title: ddRADSeq of Quercus faginea: reproductive tree leaf
design: We used a mixer mill to grind c. 50 mg of frozen leaf tissue in tubes with a tungsten bead and performed DNA extraction and purification with NucleoSpin Plant II kits (Macherey-Nagel, Duren, Germany). We processed genomic DNA into different genomic libraries (72 individuals/library) using the double-digestion restriction-site associated DNA sequencing procedure (ddRAD-seq) described in Peterson et al. (2012) (PLOS One, 7: e37135). In brief, we digested DNA with the restriction enzymes MseI and EcoRI (New England Biolabs, Ipswich, MA, USA) and ligated Illumina adaptors including unique 7-bp barcodes to the digested fragments of each individual. We pooled ligation products and size-selected them between 350-450 bp with a Pippin Prep machine (Sage Science, Beverly, MA, USA). We amplified the fragments by PCR with 12 cycles using the iProofTM High-Fidelity DNA Polymerase (BIO-RAD, Hercules, CA, USA) and sequenced the libraries in single-read 150-bp lanes on an Illumina HiSeq2500 platform at The Centre for Applied Genomics (SickKids, Toronto, ON, Canada).