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, log 2 [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
