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Biosynthesis and Regulatory Mechanism of Secondary Metabolites in Medicinal Plants: 3rd Edition

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 332

Special Issue Editor


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Guest Editor
Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
Interests: medicinal plant; bioactive compound; biosynthetic pathway; noncoding RNA; transcription factor; genome; transcriptome; metabolome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Medicinal plants are important assets to human society. However, compared with model systems and crops, research on medicinal plants has long lagged behind. Recently, driven by the increasing demand for medicinal plants and the development and application of high-throughput technologies, this research field has expanded rapidly. Significant progress has been made in genomics, epigenomics, transcriptomics, and metabolomics of medicinal plants. Numerous studies have elucidated biosynthetic pathways of secondary metabolites, genes encoding key enzymes within these pathways, and the regulatory mechanisms of secondary metabolism. These advances have enabled the production of secondary metabolites through metabolic engineering and synthetic biology. Moreover, novel technologies and strategies are being developed and applied to this field.

This Special Issue of IJMS is devoted to publishing original research and review articles on medicinal plant studies, with a focus on recent advances in the biosynthesis and regulation of secondary metabolites, particularly significant discoveries from intensive studies and the development and application of novel technologies. The aim is to provide an open-access platform for sharing important results from medicinal plant research in recent years, thereby supporting further studies on secondary metabolism, medicinal plant improvement, and the production of functionally important secondary metabolites. 

Topics of interest include, but are not limited to, the following:

  • Genomics, epigenomics, transcriptomics, and metabolomics of medicinal plants;
  • Biosynthetic pathways of secondary metabolites;
  • Key enzyme genes involved in secondary metabolite biosynthesis;
  • Epigenetic regulation of secondary metabolism, including microRNAs, long non-coding RNAs, DNA methylation, RNA methylation, and so on;
  • Transcription factors and regulatory networks in medicinal plants;
  • Metabolic engineering and synthetic biology of secondary metabolites;
  • Applications of high-throughput sequencing technologies;
  • Databases related to the biosynthesis and regulation of secondary metabolites;
  • Novel technologies and strategies for studying secondary metabolism.

Prof. Dr. Shanfa Lu
Guest Editor

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Keywords

  • biosynthetic pathway
  • epigenetic regulation
  • high-throughput sequencing
  • medicinal plant
  • metabolic engineering
  • omics
  • regulatory mechanism
  • secondary metabolite
  • synthetic biology
  • transcription factor

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Published Papers (1 paper)

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Research

16 pages, 7438 KB  
Article
Integrated Omics Analysis Revealed the Differential Metabolism of Pigments in Three Varieties of Gastrodia elata Bl
by Xiaohua Li, Huaijing Zhu, Bingbing Zhang and Dahui Liu
Int. J. Mol. Sci. 2025, 26(24), 11839; https://doi.org/10.3390/ijms262411839 - 9 Dec 2025
Viewed by 115
Abstract
Gastrodia elata Blume is a well-known traditional Chinese medicine. The color of flower and flower stalk are important characteristics in the classification of G. elata. However, the mechanisms of pigment formation in different types of G. elata are not yet elucidated. To [...] Read more.
Gastrodia elata Blume is a well-known traditional Chinese medicine. The color of flower and flower stalk are important characteristics in the classification of G. elata. However, the mechanisms of pigment formation in different types of G. elata are not yet elucidated. To understand this, targeted metabolomics as well as transcriptomics analyses were carried out in this study. The differential accumulation and the typical components of pigments in different types of G. elata were elucidated. According to our research, the accumulation of carotenoids rather than anthocyanins likely contributes to the pigment content in G. elata. The different accumulations of carotenoids including violaxanthin, lycopene, α-carotene, and α-cryptoxanthin are the main reasons that contribute to the color differences in the flowers and flower stalks of these three G. elata varieties. Integrated multi-omics analysis enriched 50 and 17 differential genes in the flavonoid–anthocyanin and carotenoid biosynthesis pathways, respectively. Among these, PSY, PDS, CCD, UGT, and ANR were identified as critical genes responsible for the differential pigment accumulation in G. elata varieties, while the MYB TFs were tightly associated with main genes expression and content of carotenoids. Overall, this study enhances the current understanding of pigments’ metabolites profiles and contributes valuable insights into the molecular mechanisms underlying G. elata carotenoid biosynthesis; these findings also provide valuable guidance for future carotenoid biofortification and molecular breeding in G. elata. Full article
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