RNA-Seq reads were processed with the Fastx toolkit for demultiplexing, barcode trimming and quality filtering (Pearson et al. 1997). Cutadapt was used to remove all residual adapter sequences (Martin 2011). Differential expression analysis of normalized FPKM (fragments per kilobase of exon per million fragments mapped) expression values was executed following standard protocols (Haas et al. 2013), with the following experiment-specific details. First, the RSEM software (Li and Dewey 2011) was used to align the quality reads to the V. vinifera PN40024 reference transcriptome (Grimplet et al. 2012). The trimmed mean of M-values (TMM) normalization method was executed in R to generate FPKM values for each transcript (Dillies et al. 2013).