These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. 7 Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001, Thermi, Macedonia, Greece. 6 Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001, Thermi, Macedonia, Greece.1 Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001, Thermi, Macedonia, Greece. 5 Perrotis College, American Farm School, GR-57001, Thessaloniki, Greece.4 Department of Vegetable Crops and Plant Genetics, Agricultural Research Organization, Newe Ya'ar Research Center, 3009500, Ramat Yishay, Israel.3 Institute for the Conservation and Breeding of Agricultural Biodiversity (COMAV-UPV), Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.2 Cavanilles Institute of Biodiversity and Evolutionary Biology (ICBiBE), Universitat de València, 46022, Valencia, Spain.1 Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization DIMITRA (ex NAGREF), GR-57001, Thermi, Macedonia, Greece.
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