De novo Sequencing and Assembly of a Winter Squash (Cucurbita pepo) Fruit Transcriptome

Squash is an important vegetable crop that is widely cultivated for the consumption of both immature and mature fruits as well as seeds.  Fruit quality is determined by the interaction of several factors, including nutrient content, flavor, sweetness, and texture.  In order to enhance the breeding of squash for improved fruit quality, it is necessary to understand the genetic basis of these traits.  Cucurbita pepo (2n = 40) has a genome of approximately 500 Mb and has a limited number of genetic resources available.  To enable the study of squash fruit quality and development, we have used transcriptome sequencing to generate a winter squash fruit transcriptome.  Our fruit transcriptome is derived from both pericarp and seed tissue of an acorn squash, sampled at five time points during fruit development.  We assembled 141,838,600 high-quality paired-end Illumina reads into 99,839 unigenes using the program Trinity.  More than 83% of these unigenes have homology with known genes and more than 69% could be functionally annotated.  We have also identified fruit quality-related genes of interest from the transcriptome; most notably, genes related to carotenoid accumulation and carbohydrate metabolism are central to fruit quality.