Genomic DNA preparation was performed as previously described (Debladis et al. 2017 (link)). After Qubit dosage (dsDNA High Sensitivity, Thermo Fisher Scientific), a second step of DNA purification was performed with the Genomic DNA Clean and Concentrator kit (Zymo Research) and precipitated. A last Qubit dosage was performed before library preparation using the 1D Genomic DNA by ligation kit SQK-LSK109 (Oxford Nanopore Technologies), following the manufacturer's instructions. The R9.5 ONT flow-cell FLO-MIN106D (Oxford Nanopore Technologies) was used. We obtained 6.4 Gb of sequences for L6F6, 0.7 Gb for L9F6, 5.9 Gb for fas1-4, and 11.4 Gb for fas2-4.
ONT reads were mapped on the TAIR10 reference genome using minimap2 with -a -Q -map-ont options (Li 2018 (link)). The alignment files were converted into BED files using BEDTools, and the coverage per 100-kb window was calculated using coverageBED (Quinlan and Hall 2010 (link)). For each 100-kb window, the ratio r = 20%rDNA coverage/wild-type Col-0 coverage was calculated. The mean (m) and standard error (SE) were calculated across the entire genome. Differentially covered regions in the 20%rDNA line were defined as regions for which r ≥ m+2SE or r ≤ m−2SE.
Additional methods can be found in theSupplemental Material .
ONT reads were mapped on the TAIR10 reference genome using minimap2 with -a -Q -map-ont options (Li 2018 (link)). The alignment files were converted into BED files using BEDTools, and the coverage per 100-kb window was calculated using coverageBED (Quinlan and Hall 2010 (link)). For each 100-kb window, the ratio r = 20%rDNA coverage/wild-type Col-0 coverage was calculated. The mean (m) and standard error (SE) were calculated across the entire genome. Differentially covered regions in the 20%rDNA line were defined as regions for which r ≥ m+2SE or r ≤ m−2SE.
Additional methods can be found in the
