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Applications of Omics and Bioinformatics in Medicinal Plants
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Applications of Omics and Bioinformatics in Medicinal Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Phytochemistry".

Deadline for manuscript submissions: 31 August 2026 | Viewed by 2901

Special Issue Editors

Dr. Kangyu Wang

E-Mail Website
Guest Editor
1. College of Life Science, Jilin Agricultural University, Changchun 130118, China
2. Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Changchun 130118, China
Interests: plant genome; transcription factor family; functional genomics; methyl jasmonate treatment
Dr. Paula C. Castilho

E-Mail Website
Guest Editor
CQM—Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
Interests: chemical composition of aromatic, medicinal, and food plants; organic chemistry hemi synthesis of bioactive compounds using natural products as raw materials; assessment of the biological activity of new compounds
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Medicinal plants have historically served as a fundamental component of both traditional and contemporary medicine, offering a substantial reservoir of bioactive compounds for disease treatment and health promotion. However, realizing their full potential necessitates the use of advanced methodologies to unravel their intricate biochemical pathways, genetic diversity, and ecological interactions. This Special Issue examines the transformative impact of omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and bioinformatics, on advancing medicinal plant research. These state-of-the-art approaches facilitate comprehensive investigations of plant systems, such as gene-to-metabolite networks, thereby fostering innovations in drug discovery, sustainable cultivation, and conservation. The integration of omics technologies has enabled researchers to identify key genes involved in the biosynthesis of pharmacologically active compounds, such as alkaloids, terpenoids, and phenolics; optimize metabolic engineering strategies; and enhance plants’ resilience to environmental stressors. We welcome submissions of original research, reviews, and methodological advancements to provide a platform to promote collaboration among biologists, bioinformaticians, pharmacologists, and agronomists. Submitted manuscripts must not be previously published or under evaluation for publication in another journal.

Dr. Kangyu Wang
Dr. Paula C. Castilho
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 submissions that pass pre-check are 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 250 words) can be sent to the Editorial Office for assessment.

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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • bioinformatics
  • medicinal plants
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • gene family
  • transcription factor

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Published Papers (3 papers)

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Research

19 pages, 4084 KB  
Article
Integrated Omic Analyses Reveal Module Networks Regulating Growth and Bioactive Component Synthesis of Sophora tonkinensis via Calcium Modulation
by Zhu Qiao, Zhan-Tao Fan, Ling-Yun Chen, Lin-Xuan Li, Fan Wei, Shuang-Shuang Qin, Jing Wang, Ben Qin and Ying Liang
Plants 2026, 15(1), 133; https://doi.org/10.3390/plants15010133 - 2 Jan 2026
Viewed by 632
Abstract
Sophora tonkinensis is a key medicinal plant endemic to the calcium-rich karst regions along the China–Vietnam border. This study investigated how calcium regulates the growth and biosynthesis of bioactive compounds in S. tonkinensis tissue culture seedlings by exposing them to a gradient of [...] Read more.
Sophora tonkinensis is a key medicinal plant endemic to the calcium-rich karst regions along the China–Vietnam border. This study investigated how calcium regulates the growth and biosynthesis of bioactive compounds in S. tonkinensis tissue culture seedlings by exposing them to a gradient of calcium concentrations. Our findings demonstrate that a moderate calcium level (T2, 2.99 mmol·L−1) promoted root development, increasing root dry weight, and significantly elevated the content of matrine and oxymatrine. In contrast, a high calcium level (T4, 5.98 mmol·L−1) inhibited root growth, reducing root length, but triggered a distinct metabolic shift, markedly increasing the accumulation of trifolirhizin and maackiain. Integrated transcriptomic, proteomic, and metabolomic analyses revealed that calcium exerts systemic regulation through multiple functional pathways. We identified four key signaling pathways—phytohormone, plant immunity, MAPK, and phospholipid signaling—as central hubs coordinating genetic information processing, vesicular transport, and metabolic reprogramming. These results provide valuable insights into the calcium-mediated regulatory networks and offer valuable targets for optimizing cultivation practices to enhance the yield of bioactive compounds in S. tonkinensis Full article
(This article belongs to the Special Issue Applications of Omics and Bioinformatics in Medicinal Plants)
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14 pages, 2886 KB  
Article
Exploration of the Donors and Specific Genes of B Subgenome in Perilla frutescens Based on Genomic Analysis
by Zhaoyuan Li, Bin Wang, Wei Wei, Yang Liu, Qiuling Wang, Zhihui Gao and Jianhe Wei
Plants 2025, 14(23), 3698; https://doi.org/10.3390/plants14233698 - 4 Dec 2025
Viewed by 639
Abstract
Perilla frutescens is an important medicinal and edible plant in Asia and was introduced in Europe and North America mainly as a spice plant. The commonly cultivated species is an allotetraploid (AABB). While the identity of its AA diploid donor has been preliminarily [...] Read more.
Perilla frutescens is an important medicinal and edible plant in Asia and was introduced in Europe and North America mainly as a spice plant. The commonly cultivated species is an allotetraploid (AABB). While the identity of its AA diploid donor has been preliminarily clarified, the other donor, BB, has not been discovered yet, and the taxonomic status and characteristics of the BB donor remain unresolved. Based on the published genomes of Perilla spp., we employed a collinearity analysis, gene structure similarity assessment, and multi-level functional annotation to infer the genomic and phenotypic features of the B subgenome. Results suggest that the protein sequences of the B and A subgenomes exhibit the highest similarity, while the protein sequences of Lavandula angustifolia or Ocimum basilicum are less similar to the B subgenome, and two subgenomes also possess the largest number of homologous genes and have similar gene structures. A total of 90 BB progenitor-specific genes were significantly enriched in pathways related to secondary metabolite biosynthesis and environmental stress response. Among these genes, the terpene synthase genes constitute the main genetic basis for the diversity of bioactive components in perilla. The discovery of a homologous gene containing the NB-ARC domain, associated with resistance to late blight, suggests that BB may contribute to key disease-resistant traits. Further gene family analysis revealed that compared with the A subgenome, the B subgenome exhibited fewer genes and lower diversity in the TPS and NB-ARC families. These findings indicate that BB may have originated from an unfound or extinct species within the Perilla spp. The BB donor might be less diversified than AA, possibly adapting to a narrow geographic and climatic range. Full article
(This article belongs to the Special Issue Applications of Omics and Bioinformatics in Medicinal Plants)
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19 pages, 2879 KB  
Article
Metabolomic Insights into Sexual Multi-Morphism of Sinomenine Accumulation in Sinomenium acutum
by Yanxian Luo, Wen Xu, Yanling Fan, Xinyu Ma, Qian Deng, Meng Li and Wei Sun
Plants 2025, 14(12), 1885; https://doi.org/10.3390/plants14121885 - 19 Jun 2025
Cited by 3 | Viewed by 1128
Abstract
Sinomenium acutum is the main raw material for sinomenine. Empirical evidence indicates a marked disparity in sinomenine content among S. acutum plants with different genders, resulting in varying medicinal potential of the processing products. However, the mechanism underlying gender-determined differences in sinomenine accumulation [...] Read more.
Sinomenium acutum is the main raw material for sinomenine. Empirical evidence indicates a marked disparity in sinomenine content among S. acutum plants with different genders, resulting in varying medicinal potential of the processing products. However, the mechanism underlying gender-determined differences in sinomenine accumulation is still elusive. In this study, untargeted metabolomics was performed among female, male, and undifferentiated S. acutum plants. In total, 1213 metabolites were identified, and most of them vary in the roots but not in the leaves among the different genders. Integrated correlation analysis on the DAMs (differentially accumulated metabolites) enriched in the isoquinoline alkaloid biosynthesis pathway suggests coclaurine as an intermediate determining gender-dependent sinomenine variation. Furthermore, hormonal profiling revealed 34 endogenous phytohormones exhibiting significant gender-based discrepancy in the roots. Among these, ABA (abscisic acid) and 5-DS (5-deoxystrigol) show significant positive correlation with sinomenine content. Then, exogenous ABA with gradient concentration was applied on S. acutum plants, and the sinomenine content in the roots increased from 31% to 166% under treatment. Our findings demonstrate that coclaurine might serve as a pivotal intermediate during sinomenine biosynthesis in S. acutum. Meanwhile, it is speculated that ABA is a key factor regulating different sinomenine accumulation, which provide a potential method to improve the yield of sinomenine. Full article
(This article belongs to the Special Issue Applications of Omics and Bioinformatics in Medicinal Plants)
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