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Advances in Genetics and Genomics of Medical Plants
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Advances in Genetics and Genomics of Medical Plants

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

Deadline for manuscript submissions: 25 March 2027 | Viewed by 1883

Editor

Dr. Mingcheng Wang

E-Mail Website
Guest Editor
Institute for Advanced Study, Chengdu University, Chengdu 610106, China
Interests: plant genomics; comparative genomic analysis; functional gene analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recent advances in genetics, genomics, and high-throughput sequencing technologies have greatly accelerated research on medicinal plants, providing new insights into their evolution, biosynthesis, and functional diversity. The rapid development of multi-omics approaches, including genomics, transcriptomics, epigenomics, and metabolomics, has enabled comprehensive investigations of nuclear and organelle genomes and their roles in regulatory mechanisms underlying important medicinal traits. These advances are driving the discovery of bioactive compounds, improvement of medicinal resources, and sustainable utilization of medical plants. This Special Issue aims to highlight cutting-edge genetic and genomic studies of medicinal plants, with a focus on genome assembly, comparative genomics, functional genomics, and integrative omics analyses. Both original research and reviews combining high-throughput data analysis with experimental validation are welcome.

Dr. Mingcheng Wang
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 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-anonymized 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

  • medicinal plant genomics
  • medicinal plant genetics
  • high-throughput sequencing
  • functional genomics
  • multi-omics integration

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Published Papers (3 papers)

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Research

25 pages, 27373 KB  
Article
Integrated Transcriptomic and Metabolomic Analyses Uncover the Molecular Mechanisms Underlying Drought Tolerance in Isodon suzhouensis
by Fawang Liu and Lei Pan
Genes 2026, 17(8), 936; https://doi.org/10.3390/genes17080936 - 11 Aug 2026
Viewed by 101
Abstract
Background/Objectives: This study aims to reveal the physiological and molecular regulatory mechanisms of the genuine medicinal herb I. suzhouensis K. F. Zhai, Z. B. Han & S. B. Zhou (Wangzaozi) of Anhui province in response to drought stress, and clarify the regulatory patterns [...] Read more.
Background/Objectives: This study aims to reveal the physiological and molecular regulatory mechanisms of the genuine medicinal herb I. suzhouensis K. F. Zhai, Z. B. Han & S. B. Zhou (Wangzaozi) of Anhui province in response to drought stress, and clarify the regulatory patterns of drought adversity on the accumulation of its medicinal active ingredients. Methods: Mild natural drought treatment was applied to I. suzhouensis. Combined with Illumina high-throughput transcriptome sequencing and HPLC-MS/MS targeted metabolomics detection, this study jointly deciphered the dynamic changes in gene expression and metabolite accumulation of I. suzhouensis under drought. Key drought-responsive metabolic pathways, core regulatory genes and marker metabolites were screened. Results: A total of 56,823 high-quality unigenes were obtained via transcriptome sequencing, among which 23,580 differentially expressed genes (DEGs) were identified. Functional enrichment analysis revealed that DEGs were predominantly enriched in pathways, including plant hormone signal transduction, phenylpropanoid biosynthesis, flavonoid biosynthesis and photosynthesis. A total of 4171 metabolites were qualitatively and quantitatively characterized via metabolomics, and 1632 differentially expressed metabolites (DEMs) were screened, mainly enriched in phenylpropanoid biosynthesis, tyrosine metabolism, flavone and flavonol biosynthesis pathways. Physiological measurements of antioxidant indices demonstrated that the activities of SOD and POD increased by approximately 2-fold, while PAL activity rose by 1.55-fold, and chlorophyll content decreased significantly. Multi-omics joint analysis indicated that mild drought stress modulates the expression of genes involved in phenylpropanoid, flavonoid and diterpenoid biosynthetic pathways, alters antioxidant enzyme activities, and coordinately regulates the formation of drought tolerance and the accumulation of bioactive compounds in I. suzhouensis. Conclusions: This study systematically elucidates the drought response mechanism of I. suzhouensis cultivated in northern Anhui province. It provides theoretical evidence and candidate core responsive gene resources for standardized cultivation of I. suzhouensis and precise regulation of medicinal quality in drought-prone production areas. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Medical Plants)
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19 pages, 3533 KB  
Article
Genome-Wide Characterization of the ALKBH Gene Family Reveals a Potential Role of PgALKBH10 in Multiple Abiotic Stress Responses in Panax ginseng C. A. Mey.
by Yiming Sun, Yadong Zhuang, Wanqing Yang, Dan Wang, Jia Hu and Wei Hao
Genes 2026, 17(7), 793; https://doi.org/10.3390/genes17070793 - 12 Jul 2026
Viewed by 370
Abstract
Background/Objectives: N6-methyladenosine (m6A) is a prevalent RNA modification that significantly influences various biological processes. AlkB homologs (ALKBHs) belong to the family of specific demethylases and, by regulating m6A methylation, are known to be involved in the modulation of plant [...] Read more.
Background/Objectives: N6-methyladenosine (m6A) is a prevalent RNA modification that significantly influences various biological processes. AlkB homologs (ALKBHs) belong to the family of specific demethylases and, by regulating m6A methylation, are known to be involved in the modulation of plant stress responses. However, the ALKBH gene family has not been systematically characterized in ginseng. Methods: A genome-wide identification and characterization of the ALKBH gene family in ginseng were performed using a telomere-to-telomere reference genome. Phylogenetic relationships, gene structures, conserved motifs, 3D structures, chromosomal distribution, syntenic relationships, cis-acting regulatory elements, protein-protein interaction (PPI) networks, and expression profiles were analyzed. Transcriptome datasets covering multiple tissues, developmental stages, cultivars, and abiotic stress treatments were examined. Candidate stress-responsive genes were further validated by qRT-PCR. Results: A total of 17 PgALKBH genes were identified and classified into seven subfamilies. Structural analyses revealed conserved motifs, exon–intron organization, and 3D structures among members within the same subfamily. Chromosomal localization and synteny analyses suggested that the PgALKBH family has been evolutionarily conserved between ginseng and Arabidopsis and has primarily undergone purifying selection during its expansion. Promoter analysis identified abundant light-, hormone-, and stress-responsive cis-elements. Expression profiling revealed distinct tissue- and developmental stage-specific patterns. The PPI analysis suggested that PgALKBH proteins, especially PgALKBH10, may play a central role in m6A-mediated RNA regulation in ginseng. Transcriptome and qRT-PCR analyses further showed that PgALKBH genes respond differentially to drought, cold, and salt stresses. Notably, PgALKBH10 was induced under all three stress conditions. Conclusions: This study provides a comprehensive characterization of the ALKBH gene family in ginseng and identifies PgALKBH10 as a promising candidate involved in multiple abiotic stress responses. These findings establish a foundation for elucidating the roles of RNA m6A demethylation in ginseng and provide valuable genetic resources for developing stress-tolerant ginseng cultivars. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Medical Plants)
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22 pages, 8242 KB  
Article
Transcriptome and Metabolome-Based Analysis Reveals the Molecular Mechanisms Underlying the Differences in Tanshinone and Salvianolic Acid Content Between Salvia miltiorrhiza Roots and Leaves
by Fawang Liu, Yingying Xu, Lei Pan, Yin Zhang and Mengping Ding
Genes 2026, 17(3), 280; https://doi.org/10.3390/genes17030280 - 27 Feb 2026
Cited by 1 | Viewed by 840
Abstract
Background/Objectives: Salvia miltiorrhiza (Danshen) is a well-known medicinal herb in traditional Chinese medicine. It produces tanshinones and salvianolic acids as key bioactive constituents in its roots, yet the molecular basis for their tissue-specific accumulation is still poorly understood. This study aims to identify [...] Read more.
Background/Objectives: Salvia miltiorrhiza (Danshen) is a well-known medicinal herb in traditional Chinese medicine. It produces tanshinones and salvianolic acids as key bioactive constituents in its roots, yet the molecular basis for their tissue-specific accumulation is still poorly understood. This study aims to identify candidate functional genes involved in the biosynthesis of tanshinones and salvianolic acids, and to reveal the molecular basis underlying their tissue-specific accumulation in S. miltiorrhiza. Methods: For this purpose, we compared transcriptomic and metabolomic differences between the roots and leaves, and further measured a set of physiological parameters, including the POD, SOD, CAT and PAL activities, as well as the total phenols and flavones contents. Results: Metabolomic analysis identified 6805 metabolites, of which 241 were differentially accumulated between roots and leaves, with 172 upregulated in roots. The elevated metabolites included gibberellin, cryptotanshinone, decursinol angelate, chalcone, and psoralenol. Transcriptome analysis identified 32,700 annotated genes, with 9895 showing differential expression between roots and leaves, including 4199 upregulated in roots. Roots exhibited higher levels of phenols and flavones, as well as significantly greater POD, SOD, CAT, and PAL activities. Conclusions: Integrated omics analysis identified putative candidate genes including CPS, KS, and P450s as potential contributors for tanshinone and salvianolic acid biosynthesis. The identified genes provide valuable resources for molecular breeding, offering opportunities to improve the medicinal quality of S. miltiorrhiza. Full article
(This article belongs to the Special Issue Advances in Genetics and Genomics of Medical Plants)
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