median, 75th percentiles and minima, and the whiskers indicate the 1.5× interquartile range. The P-values were calculated by two-sided Wilcoxon test. f An overview of ACRs across a ~ 400 kb region between tb1 and its m2 syntenic gene tcp6. Red region indicated the reported functional Hopscotch region; the blue box indicates the genes; the grey bar indicates the transposable elements. Source data are provided as a Source Data file.