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Tian C, Li J, Wu Y, Wang G, Zhang Y, Zhang X, Sun Y, Wang Y. An integrative database and its application for plant synthetic biology research. PLANT COMMUNICATIONS 2024; 5:100827. [PMID: 38297840 PMCID: PMC11121754 DOI: 10.1016/j.xplc.2024.100827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/27/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Plant synthetic biology research requires diverse bioparts that facilitate the redesign and construction of new-to-nature biological devices or systems in plants. Limited by few well-characterized bioparts for plant chassis, the development of plant synthetic biology lags behind that of its microbial counterpart. Here, we constructed a web-based Plant Synthetic BioDatabase (PSBD), which currently categorizes 1677 catalytic bioparts and 384 regulatory elements and provides information on 309 species and 850 chemicals. Online bioinformatics tools including local BLAST, chem similarity, phylogenetic analysis, and visual strength are provided to assist with the rational design of genetic circuits for manipulation of gene expression in planta. We demonstrated the utility of the PSBD by functionally characterizing taxadiene synthase 2 and its quantitative regulation in tobacco leaves. More powerful synthetic devices were then assembled to amplify the transcriptional signals, enabling enhanced expression of flavivirus non-structure 1 proteins in plants. The PSBD is expected to be an integrative and user-centered platform that provides a one-stop service for diverse applications in plant synthetic biology research.
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Affiliation(s)
- Chenfei Tian
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jianhua Li
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuhan Wu
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Guangyi Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yixin Zhang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Xiaowei Zhang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuwei Sun
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yong Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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2
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Gao Q, Zhang J, Cao J, Xiang C, Yuan C, Li X, Wang J, Zhou P, Li L, Liu J, Xie H, Li R, Huang G, Li C, Zhang G, Yang S, Zhao Y. MetaDb: a database for metabolites and their regulation in plants with an emphasis on medicinal plants. MOLECULAR HORTICULTURE 2024; 4:17. [PMID: 38679729 PMCID: PMC11057126 DOI: 10.1186/s43897-024-00095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/08/2024] [Indexed: 05/01/2024]
Affiliation(s)
- Qingqing Gao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agricultural, Honghe Vocational and Technical College, Honghe, 661199, China
| | - Jiajin Zhang
- College of Big Data, Yunnan Agricultural University, Kunming, 650201, China
| | - Juntao Cao
- College of Big Data, Yunnan Agricultural University, Kunming, 650201, China
| | - Chunfan Xiang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chengxiao Yuan
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xia Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Juan Wang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Pinhan Zhou
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Lesong Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jia Liu
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongchun Xie
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Ruolan Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guilin Huang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chaohui Li
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Guanghui Zhang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China.
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Shengchao Yang
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China.
| | - Yan Zhao
- Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation &Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China.
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, 650106, Yunnan, China.
- College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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3
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Zhao X, Ge W, Miao Z. Integrative metabolomic and transcriptomic analyses reveals the accumulation patterns of key metabolites associated with flavonoids and terpenoids of Gynostemma pentaphyllum (Thunb.) Makino. Sci Rep 2024; 14:8644. [PMID: 38622163 PMCID: PMC11018608 DOI: 10.1038/s41598-024-57716-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/21/2024] [Indexed: 04/17/2024] Open
Abstract
Gynostemma pentaphyllum (Thunb.) Makino (G. pentaphyllum) is a medicinal and edible plant with multiple functions of liver protection, anti-tumor, anti-inflammation, balancing blood sugar and blood lipids. The nutritional value of the G. pentaphyllum plant is mainly due to its rich variety of biologically active substances, such as flavonoids, terpenes and polysaccharides. In this study, we performed a comprehensive analysis combining metabolomics and root, stem and leaf transcriptomic data of G. pentaphyllum. We used transcriptomics and metabolomics data to construct a dynamic regulatory network diagram of G. pentaphyllum flavonoids and terpenoids, and screened the transcription factors involved in flavonoids and terpenoids, including basic helix-loop-helix (bHLH), myb-related, WRKY, AP2/ERF. Transcriptome analysis results showed that among the DEGs related to the synthesis of flavonoids and terpenoids, dihydroflavonol 4-reductase (DFR) and geranylgeranyl diphosphate synthases (GGPPS) were core genes. This study presents a dynamic image of gene expression in different tissues of G. pentaphyllum, elucidating the key genes and metabolites of flavonoids and terpenoids. This study is beneficial to a deeper understanding of the medicinal plants of G. pentaphyllum, and also provides a scientific basis for further regulatory mechanisms of plant natural product synthesis pathways and drug development.
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Affiliation(s)
- Xiaomeng Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Weiwei Ge
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China
| | - Zhi Miao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, People's Republic of China.
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Chen T, Yang M, Cui G, Tang J, Shen Y, Liu J, Yuan Y, Guo J, Huang L. IMP: bridging the gap for medicinal plant genomics. Nucleic Acids Res 2024; 52:D1347-D1354. [PMID: 37870445 PMCID: PMC10767881 DOI: 10.1093/nar/gkad898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/02/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
Medicinal plants have garnered significant attention in ethnomedicine and traditional medicine due to their potential antitumor, anti-inflammatory and antioxidant properties. Recent advancements in genome sequencing and synthetic biology have revitalized interest in natural products. Despite the availability of sequenced genomes and transcriptomes of these plants, the absence of publicly accessible gene annotations and tabular formatted gene expression data has hindered their effective utilization. To address this pressing issue, we have developed IMP (Integrated Medicinal Plantomics), a freely accessible platform at https://www.bic.ac.cn/IMP. IMP curated a total of 8 565 672 genes for 84 high-quality genome assemblies, and 2156 transcriptome sequencing samples encompassing various organs, tissues, developmental stages and stimulations. With the integrated 10 analysis modules, users could simply examine gene annotations, sequences, functions, distributions and expressions in IMP in a one-stop mode. We firmly believe that IMP will play a vital role in enhancing the understanding of molecular metabolic pathways in medicinal plants or plants with medicinal benefits, thereby driving advancements in synthetic biology, and facilitating the exploration of natural sources for valuable chemical constituents like drug discovery and drug production.
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Affiliation(s)
- Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Mei Yang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Guanghong Cui
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Jinfu Tang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Ye Shen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Juan Liu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Yuan Yuan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Juan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China
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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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Fathifar Z, Kalankesh LR, Ostadrahimi A, Ferdousi R. New approaches in developing medicinal herbs databases. Database (Oxford) 2023; 2023:6980759. [PMID: 36625159 PMCID: PMC9830469 DOI: 10.1093/database/baac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 11/12/2022] [Accepted: 12/17/2022] [Indexed: 01/11/2023]
Abstract
Medicinal herbs databases have become a crucial part of organizing new scientific literature generated in medicinal herbs field, as well as new drug discoveries in the information era. The aim of this review was to track the current status of medicinal herbs databases. Search for finding medicinal herbs databases was carried out via Google and PubMed. PubMed was searched for papers introducing medicinal herbs databases by the recruited search strategy. Papers with an active database on the web were included in the review. Google was also searched for medicinal herbs databases. Both retrieved papers and databases were reviewed by the authors. In this review, the current status of 25 medicinal herbs databases was reviewed, and the important characteristics of databases were mentioned. The reviewed databases had a great variety in terms of characteristics and functions. Finally, some recommendations for the efficient development of medicinal herbs databases were suggested. Although contemporary medicinal herbs databases represent much useful information, adding some features to these databases could assist them to have better functionality. This work may not cover all the necessary information, but we hope that our review can provide readers with fundamental concepts, perspectives and suggestions for constructing more useful databases.
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Affiliation(s)
- Zahra Fathifar
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Daneshgah St., Tabriz 5165665811, Iran
| | - Leila R Kalankesh
- Department of Health Information Technology, School of Management and Medical Informatics, Tabriz University of Medical Sciences, Daneshgah St., Tabriz 5165665811, Iran
| | - Alireza Ostadrahimi
- Nutrition Research Center, Department of Clinical Nutrition, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz /Ave. Golghast Atakar Neyshabouri, Tabriz 5166614711, Iran
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Yang L, Yang Y, Huang L, Cui X, Liu Y. From single- to multi-omics: future research trends in medicinal plants. Brief Bioinform 2022; 24:6840072. [PMID: 36416120 PMCID: PMC9851310 DOI: 10.1093/bib/bbac485] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/25/2022] Open
Abstract
Medicinal plants are the main source of natural metabolites with specialised pharmacological activities and have been widely examined by plant researchers. Numerous omics studies of medicinal plants have been performed to identify molecular markers of species and functional genes controlling key biological traits, as well as to understand biosynthetic pathways of bioactive metabolites and the regulatory mechanisms of environmental responses. Omics technologies have been widely applied to medicinal plants, including as taxonomics, transcriptomics, metabolomics, proteomics, genomics, pangenomics, epigenomics and mutagenomics. However, because of the complex biological regulation network, single omics usually fail to explain the specific biological phenomena. In recent years, reports of integrated multi-omics studies of medicinal plants have increased. Until now, there have few assessments of recent developments and upcoming trends in omics studies of medicinal plants. We highlight recent developments in omics research of medicinal plants, summarise the typical bioinformatics resources available for analysing omics datasets, and discuss related future directions and challenges. This information facilitates further studies of medicinal plants, refinement of current approaches and leads to new ideas.
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Affiliation(s)
- Lifang Yang
- Kunming University of Science and Technology, China
| | - Ye Yang
- Kunming University of Science and Technology, China
| | - Luqi Huang
- the academician of the Chinese Academy of Engineering, studies the development of traditional Chinese medicine, Chinese Academy of Chinese Medical Sciences, China
| | - Xiuming Cui
- Corresponding authors. X. M. Cui, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail: ; Y. Liu, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail:
| | - Yuan Liu
- Corresponding authors. X. M. Cui, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail: ; Y. Liu, Yunnan Provincial Key Laboratory of Panax notoginseng, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China. E-mail:
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Guo M, Chen H, Dong S, Zhang Z, Luo H. CRISPR-Cas gene editing technology and its application prospect in medicinal plants. Chin Med 2022; 17:33. [PMID: 35246186 PMCID: PMC8894546 DOI: 10.1186/s13020-022-00584-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/11/2022] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas gene editing technology has opened a new era of genome interrogation and genome engineering because of its ease operation and high efficiency. An increasing number of plant species have been subjected to site-directed gene editing through this technology. However, the application of CRISPR-Cas technology to medicinal plants is still in the early stages. Here, we review the research history, structural characteristics, working mechanism and the latest derivatives of CRISPR-Cas technology, and discussed their application in medicinal plants for the first time. Furthermore, we creatively put forward the development direction of CRISPR technology applied to medicinal plant gene editing. The aim is to provide a reference for the application of this technology to genome functional studies, synthetic biology, genetic improvement, and germplasm innovation of medicinal plants. CRISPR-Cas is expected to revolutionize medicinal plant biotechnology in the near future.
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Affiliation(s)
- Miaoxian Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongyu Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shuting Dong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zheng Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Hongmei Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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9
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Ye S, Feng L, Zhang S, Lu Y, Xiang G, Nian B, Wang Q, Zhang S, Song W, Yang L, Liu X, Feng B, Zhang G, Hao B, Yang S. Integrated Metabolomic and Transcriptomic Analysis and Identification of Dammarenediol-II Synthase Involved in Saponin Biosynthesis in Gynostemma longipes. FRONTIERS IN PLANT SCIENCE 2022; 13:852377. [PMID: 35401630 PMCID: PMC8990310 DOI: 10.3389/fpls.2022.852377] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/28/2022] [Indexed: 05/17/2023]
Abstract
Gynostemma longipes contains an abundance of dammarane-type ginsenosides and gypenosides that exhibit extensive pharmacological activities. Increasing attention has been paid to the elucidation of cytochrome P450 monooxygenases (CYPs) and UDP-dependent glycosyltransferases (UGTs) that participate downstream of ginsenoside biosynthesis in the Panax genus. However, information on oxidosqualene cyclases (OSCs), the upstream genes responsible for the biosynthesis of different skeletons of ginsenoside and gypenosides, is rarely reported. Here, an integrative study of the metabolome and the transcriptome in the leaf, stolon, and rattan was conducted and the function of GlOSC1 was demonstrated. In total, 46 triterpenes were detected and found to be highly abundant in the stolon, whereas gene expression analysis indicated that the upstream OSC genes responsible for saponin skeleton biosynthesis were highly expressed in the leaf. These findings indicated that the saponin skeletons were mainly biosynthesized in the leaf by OSCs, and subsequently transferred to the stolon via CYPs and UGTs biosynthesis to form various ginsenoside and gypenosides. Additionally, a new dammarane-II synthase (DDS), GlOSC1, was identified by bioinformatics analysis, yeast expression assay, and enzyme assays. The results of the liquid chromatography-mass spectrometry (LC-MS) analysis proved that GlOSC1 could catalyze 2,3-oxidosqualene to form dammarenediol-II via cyclization. This work uncovered the biosynthetic mechanism of dammarenediol-II, an important starting substrate for ginsenoside and gypenosides biosynthesis, and may achieve the increased yield of valuable ginsenosides and gypenosides produced under excess substrate in a yeast cell factory through synthetic biology strategy.
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Affiliation(s)
- Shuang Ye
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Lei Feng
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shiyu Zhang
- Centre for Mountain Futures, Kunming Institute of Botany, Kunming, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Yingchun Lu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Guisheng Xiang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Bo Nian
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Qian Wang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Shuangyan Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Wanling Song
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Ling Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiangyu Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Baowen Feng
- Honwin Pharma (Lianghe) Co., LTD., Dehong, China
| | - Guanghui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Bing Hao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- *Correspondence: Bing Hao,
| | - Shengchao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Shengchao Yang,
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