Authors: Giuseppe Andolfo1, Antimo Di Donato, Reza Darrudi, Angela Errico, Riccardo Aiese Cigliano and Maria R. Ercolano

Institutions: 

  • Department of Agriculture Sciences, University of Naples ‘Federico II’, Naples, Italy
  • Department of Horticulture, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
  • Sequentia Biotech Eureka, Barcelona, Spain

Publication: Frontiers in Genetics

Date: November 2017

Full paper: https://www.frontiersin.org/articles/10.3389/fgene.2017.00181/full

Abstract:

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 fraternaParis (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., 2011Wyatt et al., 2015Vitiello et al., 2016Xanthopoulou et al., 20162017Montero-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.

Transcriptome generation through RNA sequencing (RNA-seq) is a technology that can be used in the high resolution and broad dynamic range gene expression studies and in the simultaneous understanding of the genes function (Wang et al., 2009). Basically, the protein-coding genes function is inferred by the analysis of structure, function and evolution of the proteins they encode (Guo, 2013). For the characterization of unannotated proteins, can result particularly useful to undertake orthology analysis. Proteome data are important resources for having an overall genome vision but at the same time achieving a high level of accuracy in comparative studies (Andolfo et al., 2014a). To this end, we sequenced and assembled the first transcriptome of zucchini cultivar “True French,” founder of important pathogen resistant commercial varieties and to harness the full potential of such data we performed also an high-quality proteome annotation. A total of 33,966 protein sequences were predicted, functionally annotated and compared to cucumber, melon, watermelon and Arabidopsis proteomes. In addition, disease resistance (R) gene family was finely characterized and several specie-specific R-genes expansion was detected in C. pepo.