title: WGS of Populus  canadensis: leaves
design: Genomic DNA was extracted from leaf samples and prepared for deep-sequencing using Illumina technology, as previously described (Henry et al. 2015). Sequencing reads (150 PE) were demultiplexed into individual libraries based on their barcodes, using a custom Python script (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools), as described in previous studies (Henry et al. 2015). Next, reads were aligned to the poplar reference P. trichocarpa v3.0 (Tuskan et al. 2006), using a custom Python script based on mapping using BWA (H. Li and Durbin 2009) (http://comailab.genomecenter.ucdavis.edu/index.php/Bwa-doall). This generated an alignment file (sam file) for each sample, which was used for further analysis.