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Tian L, Gao R, Cai Y, Chen J, Dong H, Chen S, Yang Z, Wang Y, Huang L, Xu Z. A systematic review of ginsenoside biosynthesis, spatiotemporal distribution, and response to biotic and abiotic factors in American ginseng. Food Funct 2024; 15:2343-2365. [PMID: 38323507 DOI: 10.1039/d3fo03434h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
American ginseng (Panax quinquefolius) has gained recognition as a medicinal and functional food homologous product with several pharmaceutical, nutritional, and industrial applications. However, the key regulators involved in ginsenoside biosynthesis, the spatiotemporal distribution characteristics of ginsenosides, and factors influencing ginsenosides are largely unknown, which make it challenging to enhance the quality and chemical extraction processes of the cultivated American ginseng. This review presents an overview of the pharmacological effects, biosynthesis and spatiotemporal distribution of ginsenosides, with emphasis on the impacts of biotic and abiotic factors on ginsenosides in American ginseng. Modern pharmacological studies have demonstrated that American ginseng has neuroprotective, cardioprotective, antitumor, antidiabetic, and anti-obesity effects. Additionally, most genes involved in the upregulation of ginsenoside biosynthesis have been identified, while downstream regulators (OSCs, CYP450, and UGTs) require further investigation. Futhermore, limited knowledge exists regarding the molecular mechanisms of the impact of biotic and abiotic factors on ginsenosides. Notably, the nonmedicinal parts of American ginseng, particularly its flowers, fibrous roots, and leaves, exhibit higher ginsenoside content than its main roots and account for a considerable amount of weight in the whole plant, representing promising resources for ginsenosides. Herein, the prospects of molecular breeding and metabolic engineering based on multi-omics to improve the unstable quality of cultivated American ginseng and the shortage of ginsenosides are proposed. This review highlights the gaps in the current research on American ginseng and proposes solutions to address these limitations, providing a guide for future investigations into American ginseng ginsenosides.
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Affiliation(s)
- Lixia Tian
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, China
| | - Ranran Gao
- The Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100007, China
| | - Yuxiang Cai
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, China
| | - Junxian Chen
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, China
| | - Hongmei Dong
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, China
| | - Shanshan Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing, 100700, China
| | - Zaichang Yang
- School of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025, China
| | - Yu Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Linfang Huang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China.
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin, 150006, China.
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Tian L, Ou J, Sun X, Miao Y, Pei J, Zhao L, Huang L. The discovery of pivotal fungus and major determinant factor shaping soil microbial community composition associated with rot root of American ginseng. PLANT SIGNALING & BEHAVIOR 2021; 16:1952372. [PMID: 34304705 PMCID: PMC8525955 DOI: 10.1080/15592324.2021.1952372] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
American ginseng, a valuable medicinal and food plant, is threatened by rot root, which affects its yield and quality. However, limited studies have investigated the changes in soil microbial community and physiochemical properties between healthy and rot root American ginseng. Here, high-throughput sequencing and soil physiochemical properties were used to characterize these changes. The soil physiochemical properties showed significance differences between the soil of healthy and rot root, in which the pH, available potassium, available phosphorus, soil organic carbon and soil organic matter were significantly higher in healthy root soil. Besides, fungal α-diversity was also higher in healthy root soil than that in rot root. Importantly, the dominant fungal genera differed between soils of healthy and rot root of American ginseng, and LEfSe further indicated that six fungal genera (Devriesia, Chrysosporium, Dichotomopilus, Pseudeurotium, Acaulium and Scedosporium) were significantly enriched in the soil of healthy plants, whereas six fungal genera (Gibellulopsis, Fusarium, Plectosphaerella, Tetracladium, Gibberella and Ilyonectri) were significantly enriched in the soil of rot root, suggesting that an increase in the relative abundance of these pathogenic fungi (Fusarium, Plectosphaerella, and Ilyonectri) may be associated with ginseng rot root. Notably, this study is the first to report that an increase in the relative abundances of Gibellulopsis and Gibberella in the rot root soil of American ginseng may be associated with the onset of rot root symptoms in this plant. The functional profile prediction showed that the there was a significantly Pathotrophs increase in the rot root soil compared with healthy root soil and Saprotrophs were more abundant in the healthy root soil. Finally, correlation analyses revealed that soil cation exchange capacity was an important factors affecting the composition of rot root of American ginseng soil microbial communities. This study not only used a new approach to explore the new fungal associated with rot root in American ginseng but also excavated the major soil physiochemical properties affecting the microbiome diversity, providing foundation for developing biocontrol strategies against rot root.
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Affiliation(s)
- Lixia Tian
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jiarong Ou
- Tongren Municipal People’s Hospital, Tongren, China
| | - Xiao Sun
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujing Miao
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Pei
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lei Zhao
- Central Medical District of Chinese PLA General Hospital, Beijing, China
| | - Linfang Huang
- Key Research Laboratory of Traditional Chinese Medicine Resources Protection, Administration of Traditional Chinese Medicine, National Administration of Traditional Chinese Medicine, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Guo K, Chen J, Niu Y, Lin X. Full-Length Transcriptome Sequencing Provides Insights into Flavonoid Biosynthesis in Fritillaria hupehensis. Life (Basel) 2021; 11:287. [PMID: 33800612 PMCID: PMC8066755 DOI: 10.3390/life11040287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
One of the most commonly utilized medicinal plants in China is Fritillaria hupehensis (Hsiao et K.C. Hsia). However, due to a lack of genomic resources, little is known about the biosynthesis of relevant compounds, particularly the flavonoid biosynthesis pathway. A PacBio RS II sequencing generated a total of 342,044 reads from the bulb, leaf, root, and stem, of which 316,438 were full-length (FL) non-redundant reads with an average length of 1365 bp and a N50 of 1888 bp. There were also 38,607 long non-coding RNAs and 7914 simple sequence repeats detected. To improve our understanding of processes implicated in regulating secondary metabolite biosynthesis in F. hupehensis tissues, we evaluated potential metabolic pathways. Overall, this study provides a repertoire of FL transcripts in F. hupehensis for the first time, and it will be a valuable resource for marker-assisted breeding and research into bioactive compounds for medicinal and pharmacological applications.
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Affiliation(s)
- Kunyuan Guo
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China;
| | - Jie Chen
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China; (J.C.); (Y.N.)
| | - Yan Niu
- Wuhan Benagen Tech Solutions Company Limited, Wuhan 430070, China; (J.C.); (Y.N.)
| | - Xianming Lin
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi 445000, China;
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Vu DD, Shah SNM, Pham MP, Bui VT, Nguyen MT, Nguyen TPT. De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. BMC PLANT BIOLOGY 2020; 20:358. [PMID: 32727354 PMCID: PMC7391578 DOI: 10.1186/s12870-020-02571-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 07/23/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers. RESULTS In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. vietnamensis (roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances. CONCLUSION Our study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.
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Affiliation(s)
- Dinh Duy Vu
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
- Graduate University of Science and Technology (GUST), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Syed Noor Muhammad Shah
- Department of Horticulture, Faculty of Agriculture, Gomal University Dera Ismail Khan, Dera Ismail Khan, Pakistan
| | - Mai Phuong Pham
- Vietnam - Russia Tropical Centre, 63 Nguyen Van Huyen, Nghia Do, Cau Giay, Hanoi, Vietnam
| | - Van Thang Bui
- College of Forestry Biotechnology, Vietnam National University of Forestry, Xuan Mai, Hanoi, Vietnam
| | - Minh Tam Nguyen
- Department of Experimental Taxonomy & Genetic Diversity, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Thi Phuong Trang Nguyen
- Institute of Ecology and Biological Resource, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, , Cau Giay, Hanoi, Vietnam.
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Till 2018: a survey of biomolecular sequences in genus Panax. J Ginseng Res 2020; 44:33-43. [PMID: 32095095 PMCID: PMC7033366 DOI: 10.1016/j.jgr.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 06/07/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022] Open
Abstract
Ginseng is popularly known to be the king of ancient medicines and is used widely in most of the traditional medicinal compositions due to its various pharmaceutical properties. Numerous studies are being focused on this plant's curative effects to discover their potential health benefits in most human diseases, including cancer- the most life-threatening disease worldwide. Modern pharmacological research has focused mainly on ginsenosides, the major bioactive compounds of ginseng, because of their multiple therapeutic applications. Various issues on ginseng plant development, physiological processes, and agricultural issues have also been studied widely through state-of-the-art, high-throughput sequencing technologies. Since the beginning of the 21st century, the number of publications on ginseng has rapidly increased, with a recent count of more than 6,000 articles and reviews focusing notably on ginseng. Owing to the implementation of various technologies and continuous efforts, the ginseng plant genomes have been decoded effectively in recent years. Therefore, this review focuses mainly on the cellular biomolecular sequences in ginseng plants from the perspective of the central molecular dogma, with an emphasis on genomes, transcriptomes, and proteomes, together with a few other related studies.
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Liang T, Zou L, Sun S, Kuang X, Wei J, Wang L, Li Y, Sun C. Hybrid sequencing of the Gynostemma pentaphyllum transcriptome provides new insights into gypenoside biosynthesis. BMC Genomics 2019; 20:632. [PMID: 31382891 PMCID: PMC6683540 DOI: 10.1186/s12864-019-6000-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/26/2019] [Indexed: 01/03/2023] Open
Abstract
Background Gypenosides are a group of triterpene saponins from Gynostemma pentaphyllum that are the same as or very similar to ginsenosides from the Panax species. Several enzymes involved in ginsenoside biosynthesis have been characterized, which provide important clues for elucidating the gypenoside biosynthetic pathway. We suppose that gypenosides and ginsenosides may have a similar biosynthetic mechanism and that the corresponding enzymes in the two pathways may have considerable similarity in their sequences. To further understand gypenoside biosynthesis, we sequenced the G. pentaphyllum transcriptome with a hybrid sequencing-based strategy and then determined the candidate genes involved in this pathway using phylogenetic tree construction and gene expression analysis. Results Following the PacBio standard analysis pipeline, 66,046 polished consensus sequences were obtained, while Illumina data were assembled into 140,601 unigenes with Trinity software. Then, these output sequences from the two analytical routes were merged. After removing redundant data with CD-HIT software, a total of 140,157 final unigenes were obtained. After functional annotation, five 2,3-oxidosqualene cyclase genes, 145 cytochrome P450 genes and 254 UDP-glycosyltransferase genes were selected for the screening of genes involved in gypenoside biosynthesis. Using phylogenetic analysis, several genes were divided into the same subfamilies or closely related evolutionary branches with characterized enzymes involved in ginsenoside biosynthesis. Using real-time PCR technology, their expression patterns were investigated in different tissues and at different times after methyl jasmonate induction. Since the genes in the same biosynthetic pathway are generally coexpressed, we speculated that GpOSC1, GpCYP89, and GpUGT35 were the leading candidates for gypenoside biosynthesis. In addition, six GpWRKYs and one GpbHLH might play a possible role in regulating gypenoside biosynthesis. Conclusions We developed a hybrid sequencing strategy to obtain longer length transcriptomes with increased accuracy, which will greatly contribute to downstream gene screening and characterization, thus improving our ability to elucidate secondary metabolite biosynthetic pathways. With this strategy, we found several candidate genes that may be involved in gypenoside biosynthesis, which laid an important foundation for the elucidation of this biosynthetic pathway, thus greatly contributing to further research in metabolic regulation, synthetic biology and molecular breeding in this species. Electronic supplementary material The online version of this article (10.1186/s12864-019-6000-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tongtong Liang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Liqiu Zou
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Sijie Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Xuejun Kuang
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China
| | - Lizhi Wang
- Tianjin University of Traditional Chinese Medicine, No.10, Poyanghu Road, Jinghai District, Tianjin, 301617, China
| | - Ying Li
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
| | - Chao Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of, Medical Sciences, No.151, Malianwa North Road, Haidian District, Beijing, 100193, China.
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Davis MP, Behm B. Ginseng: A Qualitative Review of Benefits for Palliative Clinicians. Am J Hosp Palliat Care 2019; 36:630-659. [PMID: 30686023 DOI: 10.1177/1049909118822704] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ginseng has been used for centuries to treat various diseases and has been commercially developed and cultivated in the past 300 years. Ginseng products may be fresh, dried (white), or dried and steamed (red). Extracts may be made using water or alcohol. There are over 50 different ginsenosides identified by chromatography. We did an informal systematic qualitative review that centered on fatigue, cancer, dementia, respiratory diseases, and heart failure, and we review 113 studies in 6 tables. There are multiple potential benefits to ginseng in cancer. Ginseng, in certain circumstances, has been shown to improve dementia, chronic obstructive pulmonary disease, and heart failure through randomized trials. Most trials had biases or unknown biases and so most evidence is of low quality. We review the gaps in the evidence and make some recommendations regarding future studies.
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Affiliation(s)
- Mellar P Davis
- 1 Palliative Care Department, Knapper Cancer Center, Geisinger Medical Center, Danville, PA, USA
| | - Bertrand Behm
- 1 Palliative Care Department, Knapper Cancer Center, Geisinger Medical Center, Danville, PA, USA
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Chen W, Balan P, Popovich DG. Comparison of the ginsenoside composition of Asian ginseng (Panax ginseng) and American ginseng (Panax quinquefolius L.) and their transformation pathways. BIOACTIVE NATURAL PRODUCTS 2019. [DOI: 10.1016/b978-0-12-817901-7.00006-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Gu L, Zhang ZY, Quan H, Li MJ, Zhao FY, Xu YJ, Liu J, Sai M, Zheng WL, Lan XZ. Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in rotenoid biosynthesis in the medicinal plant Mirabilis himalaica. Mol Genet Genomics 2017; 293:635-647. [PMID: 29285563 PMCID: PMC5948277 DOI: 10.1007/s00438-017-1409-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/14/2017] [Indexed: 02/04/2023]
Abstract
Mirabilis himalaica (Edgew.) Heimerl is among the most important genuine medicinal plants in Tibet. However, the biosynthesis mechanisms of the active compounds in this species are unclear, severely limiting its application. To clarify the molecular biosynthesis mechanism of the key representative active compounds, specifically rotenoid, which is of special medicinal value for M. himalaica, RNA sequencing and TOF-MS technologies were used to construct transcriptomic and metabolomic libraries from the roots, stems, and leaves of M. himalaica plants collected from their natural habitat. As a result, each of the transcriptomic libraries from the different tissues was sequenced, generating more than 10 Gb of clean data ultimately assembled into 147,142 unigenes. In the three tissues, metabolomic analysis identified 522 candidate compounds, of which 170 metabolites involved in 114 metabolic pathways were mapped to the KEGG. Of these genes, 61 encoding enzymes were identified to function at key steps of the pathways related to rotenoid biosynthesis, where 14 intermediate metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to rotenoid biosynthesis were synthesized in the roots, stems and leaves of M. himalaica, which suggested that the use of non-medicinal tissues to extract compounds was feasible. In addition, the CHS and CHI genes were found to play important roles in rotenoid biosynthesis, especially, since CHS might be an important rate-limiting enzyme. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of rotenoid in M. himalaica.
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Affiliation(s)
- Li Gu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.,Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhong-Yi Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Hong Quan
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Ming-Jie Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Fang-Yu Zhao
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Yuan-Jiang Xu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Jiang Liu
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Man Sai
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China
| | - Wei-Lie Zheng
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.
| | - Xiao-Zhong Lan
- Agricultural and Animal Husbandry College of Tibet University, Nyingchi, 860000, People's Republic of China.
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Xin J, Zhang RC, Wang L, Zhang YQ. Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:7521363. [PMID: 28900463 PMCID: PMC5576426 DOI: 10.1155/2017/7521363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/21/2017] [Accepted: 05/16/2017] [Indexed: 12/12/2022]
Abstract
Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers.
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Affiliation(s)
- Jie Xin
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Rong-chao Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Lei Wang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yong-qing Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
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Babineau M, Mahmood K, Mathiassen SK, Kudsk P, Kristensen M. De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages. BMC Genomics 2017; 18:128. [PMID: 28166737 PMCID: PMC5294808 DOI: 10.1186/s12864-017-3538-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified. RESULTS Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively. CONCLUSIONS De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses.
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Affiliation(s)
- Marielle Babineau
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | - Khalid Mahmood
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | | | - Per Kudsk
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | - Michael Kristensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
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Li J, Zhen W, Long D, Ding L, Gong A, Xiao C, Jiang W, Liu X, Zhou T, Huang L. De Novo Sequencing and Assembly Analysis of the Pseudostellaria heterophylla Transcriptome. PLoS One 2016; 11:e0164235. [PMID: 27764127 PMCID: PMC5072632 DOI: 10.1371/journal.pone.0164235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/21/2016] [Indexed: 01/09/2023] Open
Abstract
Pseudostellaria heterophylla (Miq.) Pax is a mild tonic herb widely cultivated in the Southern part of China. The tuberous roots of P. heterophylla accumulate high levels of secondary metabolism products of medicinal value such as saponins, flavonoids, and isoquinoline alkaloids. Despite numerous studies on the pharmacological importance and purification of these compounds in P. heterophylla, their biosynthesis is not well understood. In the present study, we used Illumina HiSeq 4000 sequencing platform to sequence the RNA from flowers, leaves, stem, root cortex and xylem tissues of P. heterophylla. We obtained 616,413,316 clean reads that we assembled into 127, 334 unique sequences with an N50 length of 951 bp. Among these unigenes, 53,184 unigenes (41.76%) were annotated in a public database and 39, 795 unigenes were assigned to 356 KEGG pathways; 23,714 unigenes (8.82%) had high homology with the genes from Beta vulgaris. We discovered 32, 095 DEGs in different tissues and performed GO and KEGG enrichment analysis. The most enriched KEGG pathway of secondary metabolism showed up-regulated expression in tuberous roots as compared with the ground parts of P. heterophylla. Moreover, we identified 72 candidate genes involved in triterpenoids saponins biosynthesis in P. heterophylla. The expression profiles of 11 candidate unigenes were analyzed by quantitative real-time PCR (RT-qPCR). Our study established a global transcriptome database of P. heterophylla for gene identification and regulation. We also identified the candidate unigenes involved in triterpenoids saponins biosynthesis. Our results provide an invaluable resource for the secondary metabolites and physiological processes in different tissues of P. heterophylla.
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Affiliation(s)
- Jun Li
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Wei Zhen
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Dengkai Long
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Ling Ding
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Anhui Gong
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Chenghong Xiao
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Weike Jiang
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Xiaoqing Liu
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Tao Zhou
- Guiyang University of Chinese Medicine, Guiyang 550025, China.,National Engineering Research Center of Miao's Medicines, Guiyang 550025, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medical, China Academy of Chinese Medical Sciences, Beijing 100700, China
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13
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Liu WJ, Lv HZ, He L, Song JY, Sun C, Luo HM, Chen SL. Cloning and Bioinformatic Analysis of HMGS and HMGR Genes from Panax notoginseng. CHINESE HERBAL MEDICINES 2016. [DOI: 10.1016/s1674-6384(16)60061-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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14
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Jayakodi M, Lee SC, Lee YS, Park HS, Kim NH, Jang W, Lee HO, Joh HJ, Yang TJ. Comprehensive analysis of Panax ginseng root transcriptomes. BMC PLANT BIOLOGY 2015; 15:138. [PMID: 26063328 PMCID: PMC4464628 DOI: 10.1186/s12870-015-0527-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Korean ginseng (Panax ginseng C.A. Meyer) is a highly effective medicinal plant containing ginsenosides with various pharmacological activities, whose roots are produced commercially for crude drugs. RESULTS Here, we used the Illumina platform to generate over 232 million RNA sequencing reads from four root samples, including whole roots from one-year-old plants and three types of root tissue from six-year-old plants (i.e., main root bodies, rhizomes, and lateral roots). Through de novo assembly and reference-assisted selection, we obtained a non-redundant unigene set consisting of 55,949 transcripts with an average length of 1,250 bp. Among transcripts in the unigene set, 94 % were functionally annotated via similarity searches against protein databases. Approximately 28.6 % of the transcripts represent novel gene sequences that have not previously been reported for P. ginseng. Digital expression profiling revealed 364 genes showing differential expression patterns among the four root samples. Additionally, 32 were uniquely expressed in one-year-old roots, while seven were uniquely expressed in six-year-old root tissues. We identified 38 transcripts encoding enzymes involved in ginsenoside biosynthesis pathways and 189 encoding UDP-glycosyltransferases. CONCLUSION Our analysis provides new insights into the role of the root transcriptome in development and secondary metabolite biosynthesis in P. ginseng.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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15
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Zou LQ, Kuang XJ, Sun C. Advances in Transcriptomic Studies and Ginsenoside Biosynthesis of American Ginseng. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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16
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Chen JJ, Wang Y. Microsatellite Development and Potential Application in Authentication, Conservation, and Genetic Improvement of Chinese Medicinal Plants. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60029-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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17
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Transcriptomic analysis of American ginseng seeds during the dormancy release process by RNA-Seq. PLoS One 2015; 10:e0118558. [PMID: 25790114 PMCID: PMC4366157 DOI: 10.1371/journal.pone.0118558] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 01/20/2015] [Indexed: 01/04/2023] Open
Abstract
American ginseng (Panax quinquefolius L.) is an important herb that is cultivated in China, North American, and South Korea. It is propagated from seed, but the seed has deep dormancy characteristics described as morphophysiological dormancy. Two-stage temperature stratification, a warm (15–20°C) and cold (2°C) stratification period of 6 months, has been used successfully for seed dormancy release. However, little is known about the molecular mechanisms of seed dormancy release in the stratification process. In this study, seed development after pollination and seed development in the dormancy release process were investigated in American ginseng. The transcriptome during seed dormancy release was analyzed using RNA-Seq technology and 78,207 unigenes (mean length 531 bp) were generated. Based on similarity searches of public databases, 54,292 of the unigenes (69.4%) were functionally annotated. Further, three digital gene expression (DGE) libraries were sequenced and differences in gene expression at three stages during seed cold stratification were examined. The greatest number of differentially expressed genes occurred in the 90DCS versus 180DCS libraries, while the lowest number of differentially expressed genes occurred in the 135DCS verus 180DCS libraries. GO enrichment analysis revealed that 59, 29, and 39 GO terms were significantly enriched in the biological process, molecular function, and cell component GO categories, respectively. There were 25,190 genes with KEGG pathway annotation in the three DGE libraries and their enrichment pathways were compared. The gene expressions of 30 selected unigenes were validated using quantitative PCR. This study is the first to provide the transcriptome sequences for seed dormancy release in American ginseng, and demonstrates the successful use of DGE profiling data for analyzing transcriptomic variation during dormancy release. These data provide a basis for future researches of seed dormancy in morphophysiological dormancy seeds in non-model plants.
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Zhang GH, Ma CH, Zhang JJ, Chen JW, Tang QY, He MH, Xu XZ, Jiang NH, Yang SC. Transcriptome analysis of Panax vietnamensis var. fuscidicus discovers putative ocotillol-type ginsenosides biosynthesis genes and genetic markers. BMC Genomics 2015; 16:159. [PMID: 25765814 PMCID: PMC4355973 DOI: 10.1186/s12864-015-1332-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND P. vietnamensis var. fuscidiscus, called "Yesanqi" in Chinese, is a new variety of P. vietnamensis, which was first found in Jinping County, the southern part of Yunnan Province, China. Compared with other Panax plants, this species contains higher content of ocotillol-type saponin, majonoside R2. Despite the pharmacological importance of ocotillol-type saponins, little is known about their biosynthesis in plants. Hence, P. vietnamensis var. fuscidiscus is a suitable medicinal herbal plant species to study biosynthesis of ocotillol-type saponins. In addition, the available genomic information of this important herbal plant is lacking. RESULTS To investigate the P. vietnamensis var. fuscidiscus transcriptome, Illumina HiSeq™ 2000 sequencing platform was employed. We produced 114,703,210 clean reads, assembled into 126,758 unigenes, with an average length of 1,304 bp and N50 of 2,108 bp. Among these 126,758 unigenes, 85,214 unigenes (67.23%) were annotated based on the information available from the public databases. The transcripts encoding the known enzymes involved in triterpenoid saponins biosynthesis were identified in our Illumina dataset. A full-length cDNA of three Squalene epoxidase (SE) genes were obtained using reverse transcription PCR (RT-PCR) and the expression patterns of ten unigenes were analyzed by reverse transcription quantitative real-time PCR (RT-qPCR). Furthermore, 15 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely to involve in triterpenoid saponins biosynthesis pathway were discovered from transcriptome sequencing of P. vietnamensis var. fuscidiscus. We further analyzed the data and found 21,320 simple sequence repeats (SSRs), 30 primer pairs for SSRs were randomly selected for validation of the amplification and polymorphism in 13 P. vietnamensis var. fuscidiscus accessions. Meanwhile, five major triterpene saponins in roots of P. vietnamensis var. fuscidicus were determined using high performance liquid chromatography (HPLC) and evaporative light scattering detector (ELSD). CONCLUSIONS The genomic resources generated from P. vietnamensis var. fuscidiscus provide new insights into the identification of putative genes involved in triterpenoid saponins biosynthesis pathway. This will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level. The SSR markers identified and developed in this study show genetic diversity for this important crop and will contribute to marker-assisted breeding for P. vietnamensis var. fuscidiscus.
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Affiliation(s)
- Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Chun-Hua Ma
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Jia-Jin Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Jun-Wen Chen
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Qing-Yan Tang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Mu-Han He
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Xiang-Zeng Xu
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Ni-Hao Jiang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
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19
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Kim YJ, Zhang D, Yang DC. Biosynthesis and biotechnological production of ginsenosides. Biotechnol Adv 2015; 33:717-35. [PMID: 25747290 DOI: 10.1016/j.biotechadv.2015.03.001] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/28/2015] [Accepted: 03/01/2015] [Indexed: 12/20/2022]
Abstract
Medicinal plants are essential for improving human health, and around 75% of the population in developing countries relies mainly on herb-based medicines for health care. As the king of herb plants, ginseng has been used for nearly 5,000 years in the oriental and recently in western medicines. Among the compounds studied in ginseng plants, ginsenosides have been shown to have multiple medical effects such as anti-oxidative, anti-aging, anti-cancer, adaptogenic and other health-improving activities. Ginsenosides belong to a group of triterpene saponins (also called ginseng saponins) that are found almost exclusively in Panax species and accumulated especially in the plant roots. In this review, we update the conserved and diversified pathway/enzyme biosynthesizing ginsenosides which have been presented. Particularly, we highlight recent milestone works on functional characterization of key genes dedicated to the production of ginsenosides, and their application in engineering plants and yeast cells for large-scale production of ginsenosides.
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Affiliation(s)
- Yu-Jin Kim
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Department of Oriental Medicinal Biotechnology and Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Youngin, 446-701, South Korea
| | - Dabing Zhang
- Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia.
| | - Deok-Chun Yang
- Department of Oriental Medicinal Biotechnology and Graduate School of Biotechnology, College of Life Science, Kyung Hee University, Youngin, 446-701, South Korea.
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20
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Cao H, Nuruzzaman M, Xiu H, Huang J, Wu K, Chen X, Li J, Wang L, Jeong JH, Park SJ, Yang F, Luo J, Luo Z. Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes. Int J Mol Sci 2015; 16:3035-57. [PMID: 25642758 PMCID: PMC4346879 DOI: 10.3390/ijms16023035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/22/2015] [Indexed: 12/05/2022] Open
Abstract
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.
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Affiliation(s)
- Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Mohammed Nuruzzaman
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jingjia Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Kunlu Wu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Xianghui Chen
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jijia Li
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Li Wang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Ji-Hak Jeong
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Sun-Jin Park
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Fang Yang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Junli Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
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Dong S, Liu Y, Niu J, Ning Y, Lin S, Zhang Z. De novo transcriptome analysis of the Siberian apricot (Prunus sibirica L.) and search for potential SSR markers by 454 pyrosequencing. Gene 2014; 544:220-7. [PMID: 24746601 DOI: 10.1016/j.gene.2014.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/10/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
Abstract
The Siberian apricot, an economically and ecologically important plant in China, contains seeds high in oil and can grow on marginal land. Although this species has multiple purposes and may be a feedstock of biofuel in China, transcriptome information and molecular research on this species remain limited. RNA-Seq technology has been widely applied to transcriptomics, genomics and the development of molecular markers, and functional gene studies. In this study, we obtained 1,243,067 high-quality reads with a mean size of 425 bp in a single run, totaling 528.4 Mb of sequence data using 454 GS FLX Titanium sequencing. All reads were assembled de novo into 46,940 unigenes with a mean size of 651 bp (range: 45-5566 bp). Assembled unigenes were annotated in multiple public databases based on similarity alignments to genes and proteins. 191 unigenes involving in lipid biosynthesis and metabolism were found, among them, expression patterns of two desaturase enzymes were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR), based on six tissues from Siberian apricot, the seeds had the highest expression. 7304 simple sequence repeats (SSR) were identified from 6509 unigenes, a total of 9930 primer pairs were designed, 50 primer pairs were randomly selected to validate of the usefulness, and 24 (48%) primer pairs produced bands of the expected size. These data provide a base of sequence information to improve agronomic characters and molecular marker-assisted breeding to alter the composition of fatty acids in seeds from this plant, and hence, facilitate its utilization as a future biodiesel feedstock.
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Affiliation(s)
- Shubin Dong
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yulin Liu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jun Niu
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Yu Ning
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Shanzhi Lin
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Zhixiang Zhang
- Lab of Systematic Evolution and Biogeography of Woody Plants, College of Nature Conservation, Beijing Forestry University, Beijing 100083, China.
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22
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Ward JR, Clarke HD, Horton JL. Effects of a research-infused botanical curriculum on undergraduates' content knowledge, STEM competencies, and attitudes toward plant sciences. CBE LIFE SCIENCES EDUCATION 2014; 13:387-96. [PMID: 25185223 PMCID: PMC4152201 DOI: 10.1187/cbe.13-12-0231] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 04/11/2014] [Accepted: 04/30/2014] [Indexed: 05/19/2023]
Abstract
In response to the American Association for the Advancement of Science's Vision and Change in Undergraduate Biology Education initiative, we infused authentic, plant-based research into majors' courses at a public liberal arts university. Faculty members designed a financially sustainable pedagogical approach, utilizing vertically integrated curricular modules based on undergraduate researchers' field and laboratory projects. Our goals were to 1) teach botanical concepts, from cells to ecosystems; 2) strengthen competencies in statistical analysis and scientific writing; 3) pique plant science interest; and 4) allow all undergraduates to contribute to genuine research. Our series of inquiry-centered exercises mitigated potential faculty barriers to adopting research-rich curricula, facilitating teaching/research balance by gathering publishable scholarly data during laboratory class periods. Student competencies were assessed with pre- and postcourse quizzes and rubric-graded papers, and attitudes were evaluated with pre- and postcourse surveys. Our revised curriculum increased students' knowledge and awareness of plant science topics, improved scientific writing, enhanced statistical knowledge, and boosted interest in conducting research. More than 300 classroom students have participated in our program, and data generated from these modules' assessment allowed faculty and students to present 28 contributed talks or posters and publish three papers in 4 yr. Future steps include analyzing the effects of repeated module exposure on student learning and creating a regional consortium to increase our project's pedagogical impact.
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Affiliation(s)
- Jennifer Rhode Ward
- Biology Department, University of North Carolina-Asheville, Asheville, NC 28804
| | - H David Clarke
- Biology Department, University of North Carolina-Asheville, Asheville, NC 28804
| | - Jonathan L Horton
- Biology Department, University of North Carolina-Asheville, Asheville, NC 28804
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Punja ZK. American ginseng: research developments, opportunities, and challenges. J Ginseng Res 2013; 35:368-74. [PMID: 23717082 PMCID: PMC3659538 DOI: 10.5142/jgr.2011.35.3.368] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 07/06/2011] [Accepted: 07/09/2011] [Indexed: 11/23/2022] Open
Abstract
American ginseng (Panax quinquefolius L.) is grown in some regions of the USA and Canada and marketed for its health promoting attributes. While cultivation of this plant species has taken place in North America for over 100 years, there are many challenges that need to be addressed. In this article, the current production method used by growers is described and the challenges and opportunities for research on this valuable plant are discussed. These include studies on pharmacological activity, genetic diversity within the species, genetic improvement of currently grown plants, molecular characterization of gene expression, and management of diseases affecting plant productivity. The current research developments in these areas are reviewed and areas requiring further work are summarized. Additional research should shed light on the nature of the bioactive compounds and their clinical effects, and the molecular basis of active ingredient biosynthesis, and provide more uniform genetic material as well as improved plant growth, and potentially reduce losses due to pathogens.
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Affiliation(s)
- Zamir K Punja
- Department of Biological Sciences, Simon Fraser University, British Columbia V5A 1S6, Canada
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24
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Luo H, Sun C, Sun Y, Wu Q, Li Y, Song J, Niu Y, Cheng X, Xu H, Li C, Liu J, Steinmetz A, Chen S. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics 2011; 12 Suppl 5:S5. [PMID: 22369100 PMCID: PMC3287501 DOI: 10.1186/1471-2164-12-s5-s5] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Panax notoginseng (Burk) F.H. Chen is important medicinal plant of the Araliacease family. Triterpene saponins are the bioactive constituents in P. notoginseng. However, available genomic information regarding this plant is limited. Moreover, details of triterpene saponin biosynthesis in the Panax species are largely unknown. Results Using the 454 pyrosequencing technology, a one-quarter GS FLX titanium run resulted in 188,185 reads with an average length of 410 bases for P. notoginseng root. These reads were processed and assembled by 454 GS De Novo Assembler software into 30,852 unique sequences. A total of 70.2% of unique sequences were annotated by Basic Local Alignment Search Tool (BLAST) similarity searches against public sequence databases. The Kyoto Encyclopedia of Genes and Genomes (KEGG) assignment discovered 41 unique sequences representing 11 genes involved in triterpene saponin backbone biosynthesis in the 454-EST dataset. In particular, the transcript encoding dammarenediol synthase (DS), which is the first committed enzyme in the biosynthetic pathway of major triterpene saponins, is highly expressed in the root of four-year-old P. notoginseng. It is worth emphasizing that the candidate cytochrome P450 (Pn02132 and Pn00158) and UDP-glycosyltransferase (Pn00082) gene most likely to be involved in hydroxylation or glycosylation of aglycones for triterpene saponin biosynthesis were discovered from 174 cytochrome P450s and 242 glycosyltransferases by phylogenetic analysis, respectively. Putative transcription factors were detected in 906 unique sequences, including Myb, homeobox, WRKY, basic helix-loop-helix (bHLH), and other family proteins. Additionally, a total of 2,772 simple sequence repeat (SSR) were identified from 2,361 unique sequences, of which, di-nucleotide motifs were the most abundant motif. Conclusion This study is the first to present a large-scale EST dataset for P. notoginseng root acquired by next-generation sequencing (NGS) technology. The candidate genes involved in triterpene saponin biosynthesis, including the putative CYP450s and UGTs, were obtained in this study. Additionally, the identification of SSRs provided plenty of genetic makers for molecular breeding and genetics applications in this species. These data will provide information on gene discovery, transcriptional regulation and marker-assisted selection for P. notoginseng. The dataset establishes an important foundation for the study with the purpose of ensuring adequate drug resources for this species.
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Affiliation(s)
- Hongmei Luo
- The Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, PR China
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Tiski I, Marraccini P, Pot D, Vieira LGE, Pereira LFP. Characterization and expression of two cDNA encoding 3-Hydroxy-3-methylglutaryl coenzyme A reductase isoforms in coffee (Coffea arabica L.). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:719-27. [PMID: 21751872 DOI: 10.1089/omi.2010.0140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In higher plants there are two independent pathways for isoprenoid biosynthesis, located in the cytosol (mevalonic acid or MVA pathway) or in the plastids [methylerythritol phosphate (MEP) pathway]. The 3-hydroxy-3-methyglutaryl-CoA reductase (HMGR) is the first committed step in the MVA pathway. Using the information available from the Brazilian Coffee Genome Project, we found 13 ESTs that originated two isoforms, CaHMGR1 and CaHMGR2, for the enzyme HMGR of Coffea arabica. A complementary DNA encoding the isoform CaHMGR1 was cloned, and its complete nucleotide sequence determined. The full-length cDNA of CaHMGR1 was 2,242 bp containing a 1,812-bp ORF encoding 604 amino acids. Bioinformatic analyses revealed that the deduced CaHMGR1 had extensive homology with other plant HMGRs and contained two transmembrane domains and two putative HMGR binding sites and two NADP(H)-binding sites. Under normal growth conditions, transcripts of isoform CaHMRG1 were detected in fruit tissues (pulp, perisperm, and endosperm) only at the initial stages of development, flower buds and leaves. CaHMRG2 was expressed in all tissues and during all fruit development stages examined. These results suggest a constitutive expression of isoform CaHMGR2, while the isoform CaHMGR1 shows temporal and tissue-specific transcriptional activation.
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Affiliation(s)
- Iris Tiski
- Biotechnology Graduation Program-UEL, Londrina, PR, Brazil
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Tang Q, Ma X, Mo C, Wilson IW, Song C, Zhao H, Yang Y, Fu W, Qiu D. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics 2011; 12:343. [PMID: 21729270 PMCID: PMC3161973 DOI: 10.1186/1471-2164-12-343] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2011] [Accepted: 07/05/2011] [Indexed: 01/04/2023] Open
Abstract
Background Siraitia grosvenorii (Luohanguo) is an herbaceous perennial plant native to southern China and most prevalent in Guilin city. Its fruit contains a sweet, fleshy, edible pulp that is widely used in traditional Chinese medicine. The major bioactive constituents in the fruit extract are the cucurbitane-type triterpene saponins known as mogrosides. Among them, mogroside V is nearly 300 times sweeter than sucrose. However, little is known about mogrosides biosynthesis in S. grosvenorii, especially the late steps of the pathway. Results In this study, a cDNA library generated from of equal amount of RNA taken from S. grosvenorii fruit at 50 days after flowering (DAF) and 70 DAF were sequenced using Illumina/Solexa platform. More than 48,755,516 high-quality reads from a cDNA library were generated that was assembled into 43,891 unigenes. De novo assembly and gap-filling generated 43,891 unigenes with an average sequence length of 668 base pairs. A total of 26,308 (59.9%) unique sequences were annotated and 11,476 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. cDNA sequences for all of the known enzymes involved in mogrosides backbone synthesis were identified from our library. Additionally, a total of eighty-five cytochrome P450 (CYP450) and ninety UDP-glucosyltransferase (UDPG) unigenes were identified, some of which appear to encode enzymes responsible for the conversion of the mogroside backbone into the various mogrosides. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed on three important stages of fruit development, and based on their expression pattern, seven CYP450s and five UDPGs were selected as the candidates most likely to be involved in mogrosides biosynthesis. Conclusion A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying candidate genes encoding enzymes responsible for the biosynthesis of novel secondary metabolites in a non-model plant. Seven CYP450s and five UDPGs were selected as potential candidates involved in mogrosides biosynthesis. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the fruit extract from S. grosvenorii.
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Affiliation(s)
- Qi Tang
- Institute of Medicinal Plant, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
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Yendo ACA, de Costa F, Gosmann G, Fett-Neto AG. Production of plant bioactive triterpenoid saponins: elicitation strategies and target genes to improve yields. Mol Biotechnol 2010; 46:94-104. [PMID: 20204713 DOI: 10.1007/s12033-010-9257-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triterpenoid saponins are a class of plant secondary metabolites with structure derived from the precursor oxidosqualene in which one or more sugar residues are added. They have a wide range of pharmacological applications, such as antiplatelet, hypocholesterolemic, antitumoral, anti-HIV, immunoadjuvant, anti-inflammatory, antibacterial, insecticide, fungicide and anti-leishmanial agents. Their accumulation in plant cells is stimulated in response to changes mediated by biotic and abiotic elicitors. The enhancement of saponin yields by methyl jasmonate in plants and cell cultures in several species indicates the involvement of these metabolites in plant defence mechanisms. The elucidation of their biosynthesis at the molecular level has advanced recently. Most studies to date have focused on the participation of early enzymes in the pathway, including oxidosqualene cyclase, squalene synthase and dammarenediol synthase, as well as in isolating and characterizing genes that encode beta-amyrin synthase. Yields of bioactive saponins in various plant species and experimental systems have been successfully increased by treating cells and tissues with jasmonate or by exposing these to oxidative stress. These elicitation and molecular studies are consolidating a robust knowledge platform from which to launch the development of improved sources for commercial supply of bioactive saponins.
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Affiliation(s)
- Anna C A Yendo
- Department of Botany, Graduate Program in Botany, Federal University of Rio Grande do Sul, Av. Bento Gonçalves 9500, Porto Alegre, RS, Brazil
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Sun C, Li Y, Wu Q, Luo H, Sun Y, Song J, Lui EMK, Chen S. De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. BMC Genomics 2010; 11:262. [PMID: 20416102 PMCID: PMC2873478 DOI: 10.1186/1471-2164-11-262] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Accepted: 04/24/2010] [Indexed: 11/10/2022] Open
Abstract
Background American ginseng (Panax quinquefolius L.) is one of the most widely used herbal remedies in the world. Its major bioactive constituents are the triterpene saponins known as ginsenosides. However, little is known about ginsenoside biosynthesis in American ginseng, especially the late steps of the pathway. Results In this study, a one-quarter 454 sequencing run produced 209,747 high-quality reads with an average sequence length of 427 bases. De novo assembly generated 31,088 unique sequences containing 16,592 contigs and 14,496 singletons. About 93.1% of the high-quality reads were assembled into contigs with an average 8-fold coverage. A total of 21,684 (69.8%) unique sequences were annotated by a BLAST similarity search against four public sequence databases, and 4,097 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Based on the bioinformatic analysis described above, we found all of the known enzymes involved in ginsenoside backbone synthesis, starting from acetyl-CoA via the isoprenoid pathway. Additionally, a total of 150 cytochrome P450 (CYP450) and 235 glycosyltransferase unique sequences were found in the 454 cDNA library, some of which encode enzymes responsible for the conversion of the ginsenoside backbone into the various ginsenosides. Finally, one CYP450 and four UDP-glycosyltransferases were selected as the candidates most likely to be involved in ginsenoside biosynthesis through a methyl jasmonate (MeJA) inducibility experiment and tissue-specific expression pattern analysis based on a real-time PCR assay. Conclusions We demonstrated, with the assistance of the MeJA inducibility experiment and tissue-specific expression pattern analysis, that transcriptome analysis based on 454 pyrosequencing is a powerful tool for determining the genes encoding enzymes responsible for the biosynthesis of secondary metabolites in non-model plants. Additionally, the expressed sequence tags (ESTs) and unique sequences from this study provide an important resource for the scientific community that is interested in the molecular genetics and functional genomics of American ginseng.
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Affiliation(s)
- Chao Sun
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences, Haidian District, Beijing, China
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