Metabolomics 20 years on: what have we learned and what hurdles remain?

Alseekh, Saleh; Fernie, Alisdair R.

doi:10.1111/tpj.13950

Cited by 194 publications

(123 citation statements)

References 142 publications

(165 reference statements)

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“…However, unlike other omics technologies, no single analytical platform is capable of analyzing all metabolites simultaneously due to their extreme complexity and huge chemical diversity. Recent developments in analytical chemistry platforms such as hyphenating mass spectrometry with gas chromatography (GC), liquid chromatography (LC) or capillary electrophoresis (CE), and nuclear magnetic resonance (NMR) spectroscopy have led to a highly efficient set up for metabolome analysis [20], however, these do not yet reach comprehensibility [21]. Although huge datasets are generated from these instruments, the evolution of chemometrics and multivariate data analysis algorithms provides a powerful tool for extracting useful information from such high dimensionality results [22].…”

Section: Introductionmentioning

confidence: 99%

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

et al. 2020

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Plant-derived natural products have long been considered a valuable source of lead compounds for drug development. Natural extracts are usually composed of hundreds to thousands of metabolites, whereby the bioactivity of natural extracts can be represented by synergism between several metabolites. However, isolating every single compound from a natural extract is not always possible due to the complex chemistry and presence of most secondary metabolites at very low levels. Metabolomics has emerged in recent years as an indispensable tool for the analysis of thousands of metabolites from crude natural extracts, leading to a paradigm shift in natural products drug research. Analytical methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) are used to comprehensively annotate the constituents of plant natural products for screening, drug discovery as well as for quality control purposes such as those required for phytomedicine. In this review, the current advancements in plant sample preparation, sample measurements, and data analysis are presented alongside a few case studies of the successful applications of these processes in plant natural product drug discovery.

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Section: Introductionmentioning

confidence: 99%

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

et al. 2020

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“…Much effort has been made to dissect metabolic pathways, including screening of mutant libraries (Li et al ., ; Yonekura‐Sakakibara et al ., ), analysis of gene families (Yamamura et al ., ; Sadre et al ., ), and comparative genomics studies (Denoeud et al ., ; Huang et al ., ). To obtain deeper insights into genetic and biochemical bases of diversity in the metabolome and to artificially produce natural products with synthetic biology, linkage mapping, and association mapping based on next‐generation sequencing have been applied to metabolomics studies (Luo, ; Alseekh and Fernie, ). By discussing the development of genome‐wide association study (GWAS) and the rise of the metabolic diversity, we review two of the pre‐conditions for metabolic GWAS (mGWAS).…”

Section: Introductionmentioning

confidence: 99%

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

2018

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Plants have served as sources providing humans with metabolites for food and nutrition, biomaterials for living, and treatment for pain and disease. Plants produce a huge array of metabolites, with an immense diversity at both the population and individual levels. Dissection of the genetic bases for metabolic diversity has attracted increasing research attention. The concept of genome-wide association study (GWAS) was extended to studies on the diversity of plant metabolome that benefitted from the development of mass-spectrometry-based analytical systems and genome sequencing technologies. Metabolic genome-wide association study (mGWAS) is one of the most powerful tools for global identification of genetic determinants for diversity of plant metabolism. Recently, mGWAS has been performed for various species with continuous improvements, providing deeper insights into the genetic bases of metabolic diversity. In this review, we discuss fully the achievements to date and remaining challenges that are associated with both mGWAS and mGWAS-based multi-dimensional analysis. We begin with a summary of GWAS and its development based on statistical methods and populations. As variation in targeted traits is essential for GWAS, we review metabolic diversity and its rise at both the population and individual levels. Subsequently, the application of mGWAS for plants and its corresponding achievements are fully discussed. We address the current knowledge on mGWAS-based multi-dimensional analysis and emerging insights into the diversity of metabolism.

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“…The first papers on metabolomics in plants – the comprehensive description of the small molecule complement of the cell – were published over 20 years ago (Katona et al ., ; Fiehn et al ., ; Roberts, ; Roessner et al ., ; Aharoni et al ., ; Le Gall et al ., ; Weckwerth, ; Deferenez et al ., ; Saito and Matsuda, ); however, current methodologies only cover a small percentage of the 200 000–1 000 000 metabolites anticipated in the plant kingdom (Dixon and Strack, ; Rai et al ., ). Three methodologies are commonly used for plant metabolomics: nuclear magnetic resonance (NMR), gas chromatography mass spectrometry (GC‐MS) and liquid chromatography mass spectrometry (LC‐MS) (Obata and Fernie, ), with LC‐MS providing the most comprehensive outcomes (Alseekh and Fernie, ). Twin improvements afforded by ultra‐performance LC (UPLC) and high‐resolution mass spectrometry rendered this technique even more powerful with regards to resolution, sensitivity and throughput (Fernie and Tohge, ).…”

Section: Metabolomicsmentioning

confidence: 99%

Metabolomics should be deployed in the identification and characterization of gene‐edited crops

et al. 2020

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Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and additional consumer traits. Unlike transgenic approaches, however, it is not facile to forensically detect gene-editing events at the molecular level, as no foreign DNA exists in the elite line. These limitations in molecular detection approaches are likely to focus more attention on the products generated from the technology than on the process in itself. Rapid advances in sequencing and genome assembly increasingly facilitate genome sequencing as a means of characterizing new varieties generated by gene-editing techniques. Nevertheless, subtle edits such as single base changes or small deletions may be difficult to distinguish from normal variation within a genotype. Given these emerging scenarios, downstream 'omics' technologies reflective of edited affects, such as metabolomics, need to be used in a more prominent manner to fully assess compositional changes in novel foodstuffs. To achieve this goal, metabolomics or 'non-targeted metabolite analysis' needs to make significant advances to deliver greater representation across the metabolome. With the emergence of new edited crop varieties, we advocate: (i) concerted efforts in the advancement of 'omics' technologies, such as metabolomics, and (ii) an effort to redress the use of the technology in the regulatory assessment for metabolically engineered biotech crops.

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Metabolomics 20 years on: what have we learned and what hurdles remain?

Cited by 194 publications

References 142 publications

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

Metabolomics in the Context of Plant Natural Products Research: From Sample Preparation to Metabolite Analysis

Metabolic GWAS‐based dissection of genetic bases underlying the diversity of plant metabolism

Metabolomics should be deployed in the identification and characterization of gene‐edited crops

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