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Genomics and Genetics of Medicinal Plants
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Genomics and Genetics of Medicinal Plants

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

Deadline for manuscript submissions: 20 July 2024 | Viewed by 3614

Special Issue Editors

Dr. Qi Tang

E-Mail Website
Guest Editor
College of Horticulture, Hunan Agricultural University, Changsha 410128, China
Interests: molecular biology in medicinal plants; biosynthetic pathway; genome, transcriptome and proteome; synthetic biology
Special Issues, Collections and Topics in MDPI journals
Dr. Rufeng Wang

E-Mail Website
Guest Editor
Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
Interests: molecular biology in medicinal plants; biosynthetic pathway; biocatalysis; metabolic engineering; synthetic biology

Special Issue Information

Dear Colleagues,

Medicinal plants are an important resource for humans. However, compared with the research on model systems and crops, the number of studies on medicinal plants has fallen far behind. Recently, with the increase in demand for medicinal plants and the development and application of high-throughput technologies, the research field of medicinal plants has rapidly expanded. Significant progress has been made in studying the genomics, transcriptomics, proteomics, and metabolomics of medicinal plants. Numerous studies have contributed to elucidating the biosynthetic pathway of secondary metabolites, genes encoding key enzymes of the pathway, and regulatory mechanisms of secondary metabolites. This has enabled the production of secondary metabolites through metabolic engineering and synthetic biology. Moreover, novel technologies and strategies are being developed and applied to this research field. This open-access Special Issue of Genes is devoted to publishing original research and review articles on medicinal plant studies that highlight recent advances in the biosynthesis and regulatory mechanisms of secondary metabolites, particularly significant discoveries from intensive studies, and the development and application of novel technologies. This Special Issue aims to provide an accessible collection of research sharing innovative results from the research field of medicinal plants to aid further studies on secondary metabolism, medicinal plant improvement, and the production of functionally important secondary metabolites.

Topics of interest for this Special Issue include, but are not limited to:

  • The genomics, transcriptomics, proteomics, and metabolomics of medicinal plants;
  • Biosynthetic pathway of secondary metabolites;
  • Key enzyme genes involved in the biosynthesis of secondary metabolites;
  • Transcription factor and regulatory network in medicinal plants;
  • Metabolic engineering and synthetic biology of secondary metabolites;
  • Application of high-throughput sequencing technologies;
  • Databases associated with the biosynthesis and regulation of secondary metabolites;
  • Novel technologies and strategies for secondary metabolism studies.

Dr. Qi Tang
Dr. Rufeng Wang
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 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

  • medicinal plants
  • biosynthetic pathway
  • molecular regulatory mechanisms
  • gene annotation
  • transcription factor
  • high-throughput sequencing
  • metabolic engineering
  • secondary metabolites
  • gene editing
  • multi-omics
  • genome, transcriptome, and proteome
  • metabolomics
  • synthetic biology
  • metabolic analysis
  • metabolic outline

Published Papers (3 papers)

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Research

22 pages, 9382 KiB  
Article
Isolation, Characterization, and Expression Analysis of NAC Transcription Factor from Andrographis paniculata (Burm. f.) Nees and Their Role in Andrographolide Production
by Ramesh Kumar, Chavlesh Kumar, Debjani Roy Choudhury, Aashish Ranjan, Ritesh Kumar Raipuria, Kaushik Kumar Dhar Dubey, Ayushi Mishra, Chetan Kumar, Malik Muzafar Manzoor, Ashok Kumar, Abha Kumari, Kuldeep Singh, Gyanendra Pratap Singh and Rakesh Singh
Genes 2024, 15(4), 422; https://doi.org/10.3390/genes15040422 - 28 Mar 2024
Viewed by 1348
Abstract
Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a [...] Read more.
Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant’s leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis. Full article
(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)
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15 pages, 9252 KiB  
Article
Study of Dandelion (Taraxacum mongolicum Hand.-Mazz.) Salt Response and Caffeic Acid Metabolism under Saline Stress by Transcriptome Analysis
by Zhe Wu, Ran Meng, Wei Feng, Tassnapa Wongsnansilp, Zhaojia Li, Xuelin Lu and Xiuping Wang
Genes 2024, 15(2), 220; https://doi.org/10.3390/genes15020220 - 09 Feb 2024
Viewed by 878
Abstract
Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (Taraxacum mongolicum Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of [...] Read more.
Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (Taraxacum mongolicum Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of two dandelions, namely, “BINPU2” (dandelion A) and “TANGHAI” (dandelion B) under gradient NaCl concentrations (0, 0.3%, 0.5%, 0.7%, and 0.9%), and analyzed potential mechanisms through a comparison analysis of transcriptomes in the two dandelions. Dandelion A had a high leaf weight; high ρ-coumaric acid, caffeic acid, ferulic acid, and caffeoyl shikimic acid contents; and high activities of POD and Pro. The maximum content of four kinds of phenolic acids mostly occurred in the 0.7% NaCl treatment. In this saline treatment, 2468 and 3238 differentially expressed genes (DEGs) in dandelion A and B were found, of which 1456 and 1369 DEGs in the two dandelions, respectively, showed up-regulation, indicating that more up-regulated DEGs in dandelion A may cause its high salt tolerance. Further, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that dandelion salt response and caffeic acid metabolism were mainly enriched in the phenylpropanoid biosynthesis pathway (ko00940) and response to ethylene (GO: 0009723). The caffeic acid biosynthesis pathway was reconstructed based on DEGs which were annotated to PAL, C4H, 4CL, HCT, C3′H, and CSE. Most of these genes showed a down-regulated mode, except for parts of DEGs of 4CL (TbA05G077650 and TbA07G073600), HCT (TbA03G009110, TbA03G009080, and novel.16880), and COMT (novel.13839). In addition, more up-regulated transcription factors (TFs) of ethylene TFs in dandelion A were found, but the TFs of ERF104, CEJ1, and ERF3 in the two dandelions under saline stress showed an opposite expression pattern. These up-regulated genes could enhance dandelion salt tolerance, and down-regulated DEGs in the caffeic acid biosynthesis pathway, especially CSE (TbA08G014310) and COMT (TbA04G07330), could be important candidate genes in the synthesis of caffeic acid under saline stress. The above findings revealed the potential mechanisms of salt response and caffeic acid metabolism in dandelion under saline stress, and provide references for salt-tolerant plant breeding and cultivation on saline–alkali land in the future. Full article
(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)
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16 pages, 2062 KiB  
Article
Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR
by Jing Zhang, Xinyi He, Jun Zhou, Zhuang Dong, Han Yu, Qi Tang, Lei Yuan, Siqing Peng, Xiaohong Zhong and Yuedong He
Genes 2024, 15(1), 79; https://doi.org/10.3390/genes15010079 - 07 Jan 2024
Cited by 1 | Viewed by 999
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. [...] Read more.
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica. Full article
(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)
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