Hiseq x ten pe150 sequencing

To generate physical scaffolds for genome assembly, we generated Hi-C sequencing data by adapting published procedures^{53 (link)} (Supplementary Note 1.4.1). In brief, freshly harvested leaves were cut into 2- to 3-mm pieces and infiltrated in 2% formaldehyde, and crosslinking was stopped by adding glycine. The tissue was ground to powder and suspended in nuclei isolation buffer to obtain a nuclei suspension. Nuclei were digested with HindIII as previously described^{18 (link)}, marked by incubating with Klenow enzyme and biotin-14-dCTP^{17 (link)} generating blunt-end-repaired DNA strands, and ligated by T4 DNA polymerase. The extracted DNA was mechanically sheared to 200–300 bp sizes by ultrasound followed by size fractionation using AMPure XP beads. DNA fragments of 150–300 bp were blunt-end repaired and A-tailed, followed by purification through biotin–streptavidin-mediated pulldown^{18 (link)}. PCR amplification was performed after adapters were ligated to the Hi-C products. The PCR products were purified with AMPure XP beads, and the Hi-C libraries were quantified by quantitative PCR for Illumina HiSeq X-ten PE150 sequencing^{17 (link)}.

DNA was isolated using the DNeasy Blood and Tissue kit (Qiagen, Valencia, CA), following the manufacturer’s protocol. Sample quantity and purity were assessed with a NanoDrop spectrophotometer (260/280 > 1.46, 260/230 > 0.45) and Qubit fluorometric quantitation. Samples were sent to McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada, for Illumina HiSeq X Ten PE150 sequencing with qPCR and using Illumina TruSeq DNA v3 adaptors. The quality of the reads was tested and found to be acceptable; the average read quality had a Phred score of 36.