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Expression data from tomato fruit at three ripening stages (MG, Br, B10) in wild type lines (Alsa Craig, AC, and M82) and five tomato carotenoid mutants: apricot (at), yellow flesh (r), tangerine (t), Beta (B), and Delta (Del).

ABSTRACT: Carotenoids are essential natural compounds for human nutrition and play key roles in plants as photosynthetic pigments and as precursors of hormones and apocarotenoids. Tomato is a major model for carotenoid metabolism, where genetic variation strongly influences carotenoid composition during fruit ripening. Here we present an extensive biochemical and molecular characterization of five tomato carotenoid mutants—apricot (at), yellow flesh (r), tangerine (t), Delta (Del) and Beta (B)—across three ripening stages (mature green, breaker and red ripe). Gene-expression profiling (Affymetrix microarrays) was integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones and ABA) and correlation-based analyses. Isoprenoid profiles showed strong, stage-dependent remodeling that extended beyond expected substrate/product changes and was accompanied by substantial transcriptional variation, often independent of the position of the mutated step in the pathway. The integrated analysis highlighted regulatory links between transcripts and metabolites and pointed to lycopene cyclization as a central node in isoprenoid network rewiring during ripening, improving our understanding of mechanisms controlling isoprenoid accumulation in tomato fruit. Carotenoids are key bioactive compounds, and tomato is a major model to study how genetic variation shapes their accumulation during fruit ripening. We profiled five tomato carotenoid mutants (apricot at, yellow flesh r, tangerine t, Delta Del, Beta B) across three ripening stages using Affymetrix gene-expression arrays integrated with targeted isoprenoid metabolomics (carotenoids, chlorophylls, tocochromanols, quinones, ABA) and correlation analyses. The data reveal strong stage-dependent remodeling and highlight lycopene cyclization as a central hub in isoprenoid pathway rewiring during ripening.

ORGANISM(S): Solanum lycopersicum

PROVIDER: GSE327902 | GEO | 2026/06/03

REPOSITORIES: GEO

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Project description:Tomato fruit ripening is under the control of ethylene as well as a group of ethylene-independent transcription factors, including NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN). During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) under the control of the PHYTOENE DESATURASE (PDS) promoter resulted in increased levels of β-carotene and ABA and in decreased ethylene levels. Genes regulated by ABA, or involved in its synthesis and signaling, were overexpressed, while those associated with ethylene and cell wall remodeling were repressed. In agreement with the transcriptional data, LCYb-overexpressing fruits exhibited increased density of cell wall material containing linear, under-methylated pectins and displayed an array of additional ripening phenotypes, including delayed softening, increased turgor, enhanced shelf life and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoids also changed in the transgenics, which could be attributed to delayed fruit ripening and to ABA respectively. Network correlation analysis suggests that ABA, acting through NOR and RIN, is responsible for many of the above phenotypes. These data reinforce suggestions that ABA plays an important role in tomato fruit ripening and provide clues that fruit b-carotene, acting as a precursor for ABA, actively participates in controlling the ripening process rather than merely being an output thereof. Overexpression of a LCYb gene from Arabidopsis under the control of the ripening-associated PDS promoter leads to ripe tomato fruits accumulating high β-carotene levels. Using several independent transgenic lines, we conducted a system-wide study of the effect of increased β-carotene levels on tomato fruit ripening and shelf life. Our data suggest that β-carotene, acting through ABA, is involved in a regulatory loop within the network controlling tomato fruit ripening.

Project description:Fruit flavor and color are critical quality characteristics of tomatoes. Numerous studies have demonstrated that tomato flavor is primarily linked to the sugar-acid content and its ratio, while fruit color is predominantly determined by the composition and concentration of carotenoids and flavonoids. To elucidate the regulatory mechanisms underlying the differences in sugar-acid and color formation during fruit ripening, transcriptome analyses were conducted on the closely related yellow-fruited tomato (No.19) and red-fruited tomato (No.20) strains. This analysis aimed to identify key regulatory genes and biosynthetic pathways related to flavor and color development in tomato fruits. The transcriptome analysis revealed that 1,546 differentially expressed genes (DEGs) were identified in the Br19_vs_Br20 comparison, of which 507 were up-regulated and 1,039 were down-regulated. In the MF19_vs_MF20 comparison, 2,178 DEGs were detected, with 1,235 up-regulated and 943 down-regulated. Upon further analysis of the differentially expressed genes, we identified several key genes in the sugar-acid metabolic pathway, including sucrose synthase (SUS), phosphofructokinase (PFK), fructose-bisphosphate aldolase (FBA), citrate synthase (CS), and succinate dehydrogenase (SuDH), which may significantly influence tomato flavor. Additionally, differential genes related to carotenoid and flavonoid metabolism, such as cytochrome P450 98A (CYP98A), caffeoyl-CoA3-O-methyltransferase (CCoAMT), carotenoid isomerase (CRTISO), lycopene beta cyclase (LCYB), zeaxanthin epoxidase (ZEP), violaxanthin deepoxidase (VDE), and 9-cis-epoxycarotenoid dioxygenase (NCED), as well as genes linked to ethylene synthesis, such as 1-aminocyclopropane-1-carboxylate synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), may play a role in the color changes observed in tomatoes. The findings of this study provide insights into the underlying mechanisms of flavor and color development in tomato fruit, offering valuable information for the genetic improvement of tomatoes.

Project description:Purpose: The goals of this study was to provide genome-wide data to investigate the molecular mechanism of ABA regulation in many ripening related biological processes, including fruit color variation, antioxidant capacity, flavonoids biosynthesis and photosynthesis. Methods:By applying the next generation sequencing technology, we conducted a comparative analysis of exogenous ABA and NDGA effects on tomato fruit maturation. Results:The high throughput sequencing results showed that 25728 genes expressed across all three samples, and 10388 of them were identified as significantly differently expressed genes (DEGs). Exogenous ABA was found to enhance the transcription of genes in pigments metabolism, including carotenoids biosynthesis and chlorophyll degradation, whereas NDGA treatment inhibited these progresses. The results also revealed the crucial role of ABA in flavonoids synthesis and regulation of antioxidant system. Intriguingly, we also found that an inhibition of endogenous ABA significantly enhanced the transcriptional abundance of genes involved in fruit photosynthesis. Conclusions:next-generation sequencing enabled us to characterize the transcriptomes of tomato fruit treated with ABA and NDGA. By comparing these transcriptomes with control respectively, we observed that ABA could accelerate fruit maturation by positively regulating many genes related to ripening processes. Our study have turned spotlight on the pathways of fruit pigmentation, including carotenoid biosynthesis and chlorophyll metabolism. Exogenous ABA was able to up-regulate many genes in relation to the carotenoids accumulation and chlorophyll breakdown, thus promoting the color transition of tomato fruit. In addition, ABA has the potential to improve the genes related to antioxidant capacity, such as SODs, CATs, APXs, GSTs, GPXs, TrXs and PrxRs. Besides, the expression changes of genes involved in flavonoids biosynthesis after ABA exposure was striking, suggesting ABA could enhance the defense response by producing more secondary metabolite in tomato fruit. Moreover, the sequencing results also implied high level of ABA could negatively affect photosynthesis of tomato fruit, which needs more investigations to explore the interaction between ABA and photosynthesis in the future.

Project description:Gene-to-gene coexpression analysis is a powerful approach to infer function of uncharacterized genes. To perform non-targeted coexpression analysis of tomato genes, we collected a developmental gene expression dataset using various tissues of tomato plant. Expression data are collected from 24 different tissue types including root, hypocotyl, cotyledon, leaf at different stages, and fruit tissues at 4 different ripening stages from 4 different Solanum lycopersicum cultivars. Fruits were separated to the flesh and the peel. These two tissue types indeed showed remarkably different gene expression profiles. We also collected data from 4 different ripening stages (mature green, yellow, orange, and red) to detail the changes during ripening. By using this gene expression dataset, we calculated pair-wise Pearsonâs correlation coefficients, and performed network-based coexpression analysis. The analysis generated a number of coexpression modules, some of which showed an enrichment of genes associated with specific functional categories. This result will be useful in inferring functions of uncharacterized tomato genes, and in prioritizing genes for further experimental analysis. We used Affymetrix GeneChip Tomato genome Arrays to detail the global gene expression change using 24 different tomato tissue types (67 hybridizations). We collected gene expression data from 24 different tomato tissue types using 67 hybridizations. Root, hypocotyl, cotyledon, and leaf were sampled from 3-week-old or 5-weekâold plant of Solanum lycopersicum cultivar Micro-Tom. Fruit tissues were sampled from S. lycopersicum cultivars Micro-Tom, Anthocyanin fruit (Aft, LA1996), Line27859, and Momotaro 8 (Takii, Japan). From Micro-Tom fruit, the peel and the flesh were separately sampled from 4 different ripening stages: mature green (MG, approximately 30 day after anthesis), yellow (Y, approximately 35 days after anthesis), orange (O, approximately 38-40 days after anthesis), and red (R, approximately 45-48 days after anthesis). From fruits of Aft and Line27859, the peel and the flesh were sampled at mature green (MG, approximately 40 days after anthesis) and red (R, approximately 50-55 days after anthesis) stages. From Momotaro 8, the peel and the flesh were sampled at red (R, 50- approximately 50-55 days after anthesis) stages. For each tissue type, 2-4 biological replicates were made in RNA preparation.

Project description:The aim of this study was to elucidate the potential use of microarray technology, developed in model species, in related, yet phenotypically distinct, species where few or no information are available. Considering the high degree of sequence conservation within the Rosaceae family and, in particular, among the Prunus species we employed the first available peach oligonucleotide microarray (µPEACH 1.0) for studying the transcrptomic profile during apricot fruit development (Prunus armeniaca L., cv. 'Goldrich'). Fruit material was harvested at three distinct stages, corresponding to immature-green stage (6 weeks before fully-ripe stage), mature-firm-ripe stage (change of peel color, 1 week before fully-ripe stage) and at fully-ripe stage and designated as S1, S2 and S3 stages, respectively. Apricot targets cDNA, when applied the µPEACH1.0, were showing significant hybridization with an average of 43% of spotted targets validating the use of μPEACH1.0 to profile the transcriptome of apricot fruit during development and ripening. Microarray analysis carried out on immature and ripe peach and apricot fruit separately pointed out that 70% of genes differentially expressed was detectable the same pattern of expression in both species. This result indicates that the transcriptome of immature and ripe fruit are quite similar in apricot and peach, but also highlighted the presence of transcript changes specie-specific. When μPEACH1.0 was used to profile apricot developing fruit were identified 400 and 74 genes differetially expressed during the transition from S1 to S2 stage and from S2 to S3 stage, respectively. Intriguingly, a considerable number of auxin action regulators (AUX/IAA) and of genes coding heat shock proteins (hsp) were highly up-regulated at the onset and late of ripening phase, respectively.The comparison between the expression profiles of these apricot genes and their peach hortologues showed a similar pattern for AUX/IAA and quite different for hsps. This result suggests a similar role for AUX/IAA in both species and a more important involvement for hsps in the apricot fruit ripening.

Dataset Information

Expression data from tomato fruit at three ripening stages (MG, Br, B10) in wild type lines (Alsa Craig, AC, and M82) and five tomato carotenoid mutants: apricot (at), yellow flesh (r), tangerine (t), Beta (B), and Delta (Del).

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