A homozygous doubled haploid line TO1000DH3 derived from B. oleracea cultivar TO1434 was chosen for sequencing. High quality nuclear DNA was extracted from young leaves using a megabase-sized DNA isolation protocol as described in [34 ]. Briefly, approximately 40 g of fresh leaf tissue was homogenized in 200 ml buffer (HB; 0.01 M Trizma base, 0.08 M KCL, 0.01 M EDTA, 1 mM spermidine, 1 mM spermine, 0.5 M sucrose plus 0.15% β-mercaptoethanol, pH 9.4 to 9.5). The homogenate was filtered and the nuclei pelleted by centrifugation (1,800 g at 4°C for 20 minutes). The pellet was resuspensed (1 × HB plus 0.5% Triton-×100) and centrifuged three times. Finally, the nuclei were resuspended in 10 ml lysis buffer (100 mM TrisCl, 100 mM NaCl, 50 mM EDTA, 2% SDS). High molecular weight genomic DNA was extracted by traditional proteinase K (0.05 mg/ml; 65°C for 2 h) digestion followed by RNAase A treatment, two cycles of phenol/chloroform extraction and ethanol precipitation. Quantification of genomic DNA was performed using PicoGreen dsDNA kit (Molecular Probes, Life Technologies Inc., Burlington, ON, Canada). Genomic DNA (5 to 40 μg) was randomly sheared using one of: Covaris S2 ultrasonicator (Covaris Inc., Woburn, MA, US); Hydroshear (Genomic Solutions Inc., Ann Arbor, MI, US); or gas-driven nebulizers. For Illumina sequencing, four paired-end (PE) libraries (with median insert sizes of 273, 335, 418 and 532 bp; Table S1 in Additional file 2 ) and five short-span mate-paired (MP) libraries (from 2.5 to 8.5 kb) were constructed following the manufacturer’s instructions (TruSeq DNA sample preparation and MP library preparation kit v2 (Illumina, San Diego, CA, US), respectively). Libraries were size selected using the Pippin prep automated gel electrophoresis system (Sage Science, Beverly, MA, US), quantified using a BioAnalyzer (Agilent Technologies, Mississauga, ON, Canada) and KAPA library quantification kit for Illumina (KAPA Biosystems, Wilmington, MA, US), and sequenced from both ends (paired-end) for 100 cycles on an Illumina HiSeq 2000 instrument. For 454 pyrosequencing, two medium span MP libraries with median insert sizes of 8 and 17 kb (Table S1 in Additional file 2 ) were constructed following the method described in the GS FLX Titanium 20 kb span PE library preparation manual from Roche and sequenced using a Roche 454 FLX Titanium sequencer (454 Life Sciences, Branford, CT, US).
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