The Cucurbitaceae family is the second most large horticultural family in terms of economic importance after Solanaceae. It includes several important crops, such as melon (Cucumis melo), watermelon (Citrullus lanatus), cucumber (Cucumis sativus) and many Cucurbita species with edible fruits (Jeffrey, 1980). The genus Cucurbita (2x = 2n = 40), originated in the Americas, encompasses three economically important crop species such as Cucurbita pepo, Cucurbita moschata, and Cucurbita maxima, cultivated throughout temperate, sub-tropical, and tropical regions (Wang et al., 2011). Cucurbita pepo includes a wide assortment of varieties and cultivars, known for their unique fruit shape and color and appreciated for their culinary properties. Among different species of this genus, Cucurbita pepo have the greatest monetary value (Paris, 2008). Botanical classification based on allozyme variation recognized three subspecies in this species including: pepo, ovifera (syn. texana), and fraterna. Paris (1986) classified edible-fruited C. pepo into eight cultivar-groups: Acorn, Crookneck, Scallop, and Straightneck that belong to subsp. ovifera and Pumpkin, Zucchini, Cocozelle, and Vegetable Marrow that belong to subsp. pepo (Paris, 2010). The genome size of Cucurbita spp. is approximately 500 Mb (Arumuganathan and Earle, 1991). Recently, a high-quality draft of C. pepo (subsp. pepo cultivar-group Zucchini) genome with a sequences length of about 265 million base pairs (Mbp) was made available on CucurbiGene database as well as several C. pepo transcriptomes have been explored (Blanca et al., 2011; Wyatt et al., 2015; Vitiello et al., 2016; Xanthopoulou et al., 2016, 2017; Montero-Pau et al., 2017). However, still little is known about the genetic diversity of this noteworthy crop and even less has been done to explore its proteome. High-throughput sequencing of transcriptomes has opened the way to study the genetic and functional information stored within any organism at an unprecedented scale and speed.