The dataset submitted to NCBI include the raw read sequences of three biological replicates of Cucurbita pepo subsp. pepo cultivar-group Zucchini, variety True French, in FASTQ format. The raw reads of C. pepo can be accessed at NCBI with the following BioSample accession number: SAMN07426850 (www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP114337). The C. pepo transcriptome annotation, in GTF format, and primary protein sequences in FASTA format can be accessed at FIGSHARE with the following link (https://figshare.com/s/8a083f60df238acdbc19). The Supplementary Material (Supplementary Tables 1–5) for this article can be found online at: (https://figshare.com/s/8a083f60df238acdbc19). Users can download and use the data freely for research purpose only with acknowledgment to us and quoting this paper as reference to the data.