Distribution of mapped reads after CRISPR-Cas9-mediated repeat depletion. Libraries of L. culinaris cv. Castelluccio DNA (8-plex) were depleted using the custom gRNA set and Cas9. The gRNAs were used simultaneously (All) or were split into three groups that were used sequentially in order of increasing cutting frequency (3 grp). Bar graphs show the number (in millions) of reads mapping to repetitive DNA (A), to nuclear repetitive DNA (B), to the chloroplast genome (C), to the mitochondrial genome (D), and to the single-copy regions of the nuclear genome (E). Data are means ± SD (n = 3 for each condition; [*] P-adj ≤ 0.05, [**] P-adj ≤ 0.01, [***] P-adj ≤ 0.001, [****] P-adj ≤ 0.0001; one-way ANOVA plus Tukey's multiple comparisons test; [ns] not significant).