Fig. 1
Zones of centromere-proximal crossover suppression in Arabidopsis. A In the first row, Col/Ler crossover frequency (cM/Mb) is plotted against the Col-CEN assembly in 10-kb windows (black). CEN178 satellite density (red=forward & blue=reverse strand) and CENH3 ChIP-seq enrichment (green, log2[ChIP/input]) are plotted in the same windows. Locations of the non-recombining zones (NRZ, black), and low-recombining zones (LRZ, purple), are indicated above. Shaded blocks at the top of the plots indicate regions of Col/Ler synteny (blue) and inversions (pink) mapped by SyRI [37]. 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. Beneath, the density of genes (green) is plotted alongside %GC content (blue) per 10 kb. ATHILA retrotransposon insertions are indicated as red x-axis ticks. B As for A, but showing a zoom of the NRZ and LRZ regions. Plot annotations are the same, apart from a StainedGlass sequence identity heat map is positioned over the plots [38], and NRZ-LRZ positions are shown beneath. Histograms showing the frequency of alignments, and color correspondences, with different % sequence identity are shown above the StainedGlass heat maps. C Quantification of genomic features plotted along the ten chromosome arms that were proportionally scaled between telomeres (TEL) and NRZ midpoints. Data analyzed were gene, transposon and CEN178 density per 10 kb, CENH3 log2(ChIP/input), %GC base composition, DNA methylation, and crossovers (cM/Mb). Information on chromatin datasets analyzed is available in Additional file 6: Table S2