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Special Issue "Metabolomics in the Plant Sciences 2017"

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: closed (28 February 2018).

Special Issue Editors

Prof. Dr. Marcello Iriti
E-Mail Website
Guest Editor
Department of Agricultural and Environmental Sciences, Milan State University, Milan, Italy
Interests: crop protection; plant diseases; agrochemicals; abiotic stresses; food production; food security; food safety; global climate change; bioactive phytochemicals; agrochemicals; mycotoxins; medicinal plants; ethnobotany
Special Issues and Collections in MDPI journals
Prof. Dr. Ute Roessner
E-Mail Website
Co-Guest Editor
Metabolomics Australia, School of BioSciences, The University of Melbourne, Melbourne, Vic. 3010, Australia
Interests: metabolomics; analytical biochemistry; metabolism; crop improvement; biomarker discovery
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

In their environments, plants have to cope with a plethora of potentially detrimental conditions. They are sessile organisms and, therefore, can only produce (secondary) metabolites to protect themselves and to communicate with the components of their ecosystem: Competitive plants, microbial pathogens, phytophagous arthropods, noxious animals, pollinators, and vectors involved in seed dispersal. Therefore, in this context, chemodiversity enabled biodiversity, especially in hostile environments, where metabolite diversity of plants greatly contributed to their evolutionary success in terrestrial, marine and freshwater habitats.

In this chemoecological scenario, to study the complete set of small-molecules, commonly known as metabolites, found within a plant cell, tissue or organ, i.e., the plant metabolome, represents a reliable tool to accurately and comprehensively describe the physiological state of a biological system (cell–tissue–organ–organism), as well as its dynamic response to environmental changes.

In the field of omics, metabolomics—the large-scale study of metabolites—represents a powerful approach, because metabolites and their levels, unlike other omics measures, directly reflect the underlying global biochemical activity, (patho)physiological conditions and metabolic state of biological systems. In other words, metabolites are closely correlated to phenotype and metabolomics best represents the molecular phenotype of biological systems.

Not least of all, providing metabolome information for food and medicinal plant species is also relevant for better understanding the nutritional and healthy potential of these plants, as well as their adverse effects in human, if any. Metabolite profiling of animal/human body fluids (blood, urine, saliva) after ingestion of plant products will certainly contribute to ascertain their biological/pharmacological properties, toxicological effects, oral bioavailability and, finally, how plant product intake modifies the metabolic profile in animal/human.

In this very wide context, we invite investigators to submit both original research and review articles that explore all these aspects. Potential topics include, but are not limited to:

  • Plant secondary metabolites;
  • Chemoecology;
  • Stress physiology;
  • Crop science;
  • Food and nutrition sciences;
  • Medicinal plants;
  • Imaging Mass Spectrometry.

Prof. Dr. Marcello Iriti
Prof. Dr. Ute Roessner
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolome
  • metabolomics
  • analytical chemistry
  • metabolic engineering

Published Papers (11 papers)

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Editorial

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Open AccessEditorial
Plant Metabolomics in the Global Scenario of Food Security: A Systems-Biology Approach for Sustainable Crop Production
Int. J. Mol. Sci. 2018, 19(7), 2094; https://doi.org/10.3390/ijms19072094 - 19 Jul 2018
Cited by 2
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Research

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Open AccessArticle
Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris
Int. J. Mol. Sci. 2018, 19(4), 1049; https://doi.org/10.3390/ijms19041049 - 01 Apr 2018
Cited by 3
Abstract
RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T [...] Read more.
RpoN (or σ54) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815T formed root nodules on Phaseolus vulgaris cv. Negro jamapa, which were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by a P. phymatum rpoN Fix mutant revealed statistically significant metabolic changes compared to wild-type Fix+ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix and Fix+ nodules—combined with a search for RpoN binding sequences in promoter regions of regulated genes—confirmed the expected control of σ54 on nitrogen fixation genes in nodules. The transcriptomic data also allowed us to identify additional target genes, whose differential expression was able to explain the observed metabolite changes in numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant, and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype, as fewer but heavier nodules were formed on P. vulgaris roots. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
GC-MS Metabolomics to Evaluate the Composition of Plant Cuticular Waxes for Four Triticum aestivum Cultivars
Int. J. Mol. Sci. 2018, 19(2), 249; https://doi.org/10.3390/ijms19020249 - 23 Jan 2018
Cited by 6
Abstract
Wheat (Triticum aestivum L.) is an important food crop, and biotic and abiotic stresses significantly impact grain yield. Wheat leaf and stem surface waxes are associated with traits of biological importance, including stress resistance. Past studies have characterized the composition of wheat [...] Read more.
Wheat (Triticum aestivum L.) is an important food crop, and biotic and abiotic stresses significantly impact grain yield. Wheat leaf and stem surface waxes are associated with traits of biological importance, including stress resistance. Past studies have characterized the composition of wheat cuticular waxes, however protocols can be relatively low-throughput and narrow in the range of metabolites detected. Here, gas chromatography-mass spectrometry (GC-MS) metabolomics methods were utilized to provide a comprehensive characterization of the chemical composition of cuticular waxes in wheat leaves and stems. Further, waxes from four wheat cultivars were assayed to evaluate the potential for GC-MS metabolomics to describe wax composition attributed to differences in wheat genotype. A total of 263 putative compounds were detected and included 58 wax compounds that can be classified (e.g., alkanes and fatty acids). Many of the detected wax metabolites have known associations to important biological functions. Principal component analysis and ANOVA were used to evaluate metabolite distribution, which was attributed to both tissue type (leaf, stem) and cultivar differences. Leaves contained more primary alcohols than stems such as 6-methylheptacosan-1-ol and octacosan-1-ol. The metabolite data were validated using scanning electron microscopy of epicuticular wax crystals which detected wax tubules and platelets. Conan was the only cultivar to display alcohol-associated platelet-shaped crystals on its abaxial leaf surface. Taken together, application of GC-MS metabolomics enabled the characterization of cuticular wax content in wheat tissues and provided relative quantitative comparisons among sample types, thus contributing to the understanding of wax composition associated with important phenotypic traits in a major crop. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Identification of Conserved and Diverse Metabolic Shift of the Stylar, Intermediate and Peduncular Segments of Cucumber Fruit during Development
Int. J. Mol. Sci. 2018, 19(1), 135; https://doi.org/10.3390/ijms19010135 - 03 Jan 2018
Cited by 13
Abstract
Cucumber (Cucumis sativus L.) is one of the most important vegetables and contains a high content of nutritionally beneficial metabolites. However, little is known about the metabolic variations among different parts of cucumber fruit and their kinetics during growth. In this study, [...] Read more.
Cucumber (Cucumis sativus L.) is one of the most important vegetables and contains a high content of nutritionally beneficial metabolites. However, little is known about the metabolic variations among different parts of cucumber fruit and their kinetics during growth. In this study, the dynamic metabolic profiles in the stylar end, the intermediate segment and the peduncular end of cucumber fruit during the development were investigated by employing a non-targeted metabolomics approach, where 238 metabolites were identified. Statistical analyses revealed that both development time and tissue type influenced metabolic changes, while development time seemed to exert more effects than tissue type on the cucumber fruit metabolome. The levels of the most of the detected metabolites decreased gradually, while those of some amino acids, carbohydrates and flavonoids increased across development. The metabolomes of the stylar end and the intermediate segment were similar, although all three parts of the cucumber fruit were separated from each other in orthogonal partial least squares projection to latent structures-discriminant analysis (OPLS-DA) plots. Metabolites association analysis revealed that sn-1 and sn-2 lysophospholipids are synthesized via independent pathways in cucumber fruit. In sum, this study demonstrated both conserved and diverse metabolic kinetics of three parts of cucumber fruit, which will facilitate further study of the regulation of cucumber fruit development as well as their potential applications in nutritious quality improvement of cucumber fruit. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Sulfur-Mediated-Alleviation of Aluminum-Toxicity in Citrus grandis Seedlings
Int. J. Mol. Sci. 2017, 18(12), 2570; https://doi.org/10.3390/ijms18122570 - 03 Dec 2017
Cited by 17
Abstract
Limited data are available on the sulfur (S)-mediated-alleviation of aluminum (Al)-toxicity in higher plants. Citrus grandis seedlings were irrigated for 18 weeks with 0.5 mM MgSO4 or 0.5 mM MgSO4 + 0.5 mM Na2SO4, and 0 (−Al) [...] Read more.
Limited data are available on the sulfur (S)-mediated-alleviation of aluminum (Al)-toxicity in higher plants. Citrus grandis seedlings were irrigated for 18 weeks with 0.5 mM MgSO4 or 0.5 mM MgSO4 + 0.5 mM Na2SO4, and 0 (−Al) or 1 mM AlCl3·6H2O (+Al, Al-toxicity). Under Al-toxicity, S decreased the level of Al in leaves; increased the relative water content (RWC) of roots and leaves, the contents of phosphorus (P), calcium (Ca) and magnesium (Mg) per plant, the dry weights (DW) of roots and shoots, the ratios of root DW/shoot DW, and the Al-induced secretion of citrate from root; and alleviated the Al-induced inhibition of photosynthesis via mitigating the Al-induced decrease of electron transport capacity resulting from the impaired photosynthetic electron transport chain. In addition to decreasing the Al-stimulated H2O2 production, the S-induced upregulation of both S metabolism-related enzymes and antioxidant enzymes also contributed to the S-mediated-alleviation of oxidative damage in Al-treated roots and leaves. Decreased transport of Al from roots to shoots and relatively little accumulation of Al in leaves, and increased leaf and root RWC and P, Ca, and Mg contents per plant might also play a role in the S-mediated-alleviation of Al-toxicity. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Effect of Low Temperature Cultivation on the Phytochemical Profile and Bioactivity of Arctic Plants: A Case of Dracocephalum palmatum
Int. J. Mol. Sci. 2017, 18(12), 2579; https://doi.org/10.3390/ijms18122579 - 30 Nov 2017
Cited by 12
Abstract
The influence of climatic factors, e.g., low temperature, on the phytochemical composition and bioactivity of the arctic plant Dracocephalum palmatum Steph. ax Willd. (palmate dragonhead), a traditional food and medical herb of Northern Siberia, was investigated. D. palmatum seedlings were grown in a [...] Read more.
The influence of climatic factors, e.g., low temperature, on the phytochemical composition and bioactivity of the arctic plant Dracocephalum palmatum Steph. ax Willd. (palmate dragonhead), a traditional food and medical herb of Northern Siberia, was investigated. D. palmatum seedlings were grown in a greenhouse experiment at normal (20 °C, NT) and low (1 °C, LT) temperature levels and five groups of components that were lipophilic and hydrophilic in nature were characterized. The analyses indicated that D. palmatum under NT demonstrates high content of photosynthetic pigments, specific fatty acid (FA) profile with domination of saturated FA (53.3%) and the essential oil with trans-pinocamphone as a main component (37.9%). Phenolic compounds were identified using a combination of high performance liquid chromatography with diode array detection and electrospray ionization mass-spectrometric detection (HPLC-DAD-ESI-MS) techniques, as well as free carbohydrates and water soluble polysaccharides. For the first time, it was established that the cold acclimation of D. palmatum seedlings resulted in various changes in physiological and biochemical parameters such as membrane permeability, photosynthetic potential, membrane fluidity, leaf surface secretory function, reactive oxygen species–antioxidant balance, osmoregulator content and cell wall polymers. In brief, results showed that the adaptive strategy of D. palmatum under LT was realized on the accumulation of membrane or surface components with more fluid properties (unsaturated FA and essential oils), antioxidants (phenolic compounds and enzymes), osmoprotectants (free sugars) and cell wall components (polysaccharides). In addition, the occurrence of unusual flavonoids including two new isomeric malonyl esters of eriodictyol-7-O-glucoside was found in LT samples. Data thus obtained allow improving our understanding of ecophysiological mechanisms of cold adaptation of arctic plants. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry
Int. J. Mol. Sci. 2017, 18(10), 2196; https://doi.org/10.3390/ijms18102196 - 21 Oct 2017
Cited by 6
Abstract
Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant [...] Read more.
Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking). Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Lipidomics Unravels the Role of Leaf Lipids in Thyme Plant Response to Drought Stress
Int. J. Mol. Sci. 2017, 18(10), 2067; https://doi.org/10.3390/ijms18102067 - 28 Sep 2017
Cited by 5
Abstract
Thymus is one of the best known genera within the Labiatae (Lamiaceae) family, with more than 200 species and many medicinal and culinary uses. The effects of prolonged drought on lipid profile were investigated in tolerant and sensitive thyme plants (Thymus serpyllum [...] Read more.
Thymus is one of the best known genera within the Labiatae (Lamiaceae) family, with more than 200 species and many medicinal and culinary uses. The effects of prolonged drought on lipid profile were investigated in tolerant and sensitive thyme plants (Thymus serpyllum L. and Thymus vulgaris L., respectively). Non-targeted non-polar metabolite profiling was carried out using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry with one-month-old plants exposed to drought stress, and their morpho-physiological parameters were also evaluated. Tolerant and sensitive plants exhibited clearly different responses at a physiological level. In addition, different trends for a number of non-polar metabolites were observed when comparing stressed and control samples, for both sensitive and tolerant plants. Sensitive plants showed the highest decrease (55%) in main lipid components such as galactolipids and phospholipids. In tolerant plants, the level of lipids involved in signaling increased, while intensities of those induced by stress (e.g., oxylipins) dramatically decreased (50–60%), in particular with respect to metabolites with m/z values of 519.3331, 521.3488, and 581.3709. Partial least square discriminant analysis separated all the samples into four groups: tolerant watered, tolerant stressed, sensitive watered and sensitive stressed. The combination of lipid profiling and physiological parameters represented a promising tool for investigating the mechanisms of plant response to drought stress at non-polar metabolome level. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessArticle
Mass Spectrometry Based Profiling and Imaging of Various Ginsenosides from Panax ginseng Roots at Different Ages
Int. J. Mol. Sci. 2017, 18(6), 1114; https://doi.org/10.3390/ijms18061114 - 24 May 2017
Cited by 8
Abstract
(1) Background: Panax ginseng root is one of the most important herbal products, and the profiling of ginsenosides is critical for the quality control of ginseng roots at different ages in the herbal markets. Furthermore, interest in assessing the contents as well as [...] Read more.
(1) Background: Panax ginseng root is one of the most important herbal products, and the profiling of ginsenosides is critical for the quality control of ginseng roots at different ages in the herbal markets. Furthermore, interest in assessing the contents as well as the localization of biological compounds has been growing. The objective of this study is to carry out the mass spectrometry (MS)-based profiling and imaging of ginsenosides to assess ginseng roots at different ages; (2) Methods: Optimal ultra performance liquid chromatography coupled to quadrupole time of flight/MS (UPLC-QTOF/MS) was used to profile various ginsenosides from P. ginseng roots. Matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF)/MS-based imaging was also optimized to visualize ginsenosides in ginseng roots; (3) Results: UPLC-QTOF/MS was used to profile 30 ginsenosides with high mass accuracy, with an in-house library constructed for the fast and exact identification of ginsenosides. Using this method, the levels of 14 ginsenosides were assessed in P. ginseng roots cultivated for 4, 5, and 6 years. The optimal MALDI-imaging MS (IMS) was also applied to visualize the 14 ginsenosides in ginseng roots. As a result, the MSI cross sections showed the localization of 4 ginsenoside ions ([M + K]+) in P. ginseng roots at different ages; (4) Conclusions: The contents and localization of various ginsenosides differ depending on the cultivation years of P. ginseng roots. Furthermore, this study demonstrated the utility of MS-based profiling and imaging of ginsenosides for the quality control of ginseng roots. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Review

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Open AccessReview
Current Challenges in Plant Eco-Metabolomics
Int. J. Mol. Sci. 2018, 19(5), 1385; https://doi.org/10.3390/ijms19051385 - 06 May 2018
Cited by 12
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in [...] Read more.
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology. Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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Open AccessAddendum
Addendum: Cechová, M. et al. Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry. Int. J. Mol. Sci. 2017, 18, 2196
Int. J. Mol. Sci. 2017, 18(12), 2771; https://doi.org/10.3390/ijms18122771 - 20 Dec 2017
Abstract
It has been brought to our attention that one funding project of Ministry of Education, Youth and Sports of the Czech Republic (LO1417) was missing in the Acknowledgement section of our published paper [1], and therefore we would like to add it and [...] Read more.
It has been brought to our attention that one funding project of Ministry of Education, Youth and Sports of the Czech Republic (LO1417) was missing in the Acknowledgement section of our published paper [1], and therefore we would like to add it and report the Acknowledgements as follows [...] Full article
(This article belongs to the Special Issue Metabolomics in the Plant Sciences 2017)
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