Wounding tomato fruit elicits ripening-stage specific changes in gene expression and production of volatile compounds

Variation in ripe fruit volatiles across the tomato clade: An evolutionary framework for studying fruit scent diversity in a crop wild relative

PREMISE

The scents of volatile organic compounds (VOCs) are an important component of ripe fleshy fruit attractiveness, yet their variation across closely related wild species is poorly understood. Phylogenetic patterns in these compounds and their biosynthetic pathways offer insight into the evolutionary drivers of fruit diversity, including whether scent can communicate an honest signal of nutrient content to animal dispersers. We assessed ripe fruit VOC content across the tomato clade (Solanum sect. Lycopersicon), with implications for crop improvement since these compounds are key components of tomato flavor.

METHODS

We analyzed ripe fruit volatiles from 13 species of wild tomato grown in a common garden. Interspecific variations in 66 compounds and their biosynthetic pathways were assessed in 32 accessions, and an accession-level phylogeny was constructed to account for relatedness.

RESULTS

Wild tomato species can be differentiated by their VOCs, with Solanum pennellii notably distinct. Phylogenetic conservatism exists to a limited extent. Major cladewide patterns corresponded to divergence of the five brightly colored-fruited species from the nine green-fruited species, particularly for nitrogen-containing compounds (higher in colored-fruited) and esters (higher in green-fruited), the latter appearing to signal a sugar reward.

CONCLUSIONS

We established a framework for fruit scent evolution studies in a crop wild relative system, showing that each species in the tomato clade has a unique VOC profile. Differences between color groups align with fruit syndromes that could be driven by selection from frugivores. The evolution of colored fruits was accompanied by changes in biosynthetic pathways for esters and nitrogen-containing compounds, volatiles important to tomato flavor.

Volatilome and proteome responses to Colletotrichum lindemuthianum infection in a moderately resistant and a susceptible bean genotype

We analyzed the changes in the volatilome, proteome, stomatal conductance, salicylic and jasmonic acid contents of a susceptible and a moderately resistant genotype of common bean, Phaseoulus vulgaris L., challenged with Colletotrichum lindemuthianum, the causal agent of fungal anthracnose. Our results indicate differences at both proteome and volatilome levels between the two genotypes, before and after the infection, and different defense strategies. The moderately resistant genotype hindered pathogen infection, invasion, and replication mainly by maintaining epidermal and cell wall structure. The susceptible genotype was not able to limit the early stages of pathogen infection. Rather, stomatal conductance increased in the infected susceptible genotype, and enhanced synthesis of Green Leaf Volatiles and salicylic acid was observed, together with a strong hypersensitive response. Proteomic investigation provided a general framework for physiological changes, whereas observed variations in the volatilome suggested that volatile organic compounds may principally represent stress markers rather than defensive compounds per se.

A new perspective on plant defense against foliar gall-forming aphids through activation of the fruit abscission pathway

The peach aphid Tuberocephalus momonis seriously damages leaves and forms galls in the peach species Prunus persica f. rubro-plena, P. persica, and P. davidiana. Leaves bearing galls formed by these aphids will be abscised at least two months earlier than the healthy leaves on the same tree. Thus, we hypothesize that gall development is likely to be governed by phytohormones involved in normal organogenesis. The soluble sugar content was positively correlated between gall tissues and fruits, suggesting that the galls are sink organs. The results of UPLC-MS/MS analysis showed that higher concentrations of 6-benzylaminopurine (BAP) accumulated in both the gall-forming aphids, the galls themselves and the fruits of peach species than in healthy leaves, suggesting that BAP was being synthesized by the insects to stimulate the establishment of a gall. A significant increase in the concentrations of abscisic acid (ABA) in fruits and jasmonic acid (JA) in gall tissues indicated that these plants are defending from the galls. The concentrations of 1-amino-cyclopropane-1-carboxylic acid (ACC) significantly increased in gall tissues compared with healthy leaves, and were positively correlated with both fruit and gall development. In addition, transcriptome sequencing analysis revealed that during gall abscission, differentially expressed genes in both 'ETR-SIMKK-ERE1' and 'ABA-PYR/PYL/RCAR-PP2C-SnRK2' were significantly enriched during gall abscission. Our results showed that ethylene pathway was involved in the abscission of gall, and this gall abscission allowed the host plants to protect themselves from the gall-forming insects, at least partially.

Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information

Gene regulatory networks (GRNs) represent the regulatory links between transcription factors (TF) and their target genes. In plants, they are essential to understand transcriptional programs that control important agricultural traits such as yield or (a)biotic stress response. Although several high- and low-throughput experimental methods have been developed to map GRNs in plants, these are sometimes expensive, come with laborious protocols, and are not always optimized for tomato, one of the most important horticultural crops worldwide. In this chapter, we present a computational method that covers two protocols: one protocol to map gene identifiers between two different tomato genome assemblies, and another protocol to predict putative regulators and delineate GRNs given a set of functionally related or coregulated genes by exploiting publicly available TF-binding information. As an example, we applied the motif enrichment protocol on tomato using upregulated genes in response to jasmonate, as well as upregulated and downregulated genes in plants with genotypes OENAM1 and nam1, respectively. We found that our protocol accurately infers the expected TFs as top enriched regulators and identifies GRNs functionally enriched in biological processes related with the experimental context under study.

HS-SPME-GC/MS Analysis for Revealing Carob's Ripening

Carob's recognized nutritional and medicinal value next to its unique agriculture importance is associated with an array of social, economic, and cultural activities. The carob fruit is popular for its intense aroma due to the emitted volatile organic compounds (VOCs). The composition of VOCs released from carob fruits changes during ripening, rendering it a non-invasive tool for the determination of the ripening period and freshness of the fruit. Therefore, headspace solid-phase microextraction gas chromatography/mass spectrometry (HS-SPME-GC/MS) was applied to reveal the respective gaseous signal molecules related to fruit maturity. The sampling was implemented during weeks 26-36 from five different locations in Cyprus. Additionally, the gaseous emissions of total VOCs (TVOCs) and carbon dioxide (CO₂) were recorded next to the moisture content of the fruit. The major chemical classes in the ripening are acids, followed by esters, and ketones. More specifically, the most abundant VOCs during ripening are propanoic acid, 2-methyl-(isobutyric acid), 2-heptanone, propanoic acid, 2-methyl-, 2-methylbutyl ester, acetic acid, methyl isobutyrate, propanoic acid, 2-methyl-, 3-methylbutyl ester, 2-pentanone, butanoic acid and propanoic acid, 2-methyl-ethyl ester. Finally, CO₂ emissions and moisture content showed a rapid decline until the 31st week and then stabilized for all examined areas. The methodology revealed variations in VOCs' profile during the ripening process.

Identification of genes and metabolic pathways involved in wounding-induced kiwifruit ripening

Fruit is constantly challenged by wounding events, inducing accelerated ripening and irreversible metabolic changes. However, cognate mechanisms that regulate this process are little known. To expand our knowledge of ripening metabolism induced by wounding, an artificial-wound global transcriptome investigation combined with metabolite profiling study was conducted in postharvest kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev. 'Hayward'). Wounding treatment promoted fruit ripening, as demonstrated by changes in fruit firmness, ethylene production and respiration activity determined periodically during a ripening period of 8 d at room temperature. Calcium imaging using fluorescent probe Fluo-3 AM revealed spatial dynamics of Ca²⁺ signaling in the wounding area following 8d ripening. Several sugars including fructose, glucose, and sucrose as well as organic acids such as citric, succinic and galacturonic acid were increased by wounding. Changes of various amino acids in wounded-treated fruit, especially 5-oxoproline and valine along with alternations of soluble alcohols, like myo-inositol were detected. Gene expression analysis of the wounded fruit showed increased expression of genes that are mainly involved in defense response (e.g., AdTLP.1-3, AdPP2C.1-2, AdMALD1), calcium ion binding (e.g., AdCbEFh, AdCLR, AdANX), TCA cycle (e.g., AdMDH.1, AdMDH.2, AdCS), sugars (e.g., AdSUSA.1, AdSPS4, AdABFr), secondary metabolism (e.g., AdPAL.1-3, AdCCR, AdHCT.1-2), lipid processing (e.g., AdGELP.1-4, AdGELP) and pectin degradation (e.g., AdPE.1-2, AdPAE.1-2, AdPG.1-2) as well as in ethylene (AdERF7, AdERF1B, AdACO.1-4) and auxin (AdICE, AdAEFc, AdASII) synthesis and perception. Moreover, genes related to aquaporins, such as AdAQP2, AdAQP4 and AdAQP7 were down-regulated in fruit exposed to wounding. These results demonstrate multiple metabolic points of wounding regulatory control during kiwifruit ripening and provide insights into the molecular basis of wounding-mediated ripening.

A brief hot-water treatment alleviates chilling injury symptoms in fresh tomatoes

BACKGROUND

Reducing the negative effects of chilling injury (CI) in tomatoes after harvest is essential to ensure good quality and to minimize losses. CI is a postharvest disorder associated with the generation of reactive oxygen species (ROS) in the fruit. Therefore, antioxidant accumulation can counteract ROS, alleviating CI symptoms. In this sense, it has been confirmed that a brief hot-water (HW) immersion promotes the synthesis of antioxidants.

RESULTS

HW treatment at 52 °C for 5 min significantly reduced chilling-associated decay, from 66.7% to 17.2% in breaker turning (BT) and from 55.8% to 9.8% in mature green (MG) 'BHN-602' tomatoes stored at 5 °C for 2 weeks and from 26.7% to 6.7% in BT tomatoes stored at 5 °C for 1 week. Also, HW treatment significantly increased lycopene content by 17% in BT tomatoes stored at 5 °C for 2 weeks, as well as ascorbic acid by 11%, lipophilic phenolics by 18% and total phenolics by 6.5% in BT tomatoes stored at 12.5 °C for 1 week. Despite the increase of antioxidants, HW treatment did not enhance the sensory aromatic profile, color and antioxidant capacity. Interestingly, HW treatment reduced ripening time by 3 days in MG tomatoes stored at 5 °C for 2 weeks or at 12.5 °C for 1 week.

CONCLUSION

HW treatment applied to MG or BT 'BHN-602' tomatoes can alleviate the development of some CI symptoms, particularly decay, possibly by increasing antioxidants that scavenge ROS. © 2020 Society of Chemical Industry.

Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)

The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum L.). In this study, 11 SlWAK and 18 SlWAKL genes were identified in an uneven distribution in 9 of 12 chromosomes. GUB-WAK-bind (wall-associated receptor kinase galacturonan-binding) and epidermal growth factor (EGF) domains appear more often in SlWAK proteins. However, more SlWAKLs (wall-associated kinase like) have a WAK-assoc (wall-associated receptor kinase C-terminal) domain. Based on their phylogenetic relationships, 29 SlWAK-RLKs (wall associated kinase-receptor like kinases) were clustered into three distinct categories analogous to those in Arabidopsis thaliana. High similarities were found in conserved motifs of the genes within each group. Cis-elements in the promoter region of these 29 genes were found mainly in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), anaerobic, light, wound, and MYB transcription factors. Public tomato genome RNA-seq data indicates that multiple SlWAK-RLKs showed different expression patterns under developmental and ripening stages of fruits, such as SlWAK4, SlWAKL11, SlWAKL9, SlWAKL15, SlWAKL14, and SlWAKL1, their RPKM (Reads Per Kilo bases per Million reads) value constantly increases during the fruit expansion period, and decreases as the fruit matures. In tomato leaves, our RNA-seq data showed that nine SlWAK-RLKs transcripts (SlWAK3, SlWAK4, SlWAK10,SlWAKL1, SlWAKL2, SlWAKL3, SlWAKL5, SlWAKL14, and SlWAKL18) were significantly induced (p < 0.001), and three transcripts (SlWAK2, SlWAK5, and SlWAKL15) were significantly inhibited (p < 0.001) under mechanical wounding. The qRT-PCR (Quantitative reverse transcription polymerase chain reaction) of SlWAKL1 and SlWAKL6 verify these results.

Oligogalacturonide-accelerated healing of mechanical wounding in tomato fruit requires calcium-dependent systemic acquired resistance

Mechanical wounding causes significant economic losses of fresh produce due to accelerated senescence and spoilage as well as loss of nutritional value. Here, pre-application of oligogalacturonides (OGs) enzymatically hydrolyzed from apple pectin effectively reduced the healing times of mechanical wounds from>24 h in mock groups to 12 h, and the Botrytis cinerea infection rate was reduced from 37.5% to 12.5%. OGs accordingly increased callose deposition; SlPR1, SlPAL and SlHCT gene expression; and phenylalanine ammonia-lyase (PAL) activity around the wounds. Inhibition of Ca²⁺ signaling using the inhibitor Ruthenium Red markedly inhibited OG accelerated healing of mechanical wounding on fruit. SlPG2, SlEXP1, and SlCEL2 mRNAs accumulation was reduced in OG-elicited tomato fruit compared to water-treated fruit with subsequent retardation of the fruit softening during ripening. These results indicated that apple pectin OGs accelerate wound healing and inhibit fruit softening by activating calcium signaling in tomato fruits during postharvest storage.

Transcriptomic and Metabolic Profiling Reveals 'Green Ring' and 'Red Ring' on Jujube Fruit upon Postharvest Alternaria alternata Infection

Alternaria alternata is the major threat to postharvest storage of jujube (Ziziphus jujuba Mill.) fruit. We found that natural A. alternata infection can cause very typical phenotype of 'green ring' and 'red ring' surrounding the disease spot on the jujube fruit. The phenotype was successfully modeled and constructed on jujubes by artificial inoculation with the pathogen. Furthermore, the pathogenic infection is evidenced essential to the onset of the phenotype. The 'red ring' circle is proved to be pre-fixed to block the 'green ring' area as a battlefield combating the pathogen's attack. We monitored the global transcriptomic profiling of 'green ring' and 'red ring' tissues from jujubes infected with A. alternata, in comparison with the mock-inoculated fruit and the control intact fruit. Large amount of differentially expressed genes were obtained in 'green ring', followed by 'red ring'. Transcriptional alterations associated with the core and peripheral phenylpropanoid and lignin pathways, plant hormonal metabolisms were greatly influenced in the 'green ring' and 'red ring' by the A. alternata infection. The integrated analysis of transcriptomic profiling and metabolic changes revealed the differentially but delicately coordinated activation of these biological processes in the 'green ring' and 'red ring' on jujubes in defensing the fungal infection.

ATR-FTIR spectroscopy non-destructively detects damage-induced sour rot infection in whole tomato fruit

ATR-FTIR spectroscopy with subsequent multivariate analysis non-destructively identifies plant-pathogen interactions during disease progression, both directly and indirectly, through alterations in the spectral fingerprint. Plant-environment interactions are essential to understanding crop biology, optimizing crop use, and minimizing loss to ensure food security. Damage-induced pathogen infection of delicate fruit crops such as tomato (Solanum lycopersicum) are therefore important processes related to crop biology and modern horticulture. Fruit epidermis as a first barrier at the plant-environment interface, is specifically involved in environmental interactions and often shows substantial structural and functional changes in response to unfavourable conditions. Methods available to investigate such systems in their native form, however, are limited by often required and destructive sample preparation, or scarce amounts of molecular level information. To explore biochemical changes and evaluate diagnostic potential for damage-induced pathogen infection of cherry tomato (cv. Piccolo) both directly and indirectly, mid-infrared (MIR) spectroscopy was applied in combination with exploratory multivariate analysis. ATR-FTIR fingerprint spectra (1800-900 cm^-1) of healthy, damaged or sour rot-infected tomato fruit were acquired and distinguished using principal component analysis and linear discriminant analysis (PCA-LDA). Main biochemical constituents of healthy tomato fruit epidermis are characterized while multivariate analysis discriminated subtle biochemical changes distinguishing healthy tomato from damaged, early or late sour rot-infected tomato indirectly based solely on changes in the fruit epidermis. Sour rot causing agent Geotrichum candidum was detected directly in vivo and characterized based on spectral features distinct from tomato fruit. Diagnostic potential for indirect pathogen detection based on tomato fruit skin was evaluated using the linear discriminant classifier (PCA-LDC). Exploratory and diagnostic analysis of ATR-FTIR spectra offers biological insights and detection potential for intact plant-pathogen systems as they are found in horticultural industries.

A complex interaction between pre-harvest and post-harvest factors determines fresh-cut melon quality and aroma

Melons are prized for their characteristic aroma, however, pre-harvest growth, stage of ripening at harvest, post-harvest processing and storage conditions lead to quality changes in fresh-cut fruit. We considered changes in metabolites and gene expression over 14 days storage to assess underlying mechanisms and identify potential quality markers. Overall, 99 volatile organic compounds (VOCs) were detected and VOC profiles discriminated between two melon seasons, cut-size, storage temperatures and storage time, although season affected their discriminatory power. Abundance of two VOCs fell rapidly and was not associated with cut size, indicating their use as markers for early changes post-processing. Non-acetate to acetate ester ratio differed between the seasons and correlated with changes in alcohol acyl-transferase (CmAAT1) gene expression. Furthermore, CmAAT1 expression clustered with two ester VOCs that may be potential new products of this enzyme. Season also strongly affected post-harvest sugar content, most likely attributable to meteorological differences during growth. Storage temperature and cut size affected expression of transcription factors ERF71, ERF106, and TINY, whose expression generally rose during storage, probably related to increased stress. Thus, although time × temperature of storage are key factors, pre-harvest conditions and fruit processing impact significantly gene expression and aroma loss post-harvest.

Transcriptomic profiling of the flower scent biosynthesis pathway of Cymbidium faberi Rolfe and functional characterization of its jasmonic acid carboxyl methyltransferase gene

Background

Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to this study. Methyl jasmonate (MeJA) is one of the main volatile organic compounds (VOC) produced by the flowers of C. faberi. In this study, unigene 79,363 from comparative transcriptome analysis was selected for further investigation.

Results

A transcriptome comparison between blooming and withered flowers of C. faberi yielded a total of 9409 differentially expressed genes (DEGs), 558 of which were assigned to 258 pathways. The top ten pathways included α-linolenic acid metabolism, pyruvate metabolism and fatty acid degradation, which contributed to the conversion of α-linolenic acid to MeJA. One of the DEGs, jasmonic acid carboxyl methyltransferase (CfJMT, Unigene 79,363) was highly expressed in the blooming flower of C. faberi, but was barely detected in leaves and roots. Although the ectopic expression of CfJMT in tomato could not increase the MeJA content, the expression levels of endogenous MeJA biosynthesis genes were influenced, especially in the wound treatment, indicating that CfJMT may participate in the response to abiotic stresses.

Conclusion

This study provides a basis for elucidating the molecular mechanism of flower scent biosynthesis in C. faberi, which is beneficial for the genetically informed breeding of new cultivars of the economically valuable oriental orchids.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5501-z) contains supplementary material, which is available to authorized users.

Identification of genes involved in fruit development/ripening in Capsicum and development of functional markers

The molecular mechanism of the underlying genes involved in the process of fruit ripening in Capsicum (family Solanaceae) is not clearly known. In the present study, we identified orthologs of 32 fruit development/ripening genes of tomato in Capsicum, and validated their expression in fruit development stages in C. annuum, C. frutescens, and C. chinense. In silico expression analysis using transcriptome data identified a total of 12 out of 32 genes showing differential expression during different stages of fruit development in Capsicum. Real time expression identified gene LOC107847473 (ortholog of MADS-RIN) had substantially higher expression (>500 folds) in breaker and mature fruits, which suggested the non-climacteric ripening behaviour of Capsicum. However, differential expression of Ehtylene receptor 2-like (LOC107873245) gene during fruit maturity supported the climacteric behaviour of only C. frutescens (hot pepper). Furthermore, development of 49 gene based simple sequence repeat (SSR) markers would help in selection of identified genes in Capsicum breeding.

Gene expression analysis of rocket salad under pre-harvest and postharvest stresses: A transcriptomic resource for Diplotaxis tenuifolia

Diplotaxis tenuifolia L. is of important economic value in the fresh-cut industry for its nutraceutical and sensorial properties. However, information on the molecular mechanisms conferring tolerance of harvested leaves to pre- and postharvest stresses during processing and shelf-life have never been investigated. Here, we provide the first transcriptomic resource of rocket by de novo RNA sequencing assembly, functional annotation and stress-induced expression analysis of 33874 transcripts. Transcriptomic changes in leaves subjected to commercially-relevant pre-harvest (salinity, heat and nitrogen starvation) and postharvest stresses (cold, dehydration, dark, wounding) known to affect quality and shelf-life were analysed 24h after stress treatment, a timing relevant to subsequent processing of salad leaves. Transcription factors and genes involved in plant growth regulator signaling, autophagy, senescence and glucosinolate metabolism were the most affected by the stresses. Hundreds of genes with unknown function but uniquely expressed under stress were identified, providing candidates to investigate stress responses in rocket. Dehydration and wounding had the greatest effect on the transcriptome and different stresses elicited changes in the expression of genes related to overlapping groups of hormones. These data will allow development of approaches targeted at improving stress tolerance, quality and shelf-life of rocket with direct applications in the fresh-cut industries.

Genome-Wide Identification and Evaluation of Reference Genes for Quantitative RT-PCR Analysis during Tomato Fruit Development

Gene expression analysis in tomato fruit has drawn increasing attention nowadays. Quantitative real-time PCR (qPCR) is a routine technique for gene expression analysis. In qPCR operation, reliability of results largely depends on the choice of appropriate reference genes (RGs). Although tomato is a model for fruit biology study, few RGs for qPCR analysis in tomato fruit had yet been developed. In this study, we initially identified 38 most stably expressed genes based on tomato transcriptome data set, and their expression stabilities were further determined in a set of tomato fruit samples of four different fruit developmental stages (Immature, mature green, breaker, mature red) using qPCR analysis. Two statistical algorithms, geNorm and Normfinder, concordantly determined the superiority of these identified putative RGs. Notably, SlFRG05 (Solyc01g104170), SlFRG12 (Solyc04g009770), SlFRG16 (Solyc10g081190), SlFRG27 (Solyc06g007510), and SlFRG37 (Solyc11g005330) were proved to be suitable RGs for tomato fruit development study. Further analysis using geNorm indicate that the combined use of SlFRG03 (Solyc02g063070) and SlFRG27 would provide more reliable normalization results in qPCR experiments. The identified RGs in this study will be beneficial for future qPCR analysis of tomato fruit developmental study, as well as for the potential identification of optimal normalization controls in other plant species.

Spatially resolved metabolic distribution for unraveling the physiological change and responses in tomato fruit using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI)

Information on spatiotemporal metabolic behavior is indispensable for a precise understanding of physiological changes and responses, including those of ripening processes and wounding stress, in fruit, but such information is still limited. Here, we visualized the spatial distribution of metabolites within tissue sections of tomato (Solanum lycopersicum L.) fruit using a matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) technique combined with a matrix sublimation/recrystallization method. This technique elucidated the unique distribution patterns of more than 30 metabolite-derived ions, including primary and secondary metabolites, simultaneously. To investigate spatiotemporal metabolic alterations during physiological changes at the whole-tissue level, MALDI-MSI was performed using the different ripening phenotypes of mature green and mature red tomato fruits. Although apparent alterations in the localization and intensity of many detected metabolites were not observed between the two tomatoes, the amounts of glutamate and adenosine monophosphate, umami compounds, increased in both mesocarp and locule regions during the ripening process. In contrast, malate, a sour compound, decreased in both regions. MALDI-MSI was also applied to evaluate more local metabolic responses to wounding stress. Accumulations of a glycoalkaloid, tomatine, and a low level of its glycosylated metabolite, esculeoside A, were found in the wound region where cell death had been induced. Their inverse levels were observed in non-wounded regions. Furthermore, the amounts of both compounds differed in the developmental stages. Thus, our MALDI-MSI technique increased the understanding of the physiological changes and responses of tomato fruit through the determination of spatiotemporally resolved metabolic alterations. Graphical abstract ᅟ.