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Titova MV, Lunkova MK, Tyurina TM, Prudnikova ON, Popova EV, Klychnikov OI, Metalnikov PS, Ikhalaynen YA, Vasileva EN, Rodin IA, Nosov AM. Suspension cell cultures of Panax vietnamensis as a biotechnological source of ginsenosides: growth, cytology, and ginsenoside profile assessment. FRONTIERS IN PLANT SCIENCE 2024; 15:1349494. [PMID: 38469323 PMCID: PMC10926444 DOI: 10.3389/fpls.2024.1349494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/25/2024] [Indexed: 03/13/2024]
Abstract
Introduction Panax vietnamensis is a valuable medicinal plant and a source of a broad spectrum of biologically active ginsenosides of different structural groups. Overexploitation and low adaptability to planation cultivation have made this species vulnerable to human pressure and prompted the development of cell cultivation in vitro as a sustainable alternative to harvesting wild plants for their bioactive components. Despite high interest in biotechnological production, little is known about the main factors affecting cell growth and ginsenoside biosynthesis of this species under in vitro conditions. In this study, the potential of cell cultures of P. vietnamensis as a biotechnological source of ginsenosides was was assessed. Methods Six suspension cell lines that were developed from different sections of a single rhizome through a multi-step culture optimization process and maintained for over 3 years on media with different mineral salt base and varying contents of auxins and cytokinins. These cell lines were evaluated for productivity parameters and cytological characteristics. Ginsenoside profiles were assessed using a combination of the reversed-phase ultra-high-performance liquid chromatography-Orbitrap-tandem mass spectrometry (UHPLC-Orbitrap-MS/MS) and ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-TOF-MS). Results All lines demonstrated good growth with a specific growth rate of 0.1-0.2 day-1, economic coefficient of 0.31-0.70, productivity on dry weight (DW) of 0.30-0.83 gDW (L·day)-1, and maximum biomass accumulation varying from 10 to 22 gDW L-1. Ginsenosides of the protopanaxadiol (Rb1, Rb2/Rb3, malonyl-Rb1, and malonyl-Rb2/Rb3), oleanolic acid (R0 and chikusetsusaponin IV), and ocotillol (vinaginsenoside R1) groups and their isomers were identified in cell biomass extracts. Chikusetsusaponin IV was identified in P. vietnamensis cell culture for the first time. Discussion These results suggest that suspension cell cultures of Vietnamese ginseng have a high potential for the biotechnological production of biomass containing ginsenosides, particularly of the oleanolic acid and ocotillol groups.
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Affiliation(s)
- Maria V. Titova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Maria K. Lunkova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana M. Tyurina
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga N. Prudnikova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Elena V. Popova
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Oleg I. Klychnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biochemistry, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Pavel S. Metalnikov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri A. Ikhalaynen
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta N. Vasileva
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Igor A. Rodin
- Department of Analytical Chemistry, Faculty of Chemistry, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander M. Nosov
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
- Department of Plant Physiology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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Ma S, Sun C, Su W, Zhao W, Zhang S, Su S, Xie B, Kong L, Zheng J. Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis. BMC PLANT BIOLOGY 2024; 24:91. [PMID: 38317086 PMCID: PMC10845750 DOI: 10.1186/s12870-024-04780-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Atractylodes chinensis (DC) Koidz., a dicotyledonous and hypogeal germination species, is an important medicinal plant because its rhizome is enriched in sesquiterpenes. The development and production of A. chinensis are negatively affected by drought stress, especially at the seedling stage. Understanding the molecular mechanism of A. chinensis drought stress response plays an important role in ensuring medicinal plant production and quality. In this study, A. chinensis seedlings were subjected to drought stress treatment for 0 (control), 3 (D3), and 9 days (D9). For the control, the sample was watered every two days and collected on the second morning after watering. The integration of physiological and transcriptomic analyses was carried out to investigate the effects of drought stress on A. chinensis seedlings and to reveal the molecular mechanism of its drought stress response. RESULTS The malondialdehyde, proline, soluble sugar, and crude protein contents and antioxidative enzyme (superoxide dismutase, peroxidase, and catalase) activity were significantly increased under drought stress compared with the control. Transcriptomic analysis indicated a total of 215,665 unigenes with an average length of 759.09 bp and an N50 of 1140 bp. A total of 29,449 differentially expressed genes (DEGs) were detected between the control and D3, and 14,538 DEGs were detected between the control and D9. Under drought stress, terpenoid backbone biosynthesis had the highest number of unigenes in the metabolism of terpenoids and polyketides. To identify candidate genes involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, we observed 22 unigene-encoding enzymes in the terpenoid backbone biosynthetic pathway and 15 unigene-encoding enzymes in the sesquiterpenoid and triterpenoid biosynthetic pathways under drought stress. CONCLUSION Our study provides transcriptome profiles and candidate genes involved in sesquiterpenoid and triterpenoid biosynthesis in A. chinensis in response to drought stress. Our results improve our understanding of how drought stress might affect sesquiterpenoid and triterpenoid biosynthetic pathways in A. chinensis.
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Affiliation(s)
- Shanshan Ma
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Chengzhen Sun
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Wennan Su
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Wenjun Zhao
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Sai Zhang
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Shuyue Su
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Boyan Xie
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Lijing Kong
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China
| | - Jinshuang Zheng
- Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science & Technology, Qinhuangdao, Hebei, 066004, China.
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Wang Y, Wang B, Xu F, Ma X. Molecular Cloning and Functional Characterization of Oxidosqualene Cyclases from Panax vietnamensis. Chem Biodivers 2023; 20:e202200874. [PMID: 36635849 DOI: 10.1002/cbdv.202200874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/22/2022] [Accepted: 01/11/2023] [Indexed: 01/14/2023]
Abstract
Panax vietnamensis is a valuable medicinal resource with promising preclinical applications. Ginsenosides, which are triterpenoids, are the primary active components in P. vietnamensis. Oxidosqualene cyclases (OSCs) catalyze the formation of the basic skeleton of triterpenes from 2,3-oxidosqualene, which is a crucial step in the biosynthesis of triterpenoids. The OSCs involved in triterpenoid biosynthesis in P. vietnamensis have not yet been characterized. Four OSC genes (PvOSC1-4) were cloned from P. vietnamensis and functionally characterized via heterologous expression in yeast. Transgenic yeast expressing PvOSC1, PvOSC3, and PvOSC4 produced the corresponding products β-amyrin, cycloartenol, and dammarenediol-II, respectively. PvOSC1, PvOSC3, and PvOSC4 are monofunctional OSCs. In this study, we characterized three PvOSC genes, providing a better understanding of the biosynthesis of triterpenoids in P. vietnamensis and the multiple choices of plant OSCs for metabolic engineering in yeast and other hosts.
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Affiliation(s)
- Yibo Wang
- Key Laboratory of Yunnan Provincial Department of Education on Substance Benchmark Research of Ethnic Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China.,College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Baojie Wang
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Furong Xu
- College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xiaohui Ma
- Key Laboratory of Yunnan Provincial Department of Education on Substance Benchmark Research of Ethnic Medicines, Yunnan University of Chinese Medicine, Kunming, 650500, China.,College of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicinal Utilization, Yunnan University of Chinese Medicine, Kunming, 650500, China
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Lu S. Transcriptome analysis and development of EST-SSR markers in Anoectochilus emeiensis (Orchidaceae). PLoS One 2022; 17:e0278551. [PMID: 36472967 PMCID: PMC9725121 DOI: 10.1371/journal.pone.0278551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022] Open
Abstract
Anoectochilus emeiensis K. Y. Lang, together with other Anoectochilus species, has long been used as the main source of many traditional Chinese medicines. Owing to the shortcomings of molecular markers, the study of the genetic diversity and medicinal component synthesis mechanism of the endemic Anoectochilus species has been delayed. In this study, I carried out a transcriptome analysis of A. emeiensis. A total of 78,381 unigenes were assembled from 64.2 million reads, and 47,541 (60.65%) unigenes were matched to known proteins in the public databases. Then, 9284 expressed sequence tag-derived simple sequence repeats (EST-SSRs) were identified, and the frequency of SSRs in the A. emeiensis transcriptome was 9.88%. Trinucleotide repeats (3699, 39.84%) were the most common type, followed by dinucleotide (3251, 35.02%) and mononucleotide (1750, 18.85%) repeats. Based on the SSR sequence, 6683 primer pairs were successfully designed, 40 primer pairs were randomly selected, and 10 primer pairs were identified as polymorphic loci from 186 individuals of A. emeiensis. The EST-SSR markers examined in this study will be informative for future population genetic studies of A. emeiensis.
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Affiliation(s)
- Song Lu
- Sichuan Natural Resources Academy, Chengdu, Sichuan, China
- * E-mail:
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Wei G, Zhang G, Li M, Liu C, Wei F, Wang Y, Huang Z, Chen Z, Zheng Y, Chen S, Dong L. Core rhizosphere microbiome of Panax notoginseng and its associations with belowground biomass and saponin contents. Environ Microbiol 2022; 24:6238-6251. [PMID: 36229418 DOI: 10.1111/1462-2920.16245] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/01/2022] [Indexed: 01/12/2023]
Abstract
The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High-throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome-derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengzhi Li
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Congsheng Liu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Zhixin Huang
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Zhongjian Chen
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd, Wenshan, China
| | - Yuqing Zheng
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Fujian, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Xu J, Yang B, Li M, Li Z, Tu Y, Tang L, He G. Research on germplasm diversity of Amomum villosum. Lour in genuine producing area. PLoS One 2022; 17:e0268246. [PMID: 36044470 PMCID: PMC9432772 DOI: 10.1371/journal.pone.0268246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/25/2022] [Indexed: 12/02/2022] Open
Abstract
Background Genuine Chinese medicine is produced from medicinal plant cultivated in a specific region and is of better quality and efficacy, more consistently qualified and famous than that from the same medicinal plant cultivated in other regions. The cultivating region of genuine medicinal plant is known as the genuine producing area. Yangchun City, which is in Guangdong Province of China, is a genuine producing area for the famous Chinese medicine Amomi Fructus (also called Sharen). Amomi Fructus is the ripe and dry fruit of the Zingiberaceae plant A. villosum Lour.. A. villosum was introduced from the Persian Gulf region and has been cultivated in China for over 1000 years. Until now there are no reports on screening for good germplasm of A. villosum. Methods The contents of volatile oil and bornyl acetate of Amomi Fructus from 14 populations were determined with GC method, and the relative contents of the main chemical components in the volatile oils were determined with GC-MS method. Evaluation and variance analysis of the comprehensive quality of the 14 samples were conducted by means of a multi-indicator entropy-weight TOPSIS model (Technique for Order Preference by Similarity to an Ideal Solution) combined with OPLS-DA (Orthogonal Partial Least Squares Discrimination Analysis) and HCA (Hierarchical Clustering Analysis). The ISSR (Inter-Simple Sequence Repeat) molecular marker technique and the UPGMA (unweighted pair-group method with arithmetic means) were employed to analyze the genetic relationship among A. villosum populations. Results The contents of volatile oil and bornyl acetate differed significantly among the different populations, but the main chemical component in the volatile oil was the same in all the samples, which was bornyl acetate. OPLS-DA results showed that 9 indicators were the main factors influencing the quality differences among the 14 populations. The entropy-weight TOPSIS results showed that there were significant differences in the comprehensive qualities of the 12 populations from the genuine producing area. The best quality of fruit was found in the genuine producing area of Chunwan Town; the qualities of 33% of genuine fruits were lower than that of non-genuine fruits. Twenty-three DNA fragments were obtained by ISSR-PCR amplification using four ISSR primers, eleven of which were polymorphic loci, which accounted for 47.8%. The similarity coefficients (GS) of different populations of A. villosum ranged from 0.6087 to 0.9565. Conclusion There are significant differences among different populations of A. villosum in terms of the kinds of major chemical components and their contents, comprehensive quality and genetic diversity. The germplasm resources of A. villosum are rich in the genuine producing area. It means superior germplasm could be selected in the area. The comprehensive quality of the fruit of A. villosum from the non-genuine producing area is better than some of that from genuine producing area, proving that the non-genuine producing area can also produce Amomi Fructus with excellent quality.
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Affiliation(s)
- Jie Xu
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Guangdong Yifang Pharmaceutical Co., Ltd., Guangdong Provincial Key Laboratory of Traditional Chinese Medicine Formula Granule, Foshan, Guangdong, China
| | - Bohan Yang
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Mingxiao Li
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Zhuhai Hospital of Integrated Traditional Chinese and Western Medicine, Zhuhai, Guangdong, China
| | - Zixiang Li
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yuting Tu
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Liyun Tang
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- School of Life Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Guozhen He
- School of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- * E-mail:
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Tien NQD, Ma X, Man LQ, Chi DTK, Huy NX, Nhut DT, Rombauts S, Ut T, Loc NH. De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng ( Panax vietnamensis Ha et Grushv.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2215-2229. [PMID: 34744362 PMCID: PMC8526660 DOI: 10.1007/s12298-021-01076-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 05/04/2023]
Abstract
UNLABELLED Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted." Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01076-1.
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Affiliation(s)
- Nguyen Quang Duc Tien
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Xiao Ma
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Le Quang Man
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | - Duong Thi Kim Chi
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
| | | | - Duong-Tan Nhut
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Dalat, 670000 Vietnam
| | - Stephane Rombauts
- VIB-UGent Center for Plant Systems Biology, Ghent University, 9000 Ghent, Belgium
| | - Tran Ut
- Ngoc Linh Ginseng and Medicinal Materials Development Center, Quang Nam Quang Ngai, 51000 Vietnam
| | - Nguyen Hoang Loc
- Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
- Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000 Vietnam
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Hou M, Wang R, Zhao S, Wang Z. Ginsenosides in Panax genus and their biosynthesis. Acta Pharm Sin B 2021; 11:1813-1834. [PMID: 34386322 PMCID: PMC8343117 DOI: 10.1016/j.apsb.2020.12.017] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Ginsenosides are a series of glycosylated triterpenoids which belong to protopanaxadiol (PPD)-, protopanaxatriol (PPT)-, ocotillol (OCT)- and oleanane (OA)-type saponins known as active compounds of Panax genus. They are accumulated in plant roots, stems, leaves, and flowers. The content and composition of ginsenosides are varied in different ginseng species, and in different parts of a certain plant. In this review, we summarized the representative saponins structures, their distributions and the contents in nearly 20 Panax species, and updated the biosynthetic pathways of ginsenosides focusing on enzymes responsible for structural diversified ginsenoside biosynthesis. We also emphasized the transcription factors in ginsenoside biosynthesis and non-coding RNAs in the growth of Panax genus plants, and highlighted the current three major biotechnological applications for ginsenosides production. This review covered advances in the past four decades, providing more clues for chemical discrimination and assessment on certain ginseng plants, new perspectives for rational evaluation and utilization of ginseng resource, and potential strategies for production of specific ginsenosides.
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Key Words
- ABA, abscisic acid
- ADP, adenosine diphosphate
- AtCPR (ATR), Arabidopsis thaliana cytochrome P450 reductase
- BARS, baruol synthase
- Biosynthetic pathway
- Biotechnological approach
- CAS, cycloartenol synthase
- CDP, cytidine diphosphate
- CPQ, cucurbitadienol synthase
- CYP, cytochrome P450
- DDS, dammarenediol synthase
- DM, dammarenediol-II
- DMAPP, dimethylallyl diphosphate
- FPP, farnesyl pyrophosphate
- FPPS (FPS), farnesyl diphosphate synthase
- GDP, guanosine diphosphate
- Ginsenoside
- HEJA, 2-hydroxyethyl jasmonate
- HMGR, HMG-CoA reductase
- IPP, isopentenyl diphosphate
- ITS, internal transcribed spacer
- JA, jasmonic acid
- JA-Ile, (+)-7-iso-jasmonoyl-l-isoleucine
- JAR, JA-amino acid synthetase
- JAZ, jasmonate ZIM-domain
- KcMS, Kandelia candel multifunctional triterpene synthases
- LAS, lanosterol synthase
- LUP, lupeol synthase
- MEP, methylerythritol phosphate
- MVA, mevalonate
- MVD, mevalonate diphosphate decarboxylase
- MeJA, methyl jasmonate
- NDP, nucleotide diphosphate
- Non-coding RNAs
- OA, oleanane or oleanic acid
- OAS, oleanolic acid synthase
- OCT, ocotillol
- OSC, oxidosqualene cyclase
- PPD, protopanaxadiol
- PPDS, PPD synthase
- PPT, protopanaxatriol
- PPTS, PPT synthase
- Panax species
- RNAi, RNA interference
- SA, salicylic acid
- SE (SQE), squalene epoxidase
- SPL, squamosa promoter-binding protein-like
- SS (SQS), squalene synthase
- SUS, sucrose synthase
- TDP, thymine diphosphate
- Transcription factors
- UDP, uridine diphosphate
- UGPase, UDP-glucose pyrophosphosphprylase
- UGT, UDP-dependent glycosyltransferase
- WGD, whole genome duplication
- α-AS, α-amyrin synthase
- β-AS, β-amyrin synthase
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Affiliation(s)
- Maoqi Hou
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Rufeng Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Zhang D, Li W, Chen ZJ, Wei FG, Liu YL, Gao LZ. SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng. Sci Rep 2020; 10:15310. [PMID: 32943706 PMCID: PMC7499265 DOI: 10.1038/s41598-020-72291-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/19/2020] [Indexed: 02/08/2023] Open
Abstract
Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.
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Affiliation(s)
- Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Zhong-Jian Chen
- Wenshan Sanqi Institute of Science and Technology, Wenshan University, Wenshan, 663000, China
| | - Fu-Gang Wei
- Wenshan Miaoxiang Notoginseng Industral Co., LTD, Wenshan, 663000, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China. .,Plant Germplasm and Genomics Center, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650204, China.
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11
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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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12
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Deng MH, Zhao K, Lv JH, Huo JL, Zhang ZQ, Zhu HS, Zou XX, Wen JF. Flower transcriptome dynamics during nectary development in pepper (Capsicum annuum L.). Genet Mol Biol 2020; 43:e20180267. [PMID: 32478788 PMCID: PMC7263202 DOI: 10.1590/1678-4685-gmb-2018-0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 06/12/2019] [Indexed: 11/22/2022] Open
Abstract
The measurement of gene expression can provide important information about gene function and the molecular basis for developmental processes. We analyzed the transcriptomes at three different developmental stages of pepper flower [sporogenous cell division, stage (B1); pollen mother cell meiosis, stage (B2); and open flower (B3)]. In the cDNA libraries for B1, B2, and B3: 82718, 77061, and 91491 unigenes were assembled, respectively. A total of 34,445 unigene sequences and 128 pathways were annotated by KEGG pathway analysis. Several genes associated with nectar biosynthesis and nectary development were identified, and 8,955, 12,182, and 23,667 DEGs were identified in the B2 vs B1, B3 vs B1, and B3 vs. B2 comparisons. DEGs were involved in various metabolic processes, including flower development, nectar biosynthesis, and nectary development. According to the RNA-seq data, all 13 selected DEGs showed similar expression patterns after q-PCR analysis. Sucrose-phosphatase, galactinol-sucrose galactosyltransferase, and sucrose synthase played very important roles in nectar biosynthesis, and CRABS CLAW could potentially be involved in mediating nectary development. A significant number of simple sequence repeat and single nucleotide polymorphism markers were predicted in the Capsicum annuum sequences. The new results provide valuable genetic information about flower development in pepper.
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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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Wei G, Yang F, Wei F, Zhang L, Gao Y, Qian J, Chen Z, Jia Z, Wang Y, Su H, Dong L, Xu J, Chen S. Metabolomes and transcriptomes revealed the saponin distribution in root tissues of Panax quinquefolius and Panax notoginseng. J Ginseng Res 2019; 44:757-769. [PMID: 33192118 PMCID: PMC7655499 DOI: 10.1016/j.jgr.2019.05.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/09/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022] Open
Abstract
Background Panax quinquefolius and Panax notoginseng are widely used and well known for their pharmacological effects. As main pharmacological components, saponins have different distribution patterns in the root tissues of Panax plants. Methods In this study, the representative ginsenosides were detected and quantified by desorption electrospray ionization mass spectrometry and high-performance liquid chromatography analysis to demonstrate saponin distribution in the root tissues of P. quinquefolius and P. notoginseng, and saponin metabolite profiles were analyzed by metabolomes to obtain the biomarkers of different root tissues. Finally, the transcriptome analysis was performed to demonstrate the molecular mechanisms of saponin distribution by gene profiles. Results There was saponin distribution in the root tissues differed between P. quinquefolius and P. notoginseng. Eight-eight and 24 potential biomarkers were detected by metabolome analysis, and a total of 340 and 122 transcripts involved in saponin synthesis that were positively correlated with the saponin contents (R > 0.6, P < 0.05) in the root tissues of P. quinquefolius and P. notoginseng, respectively. Among them, GDPS1, CYP51, CYP64, and UGT11 were significantly correlated with the contents of Rg1, Re, Rc, Rb2, and Rd in P. quinquefolius. UGT255 was markedly related to the content of R1; CYP74, CYP89, CYP100, CYP103, CYP109, and UGT190 were markedly correlated with the Rd content in P. notoginseng. Conclusions These results provided the visual and quantitative profiles of and confirmed the pivotal transcripts of CYPs and UGTs regulating the saponin distribution in the root tissues of P. quinquefolius and P. notoginseng.
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Key Words
- AACT, Acetoacetyl-CoA acyltransferase
- DS, Dammarenediol-II synthase
- DXPR, 1-deoxy-o-xylulose 5-phosphate reductoisomerase
- DXPS, 1-deoxy-o-xylulose 5-phosphate synthase
- FDR, False discovery rate
- FPP, Farnesyl diphosphate
- FPS, Farnesyl pyrophosphate synthase
- GDPS, Gerenyl diphosphatesynthase
- GO, Gene Ontology
- HDS, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatesynthase
- HMGR, 3-hydroxy-3-methylglutaryl-CoA reductase
- HMGS, 3-hydroxy-3-methylglutaryl-CoA synthase
- HPLC-UV, High-performance liquid chromatography-ultraviolet detection
- IPP, Isoprenyl diphosphate
- IPPI, Isopentenyl pyrophosphate isomerase
- ISPD, 2-C-methylerythritol 4-phosphatecytidyl transferase
- ISPE, 4-(cytidine-5′-diphospho)-2-C-methylerythritol kinase
- ISPH, 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase
- MALDI-MS, Matrix-assisted laser desorption/ionization–mass spectrometry
- MECPS, 2-C-methylerythritol-2,4-cyclophosphate synthase
- MEP, 2-C-methyl-D-erythritol-4-phosphate
- MVA, Mevalonate acid
- MVD, Mevalonate diphosphate decarboxylase
- MVK, Mevalonate kinase
- Metabolome
- NCBI Nr, NCBI Non-redundant protein
- OPLS-DA, Orthogonal partial least squares-discriminant analysis
- ORF, Open read frame
- P450, P450-monooxygenase
- PMK, Phosphomevalonate kinase
- Panax plants
- Root tissues
- SE, Squalene epoxidase
- SS, Squalene synthase
- Saponin distribution
- Transcriptome
- UGTs, UDP-glycosyltransferases
- UPLC-MS, Ultrahigh-performance liquid chromatography quadrupole time of flight-mass spectrometry
- WGCNA, Weighted gene coexpression network analysis
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Affiliation(s)
- Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Feng Yang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology, Co., Ltd., Wenshan, China
| | - Lianjuan Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ying Gao
- Institute of Desertification Studies, Chinese Academy of Forestry, Beijing, China
| | - Jun Qian
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - Zhengwei Jia
- Waters Corporation Shanghai Science & Technology Co Ltd, Shanghai, China
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan, China
| | - He Su
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Tang QY, Chen G, Song WL, Fan W, Wei KH, He SM, Zhang GH, Tang JR, Li Y, Lin Y, Yang SC. Transcriptome analysis of Panax zingiberensis identifies genes encoding oleanolic acid glucuronosyltransferase involved in the biosynthesis of oleanane-type ginsenosides. PLANTA 2019; 249:393-406. [PMID: 30219960 DOI: 10.1007/s00425-018-2995-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/28/2018] [Indexed: 05/26/2023]
Abstract
Oleanolic acid glucuronosyltransferase (OAGT) genes synthesizing the direct precursor of oleanane-type ginsenosides were discovered. The four recombinant proteins of OAGT were able to transfer glucuronic acid at C-3 of oleanolic acid that yields oleanolic acid 3-O-β-glucuronide. Ginsenosides are the primary active components in the genus Panax, and great efforts have been made to elucidate the mechanisms underlying dammarane-type ginsenoside biosynthesis. However, there is limited information on oleanane-type ginsenosides. Here, high-performance liquid chromatography analysis demonstrated that oleanane-type ginsenosides (particularly ginsenoside Ro and chikusetsusaponin IV and IVa) are the abundant ginsenosides in Panax zingiberensis, an extremely endangered Panax species in southwest China. These ginsenosides are derived from oleanolic acid 3-O-β-glucuronide, which may be formed from oleanolic acid catalyzed by an unknown oleanolic acid glucuronosyltransferase (OAGT). Transcriptomic analysis of leaves, stems, main roots, and fibrous roots of P. zingiberensis was performed, and a total of 46,098 unigenes were obtained, including all the identified homologous genes involved in ginsenoside biosynthesis. The most upstream genes were highly expressed in the leaves, and the UDP-glucosyltransferase genes were highly expressed in the roots. This finding indicated that the precursors of ginsenosides are mainly synthesized in the leaves and transported to different parts for the formation of particular ginsenosides. For the first time, enzyme activity assay characterized four genes (three from P. zingiberensis and one from P. japonicus var. major, another Panax species with oleanane-type ginsenosides) encoding OAGT, which particularly transfer glucuronic acid at C-3 of oleanolic acid to form oleanolic acid 3-O-β-glucuronide. Taken together, our study provides valuable genetic information for P. zingiberensis and the genes responsible for synthesizing the direct precursor of oleanane-type ginsenosides.
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Affiliation(s)
- Qing-Yan Tang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Geng Chen
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Wan-Ling Song
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Kun-Hua Wei
- Guangxi Medicinal Resources Protection and Genetic Improvement Laboratory, Guangxi Botanical Garden of Medicinal Plant, Nanning, 530023, China
| | - Si-Mei He
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Guang-Hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Rong Tang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Ying Li
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Yuan Lin
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China
| | - Sheng-Chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasms Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201, China.
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Wei G, Wei F, Yuan C, Chen Z, Wang Y, Xu J, Zhang Y, Dong L, Chen S. Integrated Chemical and Transcriptomic Analysis Reveals the Distribution of Protopanaxadiol- and Protopanaxatriol-Type Saponins in Panax notoginseng. Molecules 2018; 23:molecules23071773. [PMID: 30029488 PMCID: PMC6099965 DOI: 10.3390/molecules23071773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 02/04/2023] Open
Abstract
Panax notoginseng is famous for its important therapeutic effects and commonly used worldwide. The active ingredients saponins have distinct contents in different tissues of P. notoginseng, and they may be related to the expression of key genes in the synthesis pathway. In our study, high-performance liquid chromatography results indicated that the contents of protopanaxadiol-(Rb1, Rc, Rb2, and Rd) and protopanaxatriol-type (R1, Rg1, and Re) saponins in below ground tissues were higher than those in above ground tissues. Clustering dendrogram and PCA analysis suggested that the below and above ground tissues were clustered into two separate groups. A total of 482 and 882 unigenes were shared in the below and above ground tissues, respectively. A total of 75 distinct expressions of CYPs transcripts (RPKM ≥ 10) were detected. Of these transcripts, 38 and 37 were highly expressed in the below ground and above ground tissues, respectively. RT-qPCR analysis showed that CYP716A47 gene was abundantly expressed in the above ground tissues, especially in the flower, whose expression was 31.5-fold higher than that in the root. CYP716A53v2 gene was predominantly expressed in the below ground tissues, especially in the rhizome, whose expression was 20.1-fold higher than that in the flower. Pearson's analysis revealed that the CYP716A47 expression was significantly correlated with the contents of ginsenoside Rc and Rb2. The CYP716A53v2 expression was associated with the saponin contents of protopanaxadiol-type (Rb1 and Rd) and protopanaxatriol-type (R1, Rg1, and Re). Results indicated that the expression patterns of CYP716A47 and CYP716A53v2 were correlated with the distribution of protopanaxadiol-type and protopanaxatriol-type saponins in P. notoginseng. This study identified the pivotal genes regulating saponin distribution and provided valuable information for further research on the mechanisms of saponin synthesis, transportation, and accumulation.
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Affiliation(s)
- Guangfei Wei
- Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Fugang Wei
- Wenshan Miaoxiang Notoginseng Technology Co., Ltd., Wenshan 663000, China.
| | - Can Yuan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Zhongjian Chen
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China.
| | - Yong Wang
- Institute of Sanqi Research, Wenshan University, Wenshan 663000, China.
| | - Jiang Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Yongqing Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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He SM, Liang YL, Cong K, Chen G, Zhao X, Zhao QM, Zhang JJ, Wang X, Dong Y, Yang JL, Zhang GH, Qian ZL, Fan W, Yang SC. Identification and Characterization of Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in Coptis Species. FRONTIERS IN PLANT SCIENCE 2018; 9:731. [PMID: 29915609 PMCID: PMC5995273 DOI: 10.3389/fpls.2018.00731] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 05/15/2018] [Indexed: 05/21/2023]
Abstract
The dried rhizomes of Coptis chinensis have been extensively used in heat clearing, dampness drying, fire draining, and detoxification by virtue of their major bioactive components, benzylisoquinoline alkaloids (BIAs). However, C. teeta and C. chinensis are occasionally interchanged, and current understanding of the molecular basis of BIA biosynthesis in these two species is limited. Here, berberine, coptisine, jatrorrhizine, and palmatine were detected in two species, and showed the highest contents in the roots, while epiberberine were found only in C. chinensis. Comprehensive transcriptome analysis of the roots and leaves of C. teeta and C. chinensis, respectively, identified 53 and 52 unigenes encoding enzymes potentially involved in BIA biosynthesis. By integrating probable biosynthetic pathways for BIAs, the jatrorrhizine biosynthesis ill-informed previously was further characterized. Two genes encoding norcoclaurine/norlaudanosoline 6-O-methyltransferases (Cc6OMT1 and Cc6OMT2) and one gene encoding norcoclaurine-7OMT (Ct7OMT) catalyzed enzymatically O-methylate (S)-norcoclaurine at C6 that yield (S)-coclaurine, along with a smaller amount of O-methylation occurred at C7, thereby forming its isomer (isococlaurine). In addition, scoulerine 9-OMT (CtSOMT) was determined to show strict substrate specificity, targeting (S)-scoulerine to yield (S)-tetrahydrocolumbamine. Taken together, the integration of the transcriptome and enzyme activity assays further provides new insight into molecular mechanisms underlying BIA biosynthesis in plants and identifies candidate genes for the study of synthetic biology in microorganisms.
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Affiliation(s)
- Si-Mei He
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Yan-Li Liang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Kun Cong
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Geng Chen
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiu Zhao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Qi-Ming Zhao
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Jia-Jin Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Yang Dong
- Province Key Laboratory, Biological Big Data College, Yunnan Agricultural University, Kunming, China
| | - Jian-Li Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Guang-Hui Zhang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Zhi-Long Qian
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
| | - Sheng-Chao Yang
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National and Local Joint Engineering Research Center on Germplasm Innovation and Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
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Jo IH, Lee J, Hong CE, Lee DJ, Bae W, Park SG, Ahn YJ, Kim YC, Kim JU, Lee JW, Hyun DY, Rhee SK, Hong CP, Bang KH, Ryu H. Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. Genes (Basel) 2017; 8:E228. [PMID: 28914759 PMCID: PMC5615361 DOI: 10.3390/genes8090228] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/17/2017] [Accepted: 09/12/2017] [Indexed: 11/17/2022] Open
Abstract
Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics in P. ginseng, we generated genome-wide transcriptome data from four different P. ginseng tissues using PacBio isoform sequencing (Iso-Seq) technology. A total of 135,317 assembled transcripts were generated with an average length of 3.2 kb and high assembly completeness. Of those unigenes, 67.5% were predicted to be complete full-length (FL) open reading frames (ORFs) and exhibited a high gene annotation rate. Furthermore, we successfully identified unique full-length genes involved in triterpenoid saponin synthesis and plant hormonal signaling pathways, including auxin and cytokinin. Studies on the functional genomics of P. ginseng seedlings have confirmed the rapid upregulation of negative feed-back loops by auxin and cytokinin signaling cues. The conserved evolutionary mechanisms in the auxin and cytokinin canonical signaling pathways of P. ginseng are more complex than those in Arabidopsis thaliana. Our analysis also revealed a more detailed view of transcriptome-wide alternative isoforms for 88 genes. Finally, transposable elements (TEs) were also identified, suggesting transcriptional activity of TEs in P. ginseng. In conclusion, our results suggest that long-read, full-length or partial-unigene data with high-quality assemblies are invaluable resources as transcriptomic references in P. ginseng and can be used for comparative analyses in closely related medicinal plants.
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Affiliation(s)
- Ick-Hyun Jo
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jinsu Lee
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Chi Eun Hong
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | | | - Wonsil Bae
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
| | - Sin-Gi Park
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Yong Ju Ahn
- TheragenEtex Bio Institute, Suwon 16229, Korea.
| | - Young Chang Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jang Uk Kim
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Jung Woo Lee
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Dong Yun Hyun
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Sung-Keun Rhee
- Department of Microbiology, Chungbuk National University, Cheongju 28644, Korea.
| | | | - Kyong Hwan Bang
- Department of Herbal Crop Research, National Institute of Horticultural and Herbal Science (NIHHS), Rural development administration (RDA), Eumseong 27709, Korea.
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheongju 28644, Korea.
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19
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Identification of candidate genes involved in isoquinoline alkaloids biosynthesis in Dactylicapnos scandens by transcriptome analysis. Sci Rep 2017; 7:9119. [PMID: 28831066 PMCID: PMC5567367 DOI: 10.1038/s41598-017-08672-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 07/12/2017] [Indexed: 12/23/2022] Open
Abstract
Dactylicapnos scandens (D. Don) Hutch (Papaveraceae) is a well-known traditional Chinese herb used for treatment of hypertension, inflammation, bleeding and pain for centuries. Although the major bioactive components in this herb are considered as isoquinoline alkaloids (IQAs), little is known about molecular basis of their biosynthesis. Here, we carried out transcriptomic analysis of roots, leaves and stems of D. scandens, and obtained a total of 96,741 unigenes. Based on gene expression and phylogenetic relationship, we proposed the biosynthetic pathways of isocorydine, corydine, glaucine and sinomenine, and identified 67 unigenes encoding enzymes potentially involved in biosynthesis of IQAs in D. scandens. High performance liquid chromatography analysis demonstrated that while isocorydine is the most abundant IQA in D. scandens, the last O-methylation biosynthesis step remains unclear. Further enzyme activity assay, for the first time, characterized a gene encoding O- methyltransferase (DsOMT), which catalyzes O-methylation at C7 of (S)-corytuberine to form isocorydine. We also identified candidate transcription factor genes belonging to WRKY and bHLH families that may be involved in the regulation of IQAs biosynthesis. Taken together, we first provided valuable genetic information for D. scandens, shedding light on candidate genes involved in IQA biosynthesis, which will be critical for further gene functional characterization.
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Liu J, Xu Y, Yang J, Wang W, Zhang J, Zhang R, Meng Q. Discovery, semisynthesis, biological activities, and metabolism of ocotillol-type saponins. J Ginseng Res 2017; 41:373-378. [PMID: 28701880 PMCID: PMC5489761 DOI: 10.1016/j.jgr.2017.01.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 12/31/2016] [Accepted: 01/02/2017] [Indexed: 11/30/2022] Open
Abstract
Ocotillol-type saponins are one kind of tetracyclic triterpenoids, sharing a tetrahydrofuran ring. Natural ocotillol-type saponins have been discovered in Panax quinquefolius L., Panax japonicus, Hana mina, and Vietnamese ginseng. In recent years, the semisynthesis of 20(S/R)-ocotillol-type saponins has been reported. The biological activities of ocotillol-type saponins include neuroprotective effect, antimyocardial ischemia, antiinflammatory, antibacterial, and antitumor activities. Owing to their chemical structure, pharmacological actions, and the stereoselective activity on antimyocardial ischemia, ocotillol-type saponins are subjected to extensive consideration. In this review, we sum up the discovery, semisynthesis, biological activities, and metabolism of ocotillol-type saponins.
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Affiliation(s)
| | | | | | | | | | | | - Qingguo Meng
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
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21
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Lee YS, Park HS, Lee DK, Jayakodi M, Kim NH, Koo HJ, Lee SC, Kim YJ, Kwon SW, Yang TJ. Integrated Transcriptomic and Metabolomic Analysis of Five Panax ginseng Cultivars Reveals the Dynamics of Ginsenoside Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:1048. [PMID: 28674547 PMCID: PMC5474932 DOI: 10.3389/fpls.2017.01048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/31/2017] [Indexed: 05/23/2023]
Abstract
Panax ginseng C.A. Meyer is a traditional medicinal herb that produces bioactive compounds such as ginsenosides. Here, we investigated the diversity of ginsenosides and related genes among five genetically fixed inbred ginseng cultivars (Chunpoong [CP], Cheongsun [CS], Gopoong [GO], Sunhyang [SH], and Sunun [SU]). To focus on the genetic diversity related to ginsenoside biosynthesis, we utilized in vitro cultured adventitious roots from the five cultivars grown under controlled environmental conditions. PCA loading plots based on secondary metabolite composition classified the five cultivars into three groups. We selected three cultivars (CS, SH, and SU) to represent the three groups and conducted further transcriptome and gas chromatography-mass spectrometry analyses to identify genes and intermediates corresponding to the variation in ginsenosides among cultivars. We quantified ginsenoside contents from the three cultivars. SH had more than 12 times the total ginsenoside content of CS, with especially large differences in the levels of panaxadiol-type ginsenosides. The expression levels of genes encoding squalene epoxidase (SQE) and dammarenediol synthase (DDS) were also significantly lower in CS than SH and SU, which is consistent with the low levels of ginsenoside produced in this cultivar. Methyl jasmonate (MeJA) treatment increased the levels of panaxadiol-type ginsenosides up to 4-, 13-, and 31-fold in SH, SU, and CS, respectively. MeJA treatment also greatly increased the quantity of major intermediates and the expression of the underlying genes in the ginsenoside biosynthesis pathway; these intermediates included squalene, 2,3-oxidosqualene, and dammarenediol II, especially in CS, which had the lowest ginsenoside content under normal culture conditions. We conclude that SQE and DDS are the most important genetic factors for ginsenoside biosynthesis with diversity among ginseng cultivars.
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Affiliation(s)
- Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Dong-Kyu Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National UniversitySeoul, South Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Hyun Jo Koo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Yeon Jeong Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
| | - Sung Won Kwon
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National UniversitySeoul, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National UniversityPyeongchang, South Korea
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22
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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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23
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Subtractive transcriptome analysis of leaf and rhizome reveals differentially expressed transcripts in Panax sokpayensis. Funct Integr Genomics 2016; 16:619-639. [PMID: 27586658 DOI: 10.1007/s10142-016-0517-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 07/16/2016] [Accepted: 07/19/2016] [Indexed: 01/01/2023]
Abstract
In the present study, suppression subtractive hybridization (SSH) strategy was used to identify rare and differentially expressed transcripts in leaf and rhizome tissues of Panax sokpayensis. Out of 1102 randomly picked clones, 513 and 374 high quality expressed sequenced tags (ESTs) were generated from leaf and rhizome subtractive libraries, respectively. Out of them, 64.92 % ESTs from leaf and 69.26 % ESTs from rhizome SSH libraries were assembled into different functional categories, while others were of unknown function. In particular, ESTs encoding galactinol synthase 2, ribosomal RNA processing Brix domain protein, and cell division cycle protein 20.1, which are involved in plant growth and development, were most abundant in the leaf SSH library. Other ESTs encoding protein KIAA0664 homologue, ubiquitin-activating enzyme e11, and major latex protein, which are involved in plant immunity and defense response, were most abundant in the rhizome SSH library. Subtractive ESTs also showed similarity with genes involved in ginsenoside biosynthetic pathway, namely farnesyl pyrophosphate synthase, squalene synthase, and dammarenediol synthase. Expression profiles of selected ESTs validated the quality of libraries and confirmed their differential expression in the leaf, stem, and rhizome tissues. In silico comparative analyses revealed that around 13.75 % of unigenes from the leaf SSH library were not represented in the available leaf transcriptome of Panax ginseng. Similarly, around 18.12, 23.75, 25, and 6.25 % of unigenes from the rhizome SSH library were not represented in available root/rhizome transcriptomes of P. ginseng, Panax notoginseng, Panax quinquefolius, and Panax vietnamensis, respectively, indicating a major fraction of novel ESTs. Therefore, these subtractive transcriptomes provide valuable resources for gene discovery in P. sokpayensis and would complement the available transcriptomes from other Panax species.
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Abstract
A total of 14 ocotillol-type ginsenosides were conveniently synthesized employing glycosylation of ocotillol sapogenin derivatives with glucosyl ortho-alkynylbenzoate donors under the promotion of a gold(I) catalyst as the key step. Relying on a rational protecting group strategy and the unexpected regioselectivity of the glycosylation of the 3,25-diol sapogenins (2a/2b, 5a/5b) for the tertiary 25-OH, mono 3-O-glucosyl ocotillol-PPD, 6-O-glucosyl ocotillol-PPT, 25-O-glucosyl ocotillol-PPD/PPT and 3,25-di-O-glucosyl ocotillol-PPD/PPT ginsenosides were prepared in which the configuration at the C-24 is either R or S.
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Affiliation(s)
- Renzeng Shen
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032, China
| | - Xin Cao
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032, China
| | - Stephane Laval
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032, China
| | - Jiansong Sun
- National Research Center for Carbohydrate Synthesis, Jiangxi Normal University , 437 West Beijing Road, Nanchang, 330027, China
| | - Biao Yu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Road, Shanghai 200032, China
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25
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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26
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Ma CH, Gao ZJ, Zhang JJ, Zhang W, Shao JH, Hai MR, Chen JW, Yang SC, Zhang GH. Candidate Genes Involved in the Biosynthesis of Triterpenoid Saponins in Platycodon grandiflorum Identified by Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:673. [PMID: 27242873 PMCID: PMC4871891 DOI: 10.3389/fpls.2016.00673] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 05/28/2023]
Abstract
BACKGROUND Platycodon grandiflorum is the only species in the genus Platycodon of the family Campanulaceae, which has been traditionally used as a medicinal plant for its lung-heat-clearing, antitussive, and expectorant properties in China, Japanese, and Korean. Oleanane-type triterpenoid saponins were the main chemical components of P. grandiflorum and platycodin D was the abundant and main bioactive component, but little is known about their biosynthesis in plants. Hence, P. grandiflorum is an ideal medicinal plant for studying the biosynthesis of Oleanane-type saponins. In addition, the genomic information of this important herbal plant is unavailable. PRINCIPAL FINDINGS A total of 58,580,566 clean reads were obtained, which were assembled into 34,053 unigenes, with an average length of 936 bp and N50 of 1,661 bp by analyzing the transcriptome data of P. grandiflorum. Among these 34,053 unigenes, 22,409 unigenes (65.80%) were annotated based on the information available from public databases, including Nr, NCBI, Swiss-Prot, KOG, and KEGG. Furthermore, 21 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely involved in triterpenoid saponins biosynthesis pathway were discovered from the transcriptome sequencing of P. grandiflorum. In addition, 10,626 SSRs were identified based on the transcriptome data, which would provide abundant candidates of molecular markers for genetic diversity and genetic map for this medicinal plant. CONCLUSION The genomic data obtained from P. grandiflorum, especially the identification of putative genes involved in triterpenoid saponins biosynthesis pathway, will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level.
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Affiliation(s)
- Chun-Hua Ma
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Zheng-Jie Gao
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Jia-Jin Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Wei Zhang
- The Life Science and Technology College, Honghe UniversityMengzi, China
| | - Jian-Hui Shao
- National Engineering Research Center for Agricultural Biodiversity Applied Technology, Yunnan Agricultural UniversityKunming, China
| | - Mei-Rong Hai
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Jun-Wen Chen
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Sheng-Chao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
| | - Guang-Hui Zhang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural UniversityKunming, China
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Huang Q, Huang X, Deng J, Liu H, Liu Y, Yu K, Huang B. Differential Gene Expression between Leaf and Rhizome in Atractylodes lancea: A Comparative Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:348. [PMID: 27066021 PMCID: PMC4811964 DOI: 10.3389/fpls.2016.00348] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/07/2016] [Indexed: 05/19/2023]
Abstract
The rhizome of Atractylodes lancea is extensively used in the practice of Traditional Chinese Medicine because of its broad pharmacological activities. This study was designed to characterize the transcriptome profiling of the rhizome and leaf of Atractylodes lancea in an attempt to uncover the molecular mechanisms regulating rhizome formation and growth. Over 270 million clean reads were assembled into 92,366 unigenes, 58% of which are homologous with sequences in public protein databases (NR, Swiss-Prot, GO, and KEGG). Analysis of expression levels showed that genes involved in photosynthesis, stress response, and translation were the most abundant transcripts in the leaf, while transcripts involved in stress response, transcription regulation, translation, and metabolism were dominant in the rhizome. Tissue-specific gene analysis identified distinct gene families active in the leaf and rhizome. Differential gene expression analysis revealed a clear difference in gene expression pattern, identifying 1518 up-regulated genes and 3464 down-regulated genes in the rhizome compared with the leaf, including a series of genes related to signal transduction, primary and secondary metabolism. Transcription factor (TF) analysis identified 42 TF families, with 67 and 60 TFs up-regulated in the rhizome and leaf, respectively. A total of 104 unigenes were identified as candidates for regulating rhizome formation and development. These data offer an overview of the gene expression pattern of the rhizome and leaf and provide essential information for future studies on the molecular mechanisms of controlling rhizome formation and growth. The extensive transcriptome data generated in this study will be a valuable resource for further functional genomics studies of A. lancea.
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Affiliation(s)
- Qianqian Huang
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Xiao Huang
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Juan Deng
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Hegang Liu
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Yanwen Liu
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Kun Yu
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
| | - Bisheng Huang
- College of Pharmacy, Hubei University of Chinese Medicine Wuhan, China
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Nguyen B, Kim K, Kim YC, Lee SC, Shin JE, Lee J, Kim NH, Jang W, Choi HI, Yang TJ. The complete chloroplast genome sequence of Panax vietnamensis Ha et Grushv (Araliaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:85-86. [PMID: 26710166 DOI: 10.3109/19401736.2015.1110810] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete chloroplast genome sequence of Panax vietnamensis, a medicinal herb belonging to Araliaceae family, was generated by de novo assembly using whole genome next-generation sequences. The chloroplast genome was a circular form of 155 992 bp long and showed typical chloroplast genome structure consisting of a large single-copy region of 86 177 bp, a small single copy region of 17 935 bp and a pair of inverted repeats of 25 940 bp. The chloroplast genome had 79 protein-coding genes, 29 tRNA genes and 4 rRNA genes. The phylogenetic analysis with the reported chloroplast genomes revealed that four Panax species were grouped in the same clade and P. vietnamensis is more closely related to P. notoginseng than P. ginseng and P. quinquefolius.
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Affiliation(s)
- Binh Nguyen
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
| | - Kyunghee Kim
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea.,b Phyzen Genomics Institute , Gwanak-Gu , Seoul , Republic of Korea
| | - Young-Chang Kim
- c Department of Herbal Crop Research , National Institute of Horticultural and Herbal Science, Rural Development Administration , Eumseong-Gun , Chungcheongbuk-Do , Republic of Korea , and
| | - Sang-Choon Lee
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
| | - Ji Eon Shin
- b Phyzen Genomics Institute , Gwanak-Gu , Seoul , Republic of Korea
| | - Junki Lee
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
| | - Nam-Hoon Kim
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
| | - Woojong Jang
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
| | - Hong-Il Choi
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea.,d Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute , Jeongeup , Republic of Korea
| | - Tae-Jin Yang
- a Department of Plant Science , Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul , Republic of Korea
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