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Medicinal Plant Research from an Omics Perspective
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Medicinal Plant Research from an Omics Perspective

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (20 June 2024) | Viewed by 3803

Special Issue Editor

Dr. Linfang Huang

E-Mail Website
Guest Editor
The Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100193, China
Interests: transcriptomics, proteomics and metabolomics of medicinal plants
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues, 

Medicinal plants face numerous challenges and difficulties in terms of resource conservation, regeneration, sustainable utilization and development. Therefore, multi-omics techniques (such as chloroplast genomics, mitochondrial genomics, microbiomics, transcriptomics, genomics, proteomics, metabolomics and phenomics) play an increasingly important role in addressing fundamental issues related to the conservation and utilization of medicinal plants.

The chloroplast genome and mitochondrial genome have become important tools for studying the evolution, species identification and genetic variation of medicinal plants. By analyzing the sequence and structural changes in the chloroplast and mitochondrial genomes, we can gain in-depth insights into the phylogenetic relationships among medicinal plant species, trace their origins and evolutionary processes, and provide valuable information for genetic improvement and conservation of medicinal plant genetic resources.

The comprehensive analysis of genomics, proteomics, metabolomics and microbiomics data provides comprehensive biological information, helping us understand the genetic characteristics of medicinal plants, the synthesis and regulatory mechanisms of bioactive compounds, and the metabolic pathways associated with therapeutic effects. These studies contribute to the discovery of new drug candidates, optimization of medicinal plant varieties, improvement of drug production processes and the modernization of traditional medicine.

This Special Issue focuses on articles covering multi-omics studies on traditional medicinal plants, including the:

  1. Chloroplast genome and mitochondrial genomes of medicinal plants
  2. Transcriptomics, proteomics and metabolomics of medicinal plants
  3. Microbiomics of medicinal plants

Dr. Linfang Huang
Guest Editor

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 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. Genes is an international peer-reviewed open access monthly 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 2600 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

  • Transcriptomics
  • Proteomics 
  • Metabolomics
  • Chloroplast genome
  • Mitochondrial genomes
  • Medicinal plants
  • Microbiomics

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Published Papers (2 papers)

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15 pages, 4108 KiB  
Article
Transcriptome and Metabolome Analysis of Isoquinoline Alkaloid Biosynthesis of Coptis chinensis in Different Years
by Xinyi Min, Ting Zhu, Xinyi Hu, Cong Hou, Jianing He and Xia Liu
Genes 2023, 14(12), 2232; https://doi.org/10.3390/genes14122232 - 18 Dec 2023
Cited by 2 | Viewed by 1766
Abstract
Coptis chinensis is a perennial herb of the Ranunculaceae family. The isoquinoline alkaloid is the main active component of C. chinensis, mainly exists in its rhizomes and has high clinical application potential. The in vitro synthesis of isoquinoline alkaloids is difficult because [...] Read more.
Coptis chinensis is a perennial herb of the Ranunculaceae family. The isoquinoline alkaloid is the main active component of C. chinensis, mainly exists in its rhizomes and has high clinical application potential. The in vitro synthesis of isoquinoline alkaloids is difficult because their structures are complex; hence, plants are still the main source of them. In this study, two-year and four-year rhizomes of C. chinensis were selected to investigate the effect of growth years on the accumulation of isoquinoline alkaloids. Two-year and four-year C. chinensis were selected for metabolomics detection and transcriptomic analysis. A total of 413 alkaloids were detected by metabolomics analysis, of which 92 were isoquinoline alkaloids. (S)-reticuline was a significantly different accumulated metabolite of the isoquinoline alkaloids biosynthetic pathway in C. chinensis between the two groups. The results of transcriptome analysis showed that a total of 464 differential genes were identified, 36 of which were associated with the isoquinoline alkaloid biosynthesis pathway of C. chinensis. Among them, 18 genes were correlated with the content of important isoquinoline alkaloids. Overall, this study provided a comprehensive metabolomic and transcriptomic analysis of the rapid growth stage of C. chinensis rhizome from the perspective of growth years. It brought new insights into the biosynthetic pathway of isoquinoline alkaloids and provided information for utilizing biotechnology to improve their contents in C. chinensis. Full article
(This article belongs to the Special Issue Medicinal Plant Research from an Omics Perspective)
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16 pages, 4334 KiB  
Article
Integrated Metabolomic and Transcriptomic Analysis of Puerarin Biosynthesis in Pueraria montana var. thomsonii at Different Growth Stages
by Xinyi Hu, Ting Zhu, Xinyi Min, Jianing He, Cong Hou and Xia Liu
Genes 2023, 14(12), 2230; https://doi.org/10.3390/genes14122230 - 18 Dec 2023
Cited by 2 | Viewed by 1555
Abstract
Puerarin, a class of isoflavonoid compounds concentrated in the roots of Puerarias, has antipyretic, sedative, and coronary blood-flow-increasing properties. Although the biosynthetic pathways of puerarin have been investigated by previous researchers, studies focusing on the influence of different growth stages on the [...] Read more.
Puerarin, a class of isoflavonoid compounds concentrated in the roots of Puerarias, has antipyretic, sedative, and coronary blood-flow-increasing properties. Although the biosynthetic pathways of puerarin have been investigated by previous researchers, studies focusing on the influence of different growth stages on the accumulation of metabolites in the puerarin pathway are not detailed, and it is still controversial at the last step of the 8-C-glycosylation reaction. In this study, we conducted a comprehensive analysis of the metabolomic and transcriptomic changes in Pueraria montana var. thomsonii during two growing years, focusing on the vigorous growth and dormant stages, to elucidate the underlying mechanisms governing the changes in metabolite and gene expression within the puerarin biosynthesis pathway. In a comparison of the two growth stages in the two groups, puerarin and daidzin, the main downstream metabolites in the puerarin biosynthesis pathway, were found to accumulate mainly during the vigorous growth stage. We also identified 67 common differentially expressed genes in this pathway based on gene expression differences at different growth stages. Furthermore, we identified four candidate 8-C-GT genes that potentially contribute to the conversion of daidzein into puerarin and eight candidate 7-O-GT genes that may be involved in the conversion of daidzein into daidzin. A co-expression network analysis of important UGTs and HIDs along with daidzein and puerarin was conducted. Overall, our study contributes to the knowledge of puerarin biosynthesis and offers information about the stage at which the 8-C-glycosylation reaction occurs in biosynthesis. These findings provide valuable insights into the cultivation and quality enhancement of Pueraria montana var. thomsonii. Full article
(This article belongs to the Special Issue Medicinal Plant Research from an Omics Perspective)
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