Metabolomics in Plants

Topic Information

Dear Colleagues,

Plant metabolomics is an emerging and rapidly expanding field within metabolomics. It involves the comprehensive study of small molecules in plant systems biology, providing a biochemical snapshot of active metabolites that reflects plant physiological status. Plant metabolomics is a powerful approach for mapping metabolite changes that correspond to functional alterations in plants arising from genetic variation, developmental stages, or environmental conditions.

This approach has broad applicability across diverse research areas, including agriculture, algae, yeast, biofuel research, environmental sciences, and marine biology. Despite its growing importance, plant metabolomics faces significant challenges due to the vast chemical diversity of plant metabolites, encompassing both primary and secondary metabolites. Consequently, there is a strong need for continued methodological development and high‑quality research contributions in this field.

Plant metabolites play essential roles in cellular signalling, defence mechanisms, and responses to environmental stresses such as drought and salinity. In addition, plant metabolomics has become a key strategy for the discovery and characterisation of natural products, many of which hold significant pharmacological and nutritional value.

This Topic is dedicated to advancing research in plant metabolomics and lipidomics, with a particular emphasis on studies addressing analytical challenges, data processing, and pathway mapping. Establishing a dedicated platform for plant metabolomics will support the dissemination of innovative research, and we look forward to receiving high‑quality contributions from the scientific community.

Dr. Thusitha W. Rupasinghe
Dr. Priyanka Reddy
Topic Editors

Keywords

Participating Journals

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
BioChem biochem	-	2.9	2021	26.4 Days	CHF 1200	Submit
Current Issues in Molecular Biology cimb	4.1	5.0	1999	15.5 Days	CHF 2400	Submit
International Journal of Molecular Sciences ijms	5.6	10.0	2000	17.5 Days	CHF 2900	Submit
Metabolites metabolites	4.5	8.1	2011	12.6 Days	CHF 2700	Submit
Plants plants	4.7	8.5	2012	14.8 Days	CHF 2700	Submit
Sci sci	4.1	5.4	2019	28.2 Days	CHF 1400	Submit

Preprints.org is a multidisciplinary platform offering a preprint service designed to facilitate the early sharing of your research. It supports and empowers your research journey from the very beginning.

MDPI Topics is collaborating with Preprints.org and has established a direct connection between MDPI journals and the platform. Authors are encouraged to take advantage of this opportunity by posting their preprints at Preprints.org prior to publication:

1. Share your research immediately: disseminate your ideas prior to publication and establish priority for your work.
2. Safeguard your intellectual contribution: Protect your ideas with a time-stamped preprint that serves as proof of your research timeline.
3. Boost visibility and impact: Increase the reach and influence of your research by making it accessible to a global audience.
4. Gain early feedback: Receive valuable input and insights from peers before submitting to a journal.
5. Ensure broad indexing: Web of Science (Preprint Citation Index), Google Scholar, Crossref, SHARE, PrePubMed, Scilit and Europe PMC.

Published Papers (6 papers)

Order results

Content type Publication Date

Result details

Normal Extended Compact

Journals

All CIMB IJMS Metabolites Plants Sci BioChem

Show export options expand_more Show export options expand_less

Select all

Export citation of selected articles as:

Plain Text BibTeX BibTeX (without abstracts) Endnote Endnote (without abstracts) Tab-delimited RIS

Error

Oops... you haven't selected anything for export.

Ok

clear

attachment

Supplementary material:
Supplementary File 1 (ZIP, 24695 KB)

19 pages, 8596 KB  

Open AccessArticle

Comprehensive Volatile Metabolite Profiling and Bioactive Marker Discovery of Saposhnikoviae Radix via HS-GC-MS/MS Integrated with Chemometrics and Network Pharmacology

by Fangliang He, Xianrui Wang, Jiating Zhang, Lizhi Wan, Haonan Wu, Xianlong Cheng, Jia Chen, Xiangri Li, Wenguang Jing and Feng Wei

Metabolites 2026, 16(9), 689; https://doi.org/10.3390/metabo16090689 (registering DOI) - 18 Sep 2026

Abstract

Background: Saposhnikoviae radix (SR), a valuable Chinese medicinal plant with high medicinal and edible value, suffers from inconsistent quality caused by growth patterns, cultivation duration, and geographical origin. Methods: In this study, comprehensive volatile metabolite profiling using HS-GC-MS/MS combined with multivariate chemometrics was [...] Read more.

Background: Saposhnikoviae radix (SR), a valuable Chinese medicinal plant with high medicinal and edible value, suffers from inconsistent quality caused by growth patterns, cultivation duration, and geographical origin. Methods: In this study, comprehensive volatile metabolite profiling using HS-GC-MS/MS combined with multivariate chemometrics was performed to characterize these quality-related differences. Results: In total, 7, 13, and 11 differential volatile compounds were identified for wild versus cultivated SR, cultivation duration, and geographical origin, respectively. By integrating the three comparisons, 11 recurrent differential compounds were selected for network pharmacology and molecular docking analyses. trans-3-Nonen-2-one, benzaldehyde, and Octanoic acid were predicted to interact with key targets, including TNF, IL1B, ALB, EGFR, and CASP3, which were mainly enriched in inflammation- and pain-related pathways, including the PI3K-Akt signaling pathway, apoptosis, and the HIF-1 signaling pathway. Molecular docking further supported favorable predicted interactions between the selected compounds and core targets. Conclusions: Overall, this study reveals volatile metabolite variation associated with major quality-related factors of SR and identifies candidate bioactive and quality-associated volatile compounds. The integration of volatile metabolite profiling, chemometrics, network pharmacology, and molecular docking provides a complementary strategy for the comprehensive quality evaluation of SR and offers a reliable reference for quality control research on other medicinal Apiaceae species. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Figure 1

attachment

Supplementary material:
Supplementary File 1 (ZIP, 1915 KB)

16 pages, 3156 KB  

Open AccessFeature PaperArticle

Metabolomics-Based Analysis of Quality Differences in Dendrobium officinale Leaves Under Different Flower Treatments

by Xiaoxu Ren, Wu Ying, Lihua Chen, Bingbin Zheng, Shouzeng Xu, Le Zhang, Xianbo Wang, Luxia Chen, Bowei He and Songlin Ruan

Metabolites 2026, 16(9), 643; https://doi.org/10.3390/metabo16090643 - 2 Sep 2026

Viewed by 171

Abstract

Background/Objectives: To elucidate how flower retention regulates leaf quality formation in Dendrobium officinale and to provide a theoretical basis for high-quality leaf cultivation and high-value utilization of byproducts, D. officinale leaves were subjected to two treatments: flower retention (FR) and flower removal [...] Read more.

Background/Objectives: To elucidate how flower retention regulates leaf quality formation in Dendrobium officinale and to provide a theoretical basis for high-quality leaf cultivation and high-value utilization of byproducts, D. officinale leaves were subjected to two treatments: flower retention (FR) and flower removal (FT). Methods: Quantitative analysis revealed significant differences in quality-related compounds between the two treatments. Specifically, the polysaccharide content in the FR group (8.72%) was significantly lower than that in the FT group (9.37%). Conversely, the FT group exhibited a significantly higher total flavonoid content (1.74%) compared to the FR group (1.41%). Additionally, the total phenol content in the FR group (0.90%) was significantly higher than that in the FT group (0.69%) (n = 3). Results: Compared with the FR group, the FT group exhibited significantly higher levels of total flavonoids, polysaccharides, tyrosine (Tyr), hydroxylysine (Hylys), lysine (Lys), histidine (His), and arginine (Arg). A total of 1999 (39.5%) of the 5062 annotated metabolites were accumulated significantly differently. The FT group was mainly characterized by upregulated secondary metabolites, including flavonoids. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that nucleotide metabolism, purine metabolism, aminoacyl-tRNA biosynthesis, and flavonoid biosynthesis were the core differential pathways. Furthermore, the differential metabolites exhibited a metabolic trade-off of “upregulated secondary metabolism and downregulated primary metabolism”. Conclusions: Our findings indicated that flower removal can significantly increase the active flavonoid components and amino acids in D. officinale leaves and optimize the quality of this medicinal leaf by regulating the source–sink relationship, carbon–nitrogen partitioning, and key metabolic pathways. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Figure 1

attachment

Supplementary material:
Supplementary File 1 (ZIP, 6973 KB)

16 pages, 11493 KB  

Open AccessArticle

Integrated Metabolomic and Transcriptomic Analyses Reveal Phenylpropanoid–Associated Variation Among Three Dendrobium huoshanense Germplasm Materials

by Peipei Wei, Binbin Du, Xingen Zhang, Guohui Li, Fang Li, Ping Zhang, Jiayi Dou, Li Zou, Junjie Yang, Yujuan Wang and Jun Dai

Metabolites 2026, 16(9), 612; https://doi.org/10.3390/metabo16090612 - 27 Aug 2026

Viewed by 257

Abstract

Background: Dendrobium huoshanense flowers are a potentially valuable medicinal resource, but metabolic variation among different germplasm materials remains incompletely characterized. This study aimed to characterize metabolic and transcriptional differences among three D. huoshanense germplasm materials and to explore gene–metabolite associations related to phenylpropanoid [...] Read more.

Background: Dendrobium huoshanense flowers are a potentially valuable medicinal resource, but metabolic variation among different germplasm materials remains incompletely characterized. This study aimed to characterize metabolic and transcriptional differences among three D. huoshanense germplasm materials and to explore gene–metabolite associations related to phenylpropanoid metabolism. Methods: Untargeted LC–MS metabolomics and transcriptome sequencing were used to comparatively profile flowers of three D. huoshanense germplasm materials (DH-1, DH-2, and DH-3). Results: Metabolomic profiling detected 4357 metabolic features putatively assigned to 12 chemical classes and revealed clear separation among the three materials. A total of 1292, 1861, and 2035 differentially accumulated metabolic features were identified in DH-1 vs. DH-2, DH-1 vs. DH-3, and DH-2 vs. DH-3, respectively. Transcriptome analysis identified 33,665 expressed genes, including 3365, 5244, and 5964 DEGs in the respective pairwise comparisons. Phenylpropanoid biosynthesis was recurrently enriched across all three DEG comparisons. Exploratory gene–metabolite analysis identified associations involving phenylpropanoid–related candidate genes, including PAL, C4H, 4CL/4CL–like, HCT–like, CSE–like, COMT/OMT–like, and CAD, with the DH-2 vs. DH-3 comparison showing the most extensive molecular differences. Conclusions: The three D. huoshanense germplasm materials exhibited distinct metabolic and transcriptional profiles, providing candidate genes and metabolic features for subsequent targeted validation. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Figure 1

attachment

Supplementary material:
Supplementary File 1 (ZIP, 124 KB)

18 pages, 6228 KB  

Open AccessArticle

Volatile Profiling and Transcriptomic Analysis of Peel and Flesh in Wampee (Clausena lansium (Lour.) Skeels)

by Ruibing Xu, Qingshan Li, Gengrui Zhu, Yi Chen and Gaoyang Zhang

Metabolites 2026, 16(8), 598; https://doi.org/10.3390/metabo16080598 - 21 Aug 2026

Viewed by 366

Abstract

Background: Wampee (Clausena lansium (Lour.) Skeels) is an understudied Rutaceae crop native to southern China, whose fruit features a complex aroma profile with simultaneous sour, sweet, bitter and astringent notes. Although bioactive compounds including flavonoids, alkaloids and volatile oils in wampee [...] Read more.

Background: Wampee (Clausena lansium (Lour.) Skeels) is an understudied Rutaceae crop native to southern China, whose fruit features a complex aroma profile with simultaneous sour, sweet, bitter and astringent notes. Although bioactive compounds including flavonoids, alkaloids and volatile oils in wampee fruit have been partially characterized, the tissue-specific metabolic and transcriptional basis underlying its distinctive aroma formation remains largely unclear. Methods: We performed an integrated volatile metabolomic and transcriptomic analysis on the pericarp (peel) and flesh of wampee fruit across three cultivars (Shanyellowpi, Heijingang, Bingtangxin). Volatile metabolites were profiled via headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS), and transcriptome profiles were generated by RNA-Seq. Multi-omics integration was conducted using Procrustes analysis, gene–metabolite correlation network construction and weighted gene co-expression network analysis (WGCNA). Results: A total of 288 volatile metabolites were identified, representing the most comprehensive volatile inventory for C. lansium reported to date. Principal component analysis and partial least squares discriminant analysis revealed distinct volatile profiles between pericarp and flesh; terpenoids were the dominant chemical class, accounting for 71.56–91.48% of total volatiles in pericarp and 61.88–67.22% in flesh. Notably, organoheterocyclic compounds were significantly enriched in Shanyellowpi flesh (40.45%), forming a cultivar-specific metabolic signature absent in the other two cultivars. Transcriptomic analysis showed that phenylpropanoid biosynthesis was the most significantly enriched pathway among differentially expressed genes, followed by monoterpene biosynthesis and sesquiterpenoid biosynthesis. Procrustes analysis demonstrated a strong global concordance between the two omics layers (M² = 0.535, p < 0.001). Gene–metabolite correlation networks identified terpene synthase (TPS) genes (HP075360, HP217350) and oxidoreductase genes (SOD1, GST, 10HGO) as candidate co-regulators of terpenoid biosynthesis. WGCNA further prioritized TPS genes, cytochrome P450 genes and MYB transcription factor genes as key regulators driving volatile metabolic divergence between tissues. Conclusion: This study provides a comprehensive volatile and transcriptomic atlas of wampee fruit, and identifies tissue-specific and cultivar-specific metabolic signatures as well as their candidate regulatory genes. These findings advance our understanding of quality differentiation in Rutaceae fruits and lay a foundation for molecular breeding and flavor improvement of wampee. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Figure 1

attachment

Supplementary material:
Supplementary File 1 (ZIP, 4035 KB)

23 pages, 15530 KB  

Open AccessArticle

Untargeted Metabolomics of Xylem Sap Exudates in Two Common Bean Genotypes with Contrasting Growth Rates Under Water Deficit During Pod Filling

by Norma Cecilia Morales-Elias, Lizandro Ramírez-Trejo, Carlos Alberto Cruz-Cruz, Juan Luis Monribot-Villanueva, José Antonio Guerrero-Analco, Monserrat Vázquez-Sánchez, José Rodolfo García-Nava, Antonio García-Esteva, María Teresa González-Arnao, José Cruz Jiménez Galindo and Daniel Padilla-Chacón

Metabolites 2026, 16(8), 564; https://doi.org/10.3390/metabo16080564 - 10 Aug 2026

Viewed by 576

Abstract

Background/Objectives: Water deficit during the pod filling stage severely limits the productivity of common beans (Phaseolus vulgaris). Although the effects of water scarcity have been extensively studied in leaves and roots, the contribution of xylem sap to systemic metabolic adaptation [...] Read more.

Background/Objectives: Water deficit during the pod filling stage severely limits the productivity of common beans (Phaseolus vulgaris). Although the effects of water scarcity have been extensively studied in leaves and roots, the contribution of xylem sap to systemic metabolic adaptation remains poorly understood. This study investigated genotype-specific metabolic changes in xylem sap exudates in response to water deficit in two common bean genotypes with contrasting growth rates. The OTI genotype has a growth cycle of 120 days, while Rosa La Bufa (RB) completes its cycle in 80 days under both well-watered and water deficit conditions. Methods: Physiological responses were evaluated, and xylem sap exudate metabolites were profiled using untargeted UPLC–ESI–QTOF–MS. Protein–metabolite interaction networks were reconstructed using STITCH v5 to identify genotype-specific metabolic organization under stress. Results: Water deficit reduced the abundance of multiple xylem metabolites, including flavonoids, isoflavones, phenolic acids, sugars, amino acids, and oxylipin-related compounds, indicating systemic metabolic contraction. OTI exhibited extensive metabolic changes characterized by enrichment of citrate, aromatic amino acids, glycolytic intermediates, flavonoid glycosides, and detoxification-associated metabolites, consistent with active carbon remobilization and oxidative stress responses. In contrast, RB accumulated isoflavones, including genistein, biochanin A, and baicalein, together with glycosylated triterpenoid saponins. Network analysis revealed that OTI developed a broad stress-responsive interactome that integrated phenylpropanoid metabolism, carbon remobilization, and detoxification pathways, whereas RB maintained a compact interactome reinforced by oxylipin-, jasmonate-, and isoflavone-associated modules. Conclusions: Xylem sap undergoes genotype-dependent metabolic adjustment under water deficit, suggesting contrasting drought adaptation strategies. Long growth cycle genotypes activate extensive metabolic plasticity, whereas reduced growth cycle genotypes rely on more specialized defense networks. These findings highlight xylem metabolomics as a valuable approach for understanding systemic drought adaptation and identifying putative metabolic biomarkers associated with drought resilience in common beans. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Graphical abstract

attachment

Supplementary material:
Supplementary File 1 (ZIP, 814 KB)

19 pages, 8472 KB  

Open AccessArticle

Comprehensive Phytochemical Characterization and Quality Evaluation of Taxillus chinensis via Integrated Widely Targeted Metabolomics, HPLC Fingerprinting, and Multi-Component Quantification

by Zhouwei Li, Hongfei Wei, Jiahui Wu, Qiyuan Yang, Jiemei Liang, Xiaoxun Wang and Li Li

Metabolites 2026, 16(7), 446; https://doi.org/10.3390/metabo16070446 - 25 Jun 2026

Viewed by 414

Abstract

Background/Objectives: This study aims to establish a systematic phytochemical characterization and quality evaluation method to systematically evaluate the influence of multiple factors on the chemical composition of Taxillus chinensis, thereby providing a scientific basis for its development, utilization, and quality control standards. [...] Read more.

Background/Objectives: This study aims to establish a systematic phytochemical characterization and quality evaluation method to systematically evaluate the influence of multiple factors on the chemical composition of Taxillus chinensis, thereby providing a scientific basis for its development, utilization, and quality control standards. Methods: To ensure a targeted and representative metabolic screening, six representative batches covering the major geographical origins and host plants were selected for initial metabolomic profiling. An integrated analytical approach combining UPLC-MS/MS-based widely targeted metabolomics, HPLC fingerprinting, and multi-component quantitative analysis with multivariate statistical analysis was employed. Results: Significant quality variations were identified across the samples. Metabolomics results indicated that while chemical component types were qualitatively consistent across growth conditions, their contents varied significantly. Unique differential metabolites clustered according to specific geographical origins or host plants. KEGG pathway analysis revealed that geographical origin primarily regulated phenylpropanoid biosynthesis, whereas host differences mainly influenced flavonoid and monoterpenoid biosynthesis. Furthermore, HPLC fingerprinting of 20 batches demonstrated similarities greater than 0.9, with 15 common peaks determined. Based on their high relative abundance, differential significance across samples, and documented pharmacological relevance to the herb’s traditional efficacy, six bioactive components—gallic acid, catechin, epicatechin, hyperoside, isoquercitrin, and quercitrin—were identified and quantified. Notably, samples originating from Wuzhou exhibited the highest total content of these components. Consistent with PCA and HCA results, gallic acid, hyperoside, isoquercitrin, and quercitrin were identified as potential markers driving quality differences. Conclusions: This integrated approach allows for a systematic analytical screening of Taxillus chinensis, clarifying chemical variations caused by environmental and biological factors, and supporting the standardization and comprehensive utilization of this medicinal plant. Full article

(This article belongs to the Topic Metabolomics in Plants)

►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less

Select all

Export citation of selected articles as:

Plain Text BibTeX BibTeX (without abstracts) Endnote Endnote (without abstracts) Tab-delimited RIS

 

Error

Oops... you haven't selected anything for export.

Ok

clear

Displaying articles 1-6