design: Total RNA from four samples per treatment was extracted following the Qiagen RNeasy plant kit protocol; samples were chosen based on both quality of RNA and qPCR results. DNA was removed from extracted RNA using the Turbo DNA-free treatment according to the manufacturers instructions (Ambion Inc., The Life Technologies Corporation, Grand Island, NY). Removal of DNA was confirmed by using RNA (1 l) as template in a qPCR targeting 18s ribosomal DNA as previously described (Burge and Friedman, 2012). RNA concentrations were quantified using the NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE). Samples were shipped to McGill University and Genome Quebec for library preparation and sequencing. RNA quality was assessed prior to library preparation using an Agilent Bioanalyzer. The Illumina TruSeq stranded cDNA kit was used for library preparation and barcoding; quality assessment of libraries indicated that one sample was not of high enough quality for sequencing. The remaining samples were distributed across two sequencing lanes on an Illumina HiSeq 4000 platform (2x150 bp paired end reads).