Differentially expressed genes during berry ripening in de novo RNA assembly of Vitis flexuosa fruits

A comparative transcriptome analysis between unripe and ripe berries of Vitis flexuosa, a Korean native wild grape, was conducted to identify differentially expressed genes (DEGs). About 12 billion nucleotides derived from unripe and ripe berries were sequenced and 180,503 contigs were obtained from the assembly results. Expression profiles of transcriptome data revealed that 5249 DEGs showed significant differences at transcript levels between unripe and ripe berries. The top five up-regulated genes in ripe berries against unripe berries were cupin family protein, cytochrome p450 79a2, HSP20-like chaperones superfamily protein, chalcone and stilbene synthase family protein, and beta-tonoplast intrinsic protein. The five most down-regulated genes in ripe berries against unripe berries were cellulose synthase family protein, laccase 17, proline-rich protein 2, subtilase 1.3, and laccase/diphenol oxidase family protein. Among DEGs, top 10 up- and down-regulated carbohydrate, organic substance, and phenylpropanoid metabolic process-related genes were selected from transcriptome analysis and their expression profiles were validated by real-time PCR. Real-time PCR analysis revealed higher expression level of DEGs encoding xyloglucan endotransglucosylase/hydrolase 32 and pectin lyase-like superfamily protein, which are related to starch and sucrose metabolism, cruciferin 3 and AGAMOUS-like 104, which are involved in organic acid metabolism, and MYB domain protein 113 and chalcone and stilbene synthase family protein, which play a role in the phenylalanine ammonia-lyase pathway in ripe than in unripe berries. Overall, we present an overview of transcriptome changes and carbohydrate, organic substance, and phenylpropanoid metabolic process-related expression patterns in unripe and ripe berries of V. flexuosa during berry ripening.