Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato

Ruggieri, Valentino; Bostan, Hamed; Barone, Amalia; Frusciante, Luigi; Chiusano, Maria Luisa

doi:10.1007/s11103-016-0469-4

Cited by 24 publications

(25 citation statements)

References 98 publications

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“…The landrace PDVIT was the best performer, with a mean value over 500 μg g −1 FW. These values are in line with the values previously reported for tomato genotypes, where AsA ranged from 100 to 880 μg g −1 FW, even though commercial cultivars are generally characterized by lower contents (from 100 to 400 μg g −1 FW), probably due to the breeding process . However, the AsA content in fresh tomato fruits is also dependent on genotype, climatic conditions, fruit development, and maturation …”

Section: Resultssupporting

confidence: 91%

Selection of tomato landraces with high fruit yield and nutritional quality under elevated temperatures

et al. 2020

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BACKGROUND Global warming and extreme or adverse events induced by climatic fluctuations are an important threat for plants growth and agricultural production. Adaptability to environmental changes prevalently derives from a large set of genetic traits affecting physiological and agronomic parameters. Therefore, the identification of genotypes that are good yield performer at high temperatures is becoming increasingly necessary for future breeding programs. Here, we analyzed the performances of different tomato landraces grown under elevated temperatures in terms of yield and nutritional quality of the fruit. Finally, we evaluated the antioxidant and anti‐inflammatory activities of fruit extracts from the tomato landraces selected. RESULTS The tomato landraces analyzed here in a hot climate differed in terms of yield performance, physicochemical parameters of fruit (pH, titratable acidity, degrees Brix, firmness), bioactive compounds (ascorbic acid, carotenoids, and polyphenols), and anti‐inflammatory potential. Three of these landraces (named E30, E94, and PDVIT) showed higher fruit quality and nutritional value. An estimated evaluation index allowed identification of PDVIT as the best performer in terms of yield and fruit quality under high temperatures. CONCLUSION The analyses performed here highlight the possibility to identify new landraces that can combine good yield performances and fruit nutritional quality at high temperatures, information that is useful for future breeding programs. © 2020 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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Section: Resultssupporting

confidence: 91%

Selection of tomato landraces with high fruit yield and nutritional quality under elevated temperatures

et al. 2020

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“…; Ruggieri et al . ). These studies show that, for example, the enzymes gluconolactonase, as well as l ‐gulonolactone oxidase, are absent in the genomes of higher plants.…”

Section: Discussionmentioning

confidence: 99%

“…The product L-gulono-1,4-lactone is then finally oxidised to L-AsA. Using bioinformatics Ruggieri et al (2016) found some candidate genes in tomato for the reductase (first step ③ in Fig. 1) but no candidate gene for the second step.…”

Section: Introductionmentioning

confidence: 99%

The Myo‐inositol pathway does not contribute to ascorbic acid synthesis

2018

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Ascorbic acid (AsA) biosynthesis in plants predominantly occurs via a pathway with d-mannose and l-galactose as intermediates. One alternative pathway for AsA synthesis, which is similar to the biosynthesis route in mammals, is controversially discussed for plants. Here, myo-inositol is cleaved to glucuronic acid and then converted via l-gulonate to AsA. In contrast to animals, plants have an effective recycling pathway for glucuronic acid, being a competitor for the metabolic rate. Recycling involves a phosphorylation at C1 by the enzyme glucuronokinase. Two previously described T-DNA insertion lines in the gene coding for glucuronokinase1 show wild type-like expression levels of the mRNA in our experiments and do not accumulate glucuronic acid in labelling experiments disproving that these lines are true knockouts. As suitable T-DNA insertion lines were not available, we generated frameshift mutations in the major expressed isoform glucuronokinase1 (At3g01640) to potentially redirect metabolites to AsA. However, radiotracer experiments with H-myo-inositol revealed that the mutants in glucuronokinase1 accumulate only glucuronic acid and incorporate less metabolite into cell wall polymers. AsA was not labelled, suggesting that Arabidopsis cannot efficiently use glucuronic acid for AsA biosynthesis. All four mutants in glucuronokinase as well as the wild type have the same level of AsA in leaves.

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“…An inventory of 378 candidate genes representing possible targets for antioxidant metabolism in tomatoes was compiled from published literature, previous research 31 , 32 and exploration of metabolic pathway databases (LycoCyc at http://solgenomics.net/and KEGG at http://www.genome.jp/kegg/). Genes were also selected to represent different gene family sizes.…”

Section: Methodsmentioning

confidence: 99%

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

Ruggieri

Anzar

Paytuví

et al. 2016

DNA Res

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The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.

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Integrated bioinformatics to decipher the ascorbic acid metabolic network in tomato

Cited by 24 publications

References 98 publications

Selection of tomato landraces with high fruit yield and nutritional quality under elevated temperatures

Selection of tomato landraces with high fruit yield and nutritional quality under elevated temperatures

The Myo‐inositol pathway does not contribute to ascorbic acid synthesis

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

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