Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis

Abstract

Tomato (Solanum lycopersicum) serves as a research model for fruit development; however, while it is an important dietary source of antioxidant nutrients, the transcriptional regulation of genes that determine nutrient levels remains poorly understood. Here, the transcriptomes of fruit at seven developmental stages (7, 14, 21, 28, 35, 42 and 49 days after flowering) from two tomato cultivars (Ailsa Craig and HG6-61) were evaluated using the Illumina sequencing platform. A total of 26,397 genes, which were expressed in at least one developmental stage, were detected in the two cultivars, and the expression patterns of those genes could be divided into 20 groups using a K-mean cluster analysis. Gene Ontology term enrichment analysis indicated that genes involved in RNA regulation, secondary metabolism, hormone metabolism and cell wall metabolism were the most highly differentially expressed genes during fruit development and ripening. A co-expression analysis revealed several transcription factors whose expression patterns correlated with those of genes associated with ascorbic acid, carotenoid and flavonoid biosynthesis. This transcriptional correlation was confirmed by agroinfiltration mediated transient expression, which showed that most of the enzymatic genes in the ascorbic acid biosynthesis were regulated by the overexpression of each of the three transcription factors that were tested. The metabolic dynamics of ascorbic acid, carotenoid and flavonoid were investigated during fruit development and ripening, and some selected transcription factors showed transcriptional correlation with the accumulation of ascorbic acid, carotenoid and flavonoid. This transcriptome study provides insight into the regulatory mechanism of fruit development and presents candidate transcription factors involved in secondary metabolism.

Structural and biochemical approaches uncover multiple evolutionary trajectories of plant quinate dehydrogenases

“…We expect this process to be more actively occurring during the early stages of plant growth and development, because an actively growing plant requires a constant supply of CGA as an antioxidant and protection from UV light, herbivory and microbial pathogens (Mondolot et al ., ; Wojciechowska et al ., ). As the plant matures there is less demand for CGA, and as such quinate can be diverted for synthesis of other compounds (Ye et al ., ). We expect the NAD + ‐specific QDH to divert the available quinate in the cytoplasm to dehydroquinate, which can then be redirected towards biosynthesis of aromatic compounds.…”

Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening

“…In addition to the extensively enriched pathways in COS and LSW177, some DEGs were found to be involved in carotenoid formation, plant hormone signal transduction, sugar metabolism and cell wall metabolism and might have unique functions in cultivated watermelon during fruit ripening. These metabolic pathways are also important for fruit ripening in melon [20], tomato [21] and orange [19]. These pathways have the ability to create an organized metabolic association that possibly cooperates during fruit ripening in cultivated watermelon.…”

An InDel in the Promoter of Al-ACTIVATED MALATE TRANSPORTER9 Selected during Tomato Domestication Determines Fruit Malate Contents and Aluminum Tolerance

“…Total RNA extractions were performed essentially as described by Ye et al (2015). Total RNAs were then sent to the Annoroad Company, where the libraries were produced and sequenced using single-ended sequencing of Illumina HiSeq 2500.…”