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Fig. 5 | Genome Biology

Fig. 5

From: Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

Fig. 5

Meiotic crossovers are associated with fine-scale genomic and chromatin features. a Left panel: Spearman’s correlation matrix for recombination rate, DNase-seq, H3K4me3, and 5mC in CHH, CHG, and CG contexts across 100-kb windows on chromosome 12. Right panel: Heatmaps of CHH, CHG, CG, H3K4me3, and DNase-seq density overlaying recombination rate across 100-kb non-overlapping windows of chromosome 12. b Left panel: Normalized DNase-seq read counts over and flanking crossovers (orange), matched cold regions (blue), and random regions (gray). Right panel: Normalized H3K4me3 read counts over and flanking crossovers (orange), matched cold regions (blue), and random regions (gray). c Comparison of normalized DNase-seq and H3K4me3 read counts for genomic features overlapping crossovers, and simulations of the analogous features near (10–1000 kb) but not overlapping crossovers. Error bars on the simulated distributions are from 10,000 permutations. d Left panel: Normalized DNase-seq read counts over and flanking genes and their promoters that overlapped crossovers (orange) and permutations of genes that did not overlap genes (blue). Right panel: Normalized H3K4me3 read counts over and flanking genes and their promoters that overlapped crossovers (orange) and permutations of genes that did not overlap genes (blue). In both panels the light blue shading for non-crossover genes reflects a simulated distribution of 100 permutations, while the statistical tests in the text are based on 10,000 permutations. Genes were split into 50 windows, while flanking regions were split into 10-bp windows. Lines reflect averaged values across genes in each group (crossover-associated and random). *Significance at P < 0.05

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