The first Illumina-based de novo transcriptome sequencing and analysis of pumpkin (Cucurbita moschata Duch.) and SSR marker development

Pumpkin (Cucurbita moschata Duch.) is an important vegetable crop cultivated worldwide. In this study, the pumpkin transcriptome was sequenced by RNA-seq using the Illumina Hiseq 2000. A total of 52,849,316 clean sequencing reads, 66,621 contigs and 62,480 unigenes were postulated. Based on similarity searches with known proteins, 47,899 genes (76.66 % of the unigenes) were annotated: 47,596, 34,368 and 16,700 mapped in Nr, Swissprot and COG classifications, respectively; 21,164 were annotated with 44 gene ontology functional categories; and 13,728 were annotated to 269 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 7,814 simple sequence repeats (SSRs) were identified in these unigenes and 4,794 pairs of primers were designed for application of SSRs. To date, 35 SSRs have been validated in 12 pumpkin varieties and can separate the pumpkin varieties into Cucurbita maxima and Cucurbita moschata. In addition, the expression of eight photoperiod-related unigenes were studied in different pumpkin plants and it was deduced that they may contribute to late flowering and light insensitiveness. This research will provide an important platform to facilitate gene discovery for functional genome studies of pumpkin and to conduct SSR discovery for breeders for use in pumpkin breeding.