Fig. 4: Broad- and fine-scale correlations between CO patterning and (epi)genomic features in R. breviuscula. | Nature Plants

Fig. 4: Broad- and fine-scale correlations between CO patterning and (epi)genomic features in R. breviuscula.

From: Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

Fig. 4

a, Chromosome distribution of the CO rate coupled with different (epi)genetic features. (Upper) Recombination landscape (black line) created with COs detected in all single-pollen nuclei (n = 1,641), coupled with Omni-C data. Synteny analysis and detected structural variants between the two haplotypes. For the y axes, all features were scaled [0, 1], with 1 indicating a maximum of 2.34 for CO frequency (cM Mb−1), 5 for Tyba array density, 6 for CENH3 domain density, 7,205 for SNP density, 88 for gene density and 227 for TE density. GC [33.3, 46.6], H3K4me3 [–1.494, 0.231], H3K9me2 [–1.20, 1.84] and H3K27me3 [–0.671, 0.491] are scaled to [0, 1] by their minima and maxima. Methylated CG (mCG), methylated CHG (mCHG) and CHH are original values (0–100%). All features were smoothed using a 1 Mbp sliding window and 250 kbp step size. b, Correlation matrix illustrating the correlation coefficients of 378 high-resolution COs detected in 63 selfed F1 offspring with all available (epi)genomic features. Blue, positive correlations; red, negative correlations. Colour intensity and the size of the circle are proportional to the correlation coefficients. Pearson correlation coefficients for each pair of all features under a 1 Mb smoothing window and 250 kb step size. c, Z-score of the overlapped CO numbers with different (epi)genetic features. d, CO frequency (blue line) at genic regions. TSS, transcription start site; TTS, transcription termination site; grey line, marker density. e, Fine-scale CO frequency at CENH3 domains. The dashed horizontal line is the genome-wide mean CO count within a 2.5 kb interval. f, Random distribution of the relative distance of CO positions to the end of the left and to the start of the right CENH3 domain. The solid blue line was predicted by local polynomial regression fitting (loess function from R) using data from 378 COs from our F1 offspring. The dashed blue band shows a range of one standard error above and below the fitted line. Pink-bordered triangles schematically represent CENH3 domains. g, Magnified view of one of the five COs placed closed to a region containing CENH3-positive chromatin and Tyba repeats. The CO resolution in this case is 200 bp. CO is indicated by the grey dashed line showing the haplotype switch (blue to orange) in the marker density track.

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