Fig. 3: Biased gene expression of homoeologs.

a The number of highly expressed genes across homoeologous chromosomes. b Expression effects of transposable elements (TEs) on flanking genes. Groups SA, SB, SC, and SD refer to chromosome groups categorized according to homoeolog expression bias and the number of highly expressed genes between homoeologous chromosomes. “Yes” indicates whether the gene category contains TEs within 2 kb; otherwise, “no.” c Proportion of homoeologs for each homoeologous expression bias category across the 10 tissues/varieties and pooled tissue. AL, pooled tissue; HE, calyx of the red variety; HG, root of the red variety; HHG, corolla of the red variety; HJ, stem of the red variety; HY, leaf of the red variety; ZE, calyx of the purple variety; ZG, root of the purple variety; ZHG, corolla of the purple variety; ZJ, stem of the purple variety; and ZY, leaf of the purple variety. d Absolute TPM gene expression abundance for the three homoeologous expression bias categories. e Distance to the nearest TEs for each of the three gene categories. f–h Ka, Ks, and the Ka/Ks ratio for each of the three gene categories. The bottom and top of each box represent the 25th and 75th percentiles, respectively. The centerline represents the 50th percentile. The whiskers indicate the minimum and maximum values. d–h Colors are consistent with cluster colors presented under (c). a, b χ² test, d–h Mann–Whitney–Wilcoxon test. *p < 0.05; **p < 0.01; ***p < 0.001