The sequencing produced a total of 69,5 millions of clean paired reads, obtaining 13,9 e12 bp of RNA-Seq data for C. pepo (Supplementary Table 1). Transcriptome assembly yielded 68,720 transcripts, with mean length of 1,534 bp. The transcripts were translated and a high-quality proteome of 33,966 primary protein sequences, with mean length of 316 AA, were obtained. DIAMOND similarity-based searches were performed against the publically available databases (SWISS-PROT, TrEMBL, TAIR10, and GenBank-NR) to annotate C. pepo proteome (Supplementary Table 2). About 85% of proteins encoded by genes had homology with four principal databases and over 75% were functionally annotated (Table 1). In addition, a GO-annotation using Blast2GO were effected and a total of 256,138 GO-terms were assigned to about 65% (21480) of the predicted proteins (Supplementary Table 3).