Genomic DNA from dried leaf samples was isolated using the CTAB-based extraction protocol [9 (link), 23 ]. DNA concentration (ng/μl), average fragment size (bp) and quality (GQN = 300 bp) were measured using Fragment Analyzer (Agilent, US).
DNA library preparation was performed through an initial enzymatic fragmentation to 200–450 bp using NEBnext® Ultra™ II FS DNA Library Prep Kit for Illumina® (New England Biolabs, US) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, US). Highly-degraded DNA samples were processed without starting fragmentation using NEBnext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, US). DNA library double-size selection (320–470 bp) was done using SPRIselect® (Beckman Coulter, US). The average fragment size (bp) and molarity (nM) of the final products were calculated using Fragment Analyzer (Agilent, US).
DNA libraries were sent to RAPiD Genomics (Florida, US) and Fasteris SA (Plan-les-Ouates, Switzerland) for paired-end sequencing at low genome coverage sequencing (0.1-10X, 2x150 bp), aiming at a minimum of 5 million reads per sample, using HiSeq® 3000, as well as HiSeq® 4000 and NovaSeq® 6000 (Illumina, US).
DNA library preparation was performed through an initial enzymatic fragmentation to 200–450 bp using NEBnext® Ultra™ II FS DNA Library Prep Kit for Illumina® (New England Biolabs, US) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, US). Highly-degraded DNA samples were processed without starting fragmentation using NEBnext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs, US). DNA library double-size selection (320–470 bp) was done using SPRIselect® (Beckman Coulter, US). The average fragment size (bp) and molarity (nM) of the final products were calculated using Fragment Analyzer (Agilent, US).
DNA libraries were sent to RAPiD Genomics (Florida, US) and Fasteris SA (Plan-les-Ouates, Switzerland) for paired-end sequencing at low genome coverage sequencing (0.1-10X, 2x150 bp), aiming at a minimum of 5 million reads per sample, using HiSeq® 3000, as well as HiSeq® 4000 and NovaSeq® 6000 (Illumina, US).
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