Fig. 5

H3K27me3-marked genes are enriched among genes downregulated in the hybrid. a Expression in A. thaliana of genes upregulated or downregulated in the hybrid. Green and red boxplots indicate genes upregulated and downregulated in the hybrid. b, c Distribution of H3K27me3 marks along a 1-Mb region on the A. thaliana chromosome 3 (b) and the A. lyrata chromosome 5 (chromosome 10 in the synthetic hybrid reference genome) (c), plotted as the ratio of normalized coverage between H3K27me3 and H3 ChIP-seq with a 100-bp window setting. d Number of genes marked by H3K27me3 in different genotypes. A gene is considered marked with H3K27me3 if more than half of its transcribed region overlaps with H3K27me3 enrichment peaks. e Fraction of H3K27me3-marked genes shared by A. thaliana and the hybrid. The pie chart on the left refers to all A. thaliana genes, the one on the right to genes downregulated in the hybrid. Genes marked with H3K27me3 both in the hybrid and parent are colored blue. f Comparison of the H3K27me3 signals over A. thaliana gene bodies in hybrid and parent. For the parent, the red dashed curve indicates the average of all H3K27me3-marked genes and the red solid curve indicates the average of the subset downregulated in the hybrid and marked with H3K27me3 in both hybrid and parent. The green curves refer to the same sets in the hybrid. Black solid and dash curves indicate the average of all A. thaliana genes in the hybrid and parent. g Ratios of H3K27me3 signals in the hybrid over the parent in A. thaliana gene bodies. Upregulated or downregulated genes are the same as in (a). p values mean Wilcoxon–Mann–Whitney tests