Fig. 4
Genetic and epigenetic haplotypes of Col and Ler and centromere-proximal crossover recombination. A CTL3.9 crossover frequency (cM/Mb) is plotted against the Col-CEN assembly, overlaid with a plot of the density of CEN178 satellite repeats (red=forward, blue=reverse strand) and 5S rDNA (purple). The positions of the CTL3.9 fluorescent T-DNAs are shown by red and green vertical lines. Above this plot, the purple and black bars indicate the positions of the LRZs and NRZ. Above is a plot of CENH3 ChIP-seq enrichment (black), with ATHILA retrotransposons indicated by red x-axis ticks. Above this is a plot of the proportion of ONT-based DNA methylation in CG (red), CHG (blue), and CHH (green) sequence contexts. A StainedGlass sequence identity heat map is shown above the CEN178 satellite arrays, together with a histogram indicating the color scale associated with % identity values. Beneath, a mirrored version is shown with data projected and aligned to the Ler-0 genome assembly. In the center of the plot, the physical positions of KASP and T-DNA markers in the Col-CEN and Ler-HiFi assemblies are connected with lines between the X-axis. B In the first row, the density of genes (green) is plotted alongside %GC content (blue) per 10 kb along the centromere-proximal regions of the Col-CEN genome assembly. ATHILA retrotransposon insertions are indicated as red x-axis ticks. In the next row, the proportion of DNA methylation mapped from ONT reads is plotted in 10-kb windows for CG (red), CHG (blue), and CHH (green) sequence contexts. In the next row, Col/Ler crossover frequency (cM/Mb) is plotted in 10-kb windows (black), with CEN178 satellite density (red=forward & blue=reverse strand), and CENH3 ChIP-seq enrichment (green, log2[ChIP/input]) plotted in the same windows. The locations of non-recombining zones (NRZ, black), and low-recombining zones (LRZ, purple), are indicated beneath. Shaded blocks at the top of these plots indicate regions of Col/Ler synteny (blue) and inversions (pink) mapped by SyRI [37]. The lower three rows are the same as above, but for the Ler genome assembly. Information on chromatin datasets analyzed is available in Additional file 6: Table S2