An acorn squash (Cucurbita pepo ssp. ovifera) fruit and seed transcriptome as a resource for the study of fruit traits in Cucurbita

Acorn squash(Cucurbita pepo)is an iconic fall vegetable in the United States,known for its unique fruit shape and also prized for its culinary properties.Little is known about the metabolism that underlies the development of fruit quality attributes such as color,sweetness,texture and nutritional qualities in acorn squash,or any other winter squash grown worldwide.To provide insight into winter squash fruit and seed development and add to the genomic resources in the Cucurbita genus,RNA sequencing was used to generate an acorn squash fruit and seed transcriptome from the cultivar Sweet REBA at critical points throughout fruit development.141838600 high-quality paired-end Illumina reads were assembled into 55949 unigenes.85%of unigenes with predicted open reading frames had homology with previously identified genes and over 62%could be functionally annotated.Comparison with the watermelon and cucumber genomes provided confirmation that the unigenes are full-length and comprehensive,covering an average of 90%of the coding sequence of their homologs and 72%of the cucumber and watermelon exomes.Key candidate genes associated with carotenoid and carbohydrate metabolism were identified toward a resource for winter squash fruit quality trait dissection.This transcriptome represents a major advance in C.pepo genomics,providing significant new sequence information and revealing the repertoire of genes expressed throughout winter squash fruit and seed development.Future studies on the genetic basis of fruit quality and future breeding efforts will be enhanced by tools and insights developed from this resource.

Comparative analysis of Cucurbita pepo metabolism throughout fruit development in acorn squash and oilseed pumpkin

Both the fruit mesocarp and the seeds of winter squash can be used for consumption,although the focus of breeding efforts varies by cultivar.Cultivars bred for fruit consumption are selected for fruit mesocarp quality traits such as carotenoid content,percent dry matter,and percent soluble solids,while these traits are essentially ignored in oilseed pumpkins.To compare fruit development in these two types of squash,we sequenced the fruit transcriptome of two cultivars bred for different purposes:an acorn squash,‘Sweet REBA’,and an oilseed pumpkin,‘Lady Godiva’.Putative metabolic pathways were developed for carotenoid,starch,and sucrose synthesis in winter squash fruit and squash homologs were identified for each of the structural genes in the pathways.Gene expression,especially of known rate-limiting and branch point genes,corresponded with metabolite accumulation both across development and between the two cultivars.Thus,developmental regulation of metabolite genes is an important factor in winter squash fruit quality.