DNA- seq of  Solidago altissima plant species
DNA quantity was assessed (&gt;8.5 ng/l) using a QuBit broad-sensitivity DNA quantification system (Invitrogen, Carlsbad, CA, USA). We performed double-digest genotype-by-sequencing library preparation by adding 200 ng of high-quality DNA in 7.2 L water to 2.0 L CutSmart Buffer 10x, 0.4 L Pst-1 HF (NEB), 0.4 L Msp1. Samples were digested for 8h at 37C, 20 minutes at 65C with 2.0 L 10x CutSmart Buffer, 4.0 L 10mM ATP, 0.5L T4 DNA Ligase, 8 L H2O, 1L 10mM common adaptor and 5L 0.6ng/L barcoded adaptor. We ligated samples for 3h at 22C and 20 minutes at 65C, and mixed all samples with 6144 L Sera-Mag beads (Thermo Fisher). After 15-minute incubation at room temperature, we allotted samples to seven 1.5mL tubes and placed these in Dyna-Mag 2 (Thermo Fisher) magnet for 4 minutes. Clear liquid was then removed, and washed three times using 80% EtOH and once with 100% EtOH, and eluted in 150 L 10mM Tris pH 8.0. We amplified eight reactions each with 3L of elution and 7.5uL H2O, 12.5 L KAPA 2x MasterMix, 1L of 12.5mM each PCR primers f &amp; r. Reaction cycle was 98C for 1 minute, followed by 20s at 62C and 30s at 72C. Following 16 cycles, we additionally kept samples at 72C for 5 minutes. After amplification, we cleaned up 30 L from each well using the Bioline PCR and Gel kit (Bioline), and eluted the purified product in 30L buffer. Size selection was performed by running the cleaned PCR product on a 2% agarose gel and removing the 400-600bp fragment. This gel fragment was cleaned up using the Bioline PCR and Gel Kit (Biolin1) and eluted in 20 L H2O. The ddGBS libraries were paired-end sequenced by Genome Quebec on the Illumina HiSeq 2000 platform.