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Molecular Genetics and Multi-omics in Medicinal Plants
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Molecular Genetics and Multi-omics in 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: closed (25 November 2024) | Viewed by 6411

Special Issue Editors

Dr. Zhihua Wu

E-Mail Website
Guest Editor
College of Life Science, Zhejiang Normal University, Jinhua, China
Interests: bioinformatics; genomics; medicinal plants
Prof. Dr. Xiaofei Ma

E-Mail Website
Guest Editor
Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
Interests: ecological genetics; population genetics; multi-omics

Special Issue Information

Dear Colleagues,

Medicinal plants are essential for human health around the world as they contain secondary metabolites. As a staple pharmaceutical source, medicinal plants play an important role in the prevention and treatment of various diseases due to the diversity of secondary metabolites. However, research on the biosynthetic mechanisms of special components in medicinal plants is insufficient, and the development and utilization of genetic germplasm resources of medicinal plants lag behind those of crops due to their short breeding history.

The development of high-throughput sequencing has promoted the application of multiple omics such as genomics, transcriptomics, metabolomics, proteomics, and methylomics in medicinal plants. This helps us to clarify the genetic characteristics, and reveal the regulatory mechanisms of special metabolites in medicinal plants. As a result, genetic and multi-omics research will significantly improve the efficiency of functional gene mining responsible for secondary metabolite biosynthesis, and further accelerate the process of molecular breeding based on the molecular markers associated with functional genes. In addition, the identified functional genes could be applied in bthe iosynthesis of natural product monomers using synthetic biology to meet clinical needs.

This Special Issue aims to feature cutting-edge research on molecular genetics and multi-omics of medicinal plants. We invite researchers to contribute their original research articles, reviews, and perspectives to this Special Issue. By sharing the latest findings and advancements in this field, we aspire to establish a comprehensive platform for researchers to further our understanding of genetic germplasm resources and biosynthesis of secondary metabolites in medicinal plants.

Topics covered by this Special Issue could include but are not limited to the following:

  • Genetic diversity and breeding of medicinal plants;
  • Nuclear, chloroplast and mitochondrial genomes of medicinal plants;
  • Integrated analysis of multi-omics in medicinal plants;
  • Tools and methods of molecular genetics and multi-omics for medicinal plants.

Dr. Zhihua Wu
Prof. Dr. Xiaofei Ma
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
  • secondary metabolism
  • genetic diversity
  • genome
  • multi-omics analysis
  • molecular regulation
  • gene mining

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Published Papers (5 papers)

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Research

13 pages, 2256 KiB  
Article
Identification of Key Genes Involved in Sesquiterpene Synthesis in Nardostachys jatamansi Based on Transcriptome and Component Analysis
by Xiaohui Tang, Tingju Li, Zhiyu Hao, Wenji Zhao, Yanlong Han, Guofu Jia, Zhengjun He, Chaoxiang Ren, Ke Rao, Jin Pei and Jiang Chen
Genes 2024, 15(12), 1539; https://doi.org/10.3390/genes15121539 - 28 Nov 2024
Viewed by 786
Abstract
Background: Nardostachys jatamansi (D. Don) DC. (N. jatamansi.) is an endangered medicinal plant native to the Himalayas that is widely used in traditional medicine due to its terpenoid compounds, especially sesquiterpenes, which are abundant in N. jatamansi. However, the [...] Read more.
Background: Nardostachys jatamansi (D. Don) DC. (N. jatamansi.) is an endangered medicinal plant native to the Himalayas that is widely used in traditional medicine due to its terpenoid compounds, especially sesquiterpenes, which are abundant in N. jatamansi. However, the mechanism of sesquiterpene metabolism remains unclear. Methods: Transcriptome sequencing analyses of different parts (roots and rhizomes, leaves, anthocaulus and flowers) and developmental stages (rejuvenation, budding, flowering, fruiting and withering) of cultivated N. jatamansi were conducted using the Illumina platform. Key genes involved in regulating the sesquiterpene metabolism pathway in N. jatamansi were identified by combining component analyses of various tissues and developmental stages. Furthermore, these key genes were validated through MeJA treatment and a chemical composition analysis. Results: A transcriptome sequencing analysis was performed on 24 samples from four tissues and in five developmental stages, yielding 183.18 Gb of clean data with a Q30 base percentage of 92% or above. A total of 269,136 UniGenes were obtained and annotated. Genes related to sesquiterpene synthesis were screened and validated by RT–qPCR using annotation results from various databases. Twelve candidate genes involved in sesquiterpene synthase were identified. Following MeJA treatment, an RT–qPCR analysis revealed that the expression of the NjTPS-49, NjTPS-54, NjTPS-56, NjTPS-57 and NjTPS-59 genes was positively regulated. Additionally, an HPLC analysis indicated an increase in the nardosinone content after MeJA treatment. This study demonstrates that NjTPS-49, NjTPS-54, NjTPS-56, NjTPS-57 and NjTPS-59 are potential candidate genes for sesquiterpene synthesis. Conclusion: The obtained findings establish the groundwork for elucidating the mechanism of sesquiterpene synthesis in N. jatamansi and contribute to the conservation of N. jatamansi resources. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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18 pages, 3968 KiB  
Article
Comparative and Spatial Transcriptome Analysis of Rhododendron decorum Franch. During the Flowering Period and Revelation of the Plant Defense Mechanism
by Weiwei Liu, Chenghua Yu, Kaiye Yang, Ling Wang, Zhongyu Fan and Xinchun Mo
Genes 2024, 15(11), 1482; https://doi.org/10.3390/genes15111482 - 18 Nov 2024
Viewed by 1111
Abstract
Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized [...] Read more.
Background: Rhododendron is a globally distributed and extensive genus, comprising over 1000 species. In the southwestern mountains of China, there exists a remarkable diversity of Rhododendron, with Yunnan Province alone harboring more than 600 species. R. decorum Franch. has long been utilized by local communities for its medicinal and edible properties. However, the transcriptional regulation function, medicinal properties, and edibility characteristics of R. decorum Franch. currently lack a solid theoretical basis. Methods: Total RNA was extracted from leaves, corollas and androecium/gynoecium of R. decorum Franch. in Heqing county, followed by the construction of cDNA libraries and the de novo assembly of transcriptomes. Results: A total of 63,050 unigenes were extracted from the flowers and leaf organs of R. decorum Franch. Among these unigenes, 43,517 were predicted to be coding sequences, with 32,690 being effectively annotated. Differential gene expression enrichment was observed among different organs within their respective transcriptomes; notably floral organs exhibited significant defense against plant diseases along with signal transduction functions. Furthermore, during the flower harvesting period, all floral organs exhibited gene enrichment pathways associated with carbohydrate metabolism. Additionally, the stamen and pistil displayed flavonoid metabolism pathways, suggesting their potential applications as functional food or medicine. Conclusions: Our results shed light on plant–pathogen defense mechanisms and the molecular bias of flavonoids biosynthesis on flower organs during the flowering period, which might help to understand the consumption of R. decorum Franch. corollas by the Bai nationality of Heqing county. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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17 pages, 9424 KiB  
Article
Flavonoid Synthesis Pathway Response to Low-Temperature Stress in a Desert Medicinal Plant, Agriophyllum Squarrosum (Sandrice)
by Pengshu Zhao, Xia Yan, Chaoju Qian, Guorong Ma, Xingke Fan, Xiaoyue Yin, Yuqiu Liao, Tingzhou Fang, Shanshan Zhou, Ibrahim Awuku and Xiao-Fei Ma
Genes 2024, 15(9), 1228; https://doi.org/10.3390/genes15091228 - 20 Sep 2024
Cited by 5 | Viewed by 1479
Abstract
Background/Objectives: Agriophyllum squarrosum (L.) Moq. (A. squarrosum), also known as sandrice, is an important medicinal plant widely distributed in dunes across all the deserts of China. Common garden trials have shown content variations in flavonoids among the ecotypes of sandrice, [...] Read more.
Background/Objectives: Agriophyllum squarrosum (L.) Moq. (A. squarrosum), also known as sandrice, is an important medicinal plant widely distributed in dunes across all the deserts of China. Common garden trials have shown content variations in flavonoids among the ecotypes of sandrice, which correlated with temperature heterogeneity in situ. However, there have not been any environmental control experiments to further elucidate whether the accumulation of flavonoids was triggered by cold stress; Methods: This study conducted a four-day ambient 4 °C low-temperature treatment on three ecotypes along with an in situ annual mean temperature gradient (Dulan (DL), Aerxiang (AEX), and Dengkou (DK)); Results: Target metabolomics showed that 12 out of 14 flavonoids in sandrice were driven by cold stress. Among them, several flavonoids were significantly up-regulated, such as naringenin and naringenin chalcone in all three ecotypes; isorhamnetin, quercetin, dihydroquercetin, and kaempferol in DL and AEX; and astragalin in DK. They were accompanied by 19 structural genes of flavonoid synthesis and 33 transcription factors were markedly triggered by cold stress in sandrice. The upstream genes, AsqAEX006535−CHS, AsqAEX016074−C4H, and AsqAEX004011−4CL, were highly correlated with the enrichment of naringenin, which could be fine-tuned by AsqAEX015868−bHLH62, AsqAEX001711−MYB12, and AsqAEX002220−MYB1R1; Conclusions: This study sheds light on how desert plants like sandrice adapt to cold stress by relying on a unique flavonoid biosynthesis mechanism that regulating the accumulation of naringenin. It also supports the precise development of sandrice for the medicinal industry. Specifically, quercetin and isorhamnetin should be targeted for development in DL and AEX, while astragalin should be precisely developed in DK. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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13 pages, 3060 KiB  
Article
Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Saussurea inversa (Asteraceae)
by Wubin Dai, Xiuting Ju, Guomin Shi and Tao He
Genes 2024, 15(8), 1074; https://doi.org/10.3390/genes15081074 - 14 Aug 2024
Viewed by 1052
Abstract
Saussurea inversa is a perennial herb used in traditional Chinese medicine and is effective against rheumatoid arthritis. In this study, we sequenced the complete mitochondrial (mt) genome of S. inversa (GenBank accession number: ON584565.1). The circular mt genome of S. inversa was 335,372 [...] Read more.
Saussurea inversa is a perennial herb used in traditional Chinese medicine and is effective against rheumatoid arthritis. In this study, we sequenced the complete mitochondrial (mt) genome of S. inversa (GenBank accession number: ON584565.1). The circular mt genome of S. inversa was 335,372 bp in length, containing 62 genes, including 33 mRNAs, 22 tRNAs, 6 rRNAs, and 1 pseudogene, along with 1626 open reading frames. The GC content was 45.14%. Predictive analysis revealed substantial RNA editing, with ccmFn being the most abundantly edited gene, showing 36 sites. Gene migration between the mt and chloroplast (cp) genomes of S. inversa was observed through the detection of homologous gene fragments. Phylogenetic analysis revealed that S. inversa was clustered with Arctium tomentosum (Asteraceae). Our findings provide extensive information regarding the mt genome of S. inversa and help lay the foundation for future studies on its genetic variations, phylogeny, and breeding via the analysis of the mt genome. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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16 pages, 5266 KiB  
Article
Integrated Analyses of Metabolome and RNA-seq Data Revealing Flower Color Variation in Ornamental Rhododendron simsii Planchon
by Zhiliang Li, Siduo Xu, Hongmei Wu, Xuchun Wan, Hanhan Lei, Jiaojun Yu, Jun Fu, Jialiang Zhang and Shuzhen Wang
Genes 2024, 15(8), 1041; https://doi.org/10.3390/genes15081041 - 7 Aug 2024
Cited by 2 | Viewed by 1296
Abstract
Rhododendron simsii Planchon is an important ornamental species in the northern hemisphere. Flower color is an important objective of Rhododendron breeding programs. However, information on anthocyanin synthesis in R. simsii is limited. In this research, the regulatory mechanism of anthocyanin biosynthesis in R. [...] Read more.
Rhododendron simsii Planchon is an important ornamental species in the northern hemisphere. Flower color is an important objective of Rhododendron breeding programs. However, information on anthocyanin synthesis in R. simsii is limited. In this research, the regulatory mechanism of anthocyanin biosynthesis in R. simsii was performed through the integrated analysis of metabolome and RNA-seq. A total of 805 and 513 metabolites were screened by positive and negative ionization modes, respectively, In total, 79 flavonoids contained seven anthocyanidins, 42 flavanones, 10 flavans, 13 flavones, and seven flavonols. Methylated and glycosylated derivatives took up the most. Differentially accumulated metabolites were mainly involved in “flavone and flavonol biosynthesis”, “cyanoamino acid metabolism”, “pyrimidine metabolism”, and “phenylalanine metabolism” pathways. For flavonoid biosynthesis, different expression of shikimate O-hydroxycinnamoyltransferase, caffeoyl-CoA O-methyltransferase, flavonoid 3′-monooxygenase, flavonol synthase, dihydroflavonol 4-reductase/flavanone 4-reductase, F3′5′H, chalcone synthase, leucoanthocyanidin reductase, and 5-O-(4-coumaroyl)-D-quinate 3′-monooxygenase genes ultimately led to different accumulations of quercetin, myricetin, cyanidin, and eriodictyol. In flavone and flavonol biosynthesis pathway, differential expression of F3′5′H, flavonoid 3′-monooxygenase and flavonol-3-O-glucoside/galactoside glucosyltransferase genes led to the differential accumulation of quercetin, isovitexin, and laricitrin. This research will provide a biochemical basis for further modification of flower color and genetic breeding in R. simsii and related Rhododendron species. Full article
(This article belongs to the Special Issue Molecular Genetics and Multi-omics in Medicinal Plants)
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