Fig. 2
Gene and transposon content of the Arabidopsis LRZs and NRZs. A Meta-profiles of leaf RNA-seq (blue, Log2[RNA-seq (TPM)], SPO11-1-oligos (pink, Log2[SPO11-1-oligos/genomic DNA]), ASY1 (green, Log2[ChIP-seq/input]), REC8 (red, Log2[ChIP-seq/input]), DNA methylation (%, CG=dark blue, CHG=blue, CHH=light blue), and H3K9me2 (blue, Log2[ChIP-seq/input]), across genes located in the chromosome arms (n=27,499), the LRZs (n=542), and the NRZs (n=132) and in 2-kb flanking regions. For each gene set, the same number of random windows of the same widths was compared within the same regions. Plot ribbons denote 95% confidence intervals for windowed values. Information on chromatin datasets analyzed is available in Additional file 6: Table S2. B Observed number of LRZ crossovers overlapping the listed gene features are shown (blue), compared to 10,000 sets of randomly positioned loci of the same number and width distribution as the LRZ crossovers. The α=0.05 significance thresholds are indicated (red), and the means of the permuted sets of loci (black) (P-values from all comparisons were <0.0001). C The observed median Pi (π) value for genes located in the LRZs (n=336) and NRZs (n=58) (blue), compared to 1000 sets of randomly chosen genes in the chromosome arms (gray). α=0.05 significance thresholds are indicated (red), and the medians of the permuted loci sets (black). P-values for both comparisons were <0.0001. Pi was calculated using 1001 Genomes Project SNPs [46]. D Plots of retrotransposon density per 100 kb along the Col-CEN assembly, showing Gypsy (black), Copia (purple), and LINE (green) superfamilies. The locations of the LRZs (purple) and NRZs (black) are indicated above the plots, and the CEN178 satellite arrays (red, blue) are indicated along the x-axis