Characterization of Cucurbita maxima Fruit Metabolomic Profiling and Transcriptome to Reveal Fruit Quality and Ripening Gene Expression Patterns

Pumpkin (Cucurbita maxima) fruit is the important dietary source of carotenoid and is known for the good flavour and texture due to the accumulation of sugar and starch. However, lack of transcriptional information hinders our understanding of the molecular mechanisms underlying fruit quality attributes and nutrition in C. maxima. To provide insight into transcriptional regulation of fruit quality formation of C. maxima, quality analysis and high-throughput RNA sequencing of fruits at different developing stages were characterized. The quality analyses consist of dry matter values, percent soluble solids, carotenoid contents, and starch and sugar contents in seven stages of fruit development. Fruit transcriptome of C. maxima at five stages throughout development was assembled to elucidate the molecular regulation of fruit development. Almost 18 billion nucleotide bases were sequenced in total, and 48,471 unigenes were detected. A total of 32,397 (66.8%) unigenes were identified to be differentially expressed. We found there was a correlation between ripening-associated transcripts and metabolites and the functions of regulating genes. KEGG analysis showed there are multiple transcripts enriched in starch, sugar, carotenoid, plant hormone signal transduction and pectin pathways and several pathways regulating quality formation were identified. Candidate genes involving in sugar, starch, pectin, fruit softening and carotenoid metabolism in fruit were firstly identified for the species of C. maxima. Combining the sugar, starch and carotenoid accumulating patterns during fruit development, a series of possible rate limiting genes were identified. These findings will provide valuable information for further studies regarding fruit quality and development.