The quality control checks on raw sequence data (75,22 millions of paired reads totalling 15 e12 bp) from all the three data sets was performed using FastQC (Andrews, 2010). Raw reads were filtered to remove the adapter sequences and the poorer quality regions with sequence pre-processing tool, Trimmomatic (Bolger et al., 2014). Paired-end read duplicates from the PCR amplification step in the sequencing process were removed and only those reads with a mapping score ≥ 30 were kept in the alignments. The high quality reads were aligned against the C. pepo reference genome sequence version 3.2 (https://cucurbigene.upv.es/) with STAR aligner (version 2.4.0j). The resulting alignment was used as input to Cufflinks (version 2.2.1) for transcript assembly. PASA pipeline (version 2.0.2) was used to combine Cufflinks results with the public transcriptome version 3.0 (https://cucurbigene.upv.es/).