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El Menyiy N, Elouafy Y, Moubachir R, Abdnim R, Benali T, Taha D, Khalid A, Abdalla AN, Hamza SMA, Elhadi Ibrahim S, El-Shazly M, Zengin G, Bouyahya A. Chemistry, Biological Activities, and Pharmacological Properties of Gastrodin: Mechanism Insights. Chem Biodivers 2024; 21:e202400402. [PMID: 38573028 DOI: 10.1002/cbdv.202400402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/30/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024]
Abstract
Gastrodin, a bioactive compound derived from the rhizome of the orchid Gastrodia elata, exhibits a diverse range of biological activities. With documented neuroprotective, anti-inflammatory, antioxidant, anti-apoptotic, and anti-tumor effects, gastrodin stands out as a multifaceted therapeutic agent. Notably, it has demonstrated efficacy in protecting against neuronal damage and enhancing cognitive function in animal models of Alzheimer's disease, Parkinson's disease, and cerebral ischemia. Additionally, gastrodin showcases immunomodulatory effects by mitigating inflammation and suppressing the expression of inflammatory cytokines. Its cytotoxic activity involves the inhibition of angiogenesis, suppression of tumor growth, and induction of apoptosis. This comprehensive review seeks to elucidate the myriad potential effects of Gastrodin, delving into the intricate molecular mechanisms underpinning its pharmacological properties. The findings underscore the therapeutic potential of gastrodin in addressing various conditions linked to neuroinflammation and cancer.
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Affiliation(s)
- Naoual El Menyiy
- Laboratory of Pharmacology, National Agency of Medicinal and Aromatic Plants, Taounate, 34025, Morocco
| | - Youssef Elouafy
- Laboratory of Materials, Nanotechnology and Environment LMNE, Faculty of Sciences, Mohammed V University in Rabat, Rabat, BP 1014, Morocco
| | - Rania Moubachir
- Bioactives and Environmental Health Laboratory, Faculty of Sciences, Moulay Ismail University, 11201, Meknes, Marocco
| | - Rhizlan Abdnim
- Laboratoire de bioressources, biotechnologie, ethnopharmacologie et santé, Département de biologie, Faculté des sciences, Université Mohamed premier, Boulevard Mohamed VI; BP:717, 60000, Oujda, Marocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Marrakesh-Safi, 46030, Morocco
| | - Douae Taha
- Molecular Modeling, Materials, Nanomaterials, Water and Environment Laboratory, CERNE2D, Department of Chemistry, Faculty of Sciences, Mohammed V University, Rabat, Rabat, 10106, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Unit, Health Research Cener, Jazan University, P.O. Box: 114, Jazan, 11111, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P. O. Box 2404, 11111, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Siddiqa M A Hamza
- Department of Pathology, College of Medicine, Umm Alqura University, 24832, Alqunfudah, Saudi Arabia
| | - Salma Elhadi Ibrahim
- Department of Physiology, College of Medicine, Umm Alqura University, 24832, Alqunfudah, Saudi Arabia
| | - Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, 11566, Cairo, Egypt
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, 42130, Konya, Turkey
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, 10106, Morocco
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Leng C, Hou M, Xing Y, Chen J. Perspective and challenges of mycorrhizal symbiosis in orchid medicinal plants. CHINESE HERBAL MEDICINES 2024; 16:172-179. [PMID: 38706832 PMCID: PMC11064572 DOI: 10.1016/j.chmed.2024.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 05/07/2024] Open
Abstract
The family Orchidaceae is of the most diverse taxon in the plant kingdom, and most of its members are highly valuable herbal medicines. Orchids have a unique mycorrhizal symbiotic relationship with specific fungi for carbohydrate and nutrient supplies in their whole lifecycle. The large-scale cultivation of the medicinal plant Gastodia elata is a successful example of using mycorrhizal symbiotic technology. In this review, we adopted G. elata and Dendrobium officinale as examples to describe the characteristics of orchid mycorrhiza and mycorrhizal benefits for host plants' growth and health (e.g. biotic and abiotic stress and secondary metabolite accumulation). The challenges in applying mycorrhizal technology to the cultivation of orchid medicinal plants in the future were also discussed. This review aims to serve as a theoretical guide for the cultivation of mycorrhizal technology in medicinal orchid plants.
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Affiliation(s)
- Chunyan Leng
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Mengyan Hou
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yongmei Xing
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Cai G, Cao Y, Tian M, Mo H, Chen X, Li Z, Ji Q, He K, Du G, Yang H. Characterization of the transcriptional responses of Armillaria gallica 012m to GA3. Arch Microbiol 2023; 205:308. [PMID: 37594611 DOI: 10.1007/s00203-023-03621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/19/2023]
Abstract
Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.
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Affiliation(s)
- Guolei Cai
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Yapu Cao
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Menghua Tian
- Zhaotong Tianma Research Institute, Zhaotong, Yunnan, China
| | - Haiying Mo
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Xin Chen
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Zhihao Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Qiaolin Ji
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Kaixiang He
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China
| | - Gang Du
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China.
| | - Haiying Yang
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China.
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Wang Y, Shahid MQ. Insights into the nutritional properties and molecular basis of biosynthesis of amino acids and vitamins of Gastrodia elata offered by metabolomic and transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1183139. [PMID: 37434605 PMCID: PMC10331839 DOI: 10.3389/fpls.2023.1183139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023]
Abstract
Gastrodia elata Blume (GE), a traditional and precious Chinese medicinal material, has been approved as a functional food. However, understanding GE's nutritional properties and its molecular basis remains limited. Here, metabolomic and transcriptomic analyses were performed on young and mature tubers of G. elata.f.elata (GEEy and GEEm) and G. elata.f.glauca (GEGy and GEGm). A total of 345 metabolites were detected, including 76 different amino acids and their derivatives containing all human essential amino acids (e.g., l-(+)-lysine, l-leucine), 13 vitamins (e.g., nicotinamide, thiamine), and 34 alkaloids (e.g., spermine, choline). GEGm has higher amino acid accumulation than GEEy, GEEm and GEGy, and vitamin contents were also slightly different in all four samples. Implying that GE, especially GEGm, is a kind of excellent complementary food as amino acid nutrition provider. From assembled 21,513 transcripts (genes) based on the transcriptome, we identified many genes that encode enzymes (e.g., pfkA, bglX, tyrAa, lysA, his B, aroA), which are responsible for the biosynthesis of amino acids and enzymes (e.g., nadA, URH1, NAPRT1, punA, rsgA) that related to vitamins metabolism. A total of 16 pairs of the differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) (e.g., gene-tia006709 coding GAPDH and l-(+)-arginine, and gene-tia010180 coding tyrA and l-(+)-arginine) and three DEG-DAM pairs (e.g., gene-tia015379 coding NadA and nicotinate d-ribonucleoside) show significant similar positive or negative correlation based on three, and two comparisons of GEEy vs. GEGy, GEGy vs. GEGm, GEEy vs. GEGy and GEEm vs. GEGm, which involved into amino acid biosynthesis, and nicotinate nicotinamide metabolism, respectively. These results prove that the enzyme coded by these DEG promotes (positive correlation) or inhibits (negative correlation) the biosynthesis of parallel DAM in GE. Overall, the data and corresponding analysis in this study provide new insights into the nutritional properties of GE and the related molecular basis.
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Affiliation(s)
- Yunsheng Wang
- School of Health and Life Science, Kaili University, Kaili City, Guizhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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Cui C, Yan J, Liu Y, Zhang Z, Su Q, Kong M, Zhou C, Ming H. One-pot biosynthesis of gastrodin using UDP-glycosyltransferase itUGT2 with an in situ UDP-glucose recycling system. Enzyme Microb Technol 2023; 166:110226. [PMID: 36913860 DOI: 10.1016/j.enzmictec.2023.110226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/11/2023]
Abstract
Gastrodin, the major effective ingredient in Tianma (Gastrodia elata), is a p-hydroxybenzoic acid derivative with various activities. Gastrodin has been widely investigated for food and medical applications. The last biosynthetic step for gastrodin is UDP-glycosyltransferase (UGT)-mediated glycosylation with UDP-glucose (UDPG) as glycosyl donor. In this study, we performed a one-pot reaction both in vitro and in vivo to synthesize gastrodin from p-hydroxybenzyl alcohol (pHBA) by coupling UDP-glucosyltransferase from Indigofera tinctoria (itUGT2) to sucrose synthase from Glycine max (GmSuSy) for regeneration of UDPG. The in vitro results showed that itUGT2 transferred a glucosyl group to pHBA to generate gastrodin. After 37 UDPG regeneration cycles with 2.5% (molar ratio) UDP, the pHBA conversion reached 93% at 8 h. Furthermore, a recombinant strain with itUGT2 and GmSuSy genes was constructed. Through optimizing the incubation conditions, a 95% pHBA conversion rate (220 mg/L gastrodin titer) was achieved in vivo without addition of UDPG, which was 2.6-fold higher than that without GmSuSy. This in situ system for gastrodin biosynthesis provides a highly efficient strategy for both in vitro gastrodin synthesis and in vivo biosynthesis of gastrodin in E. coli with UDPG regeneration.
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Affiliation(s)
- Caixia Cui
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China.
| | - Jinyuan Yan
- Changdu Bureau of Science and Technology, Changdu 854000, PR China
| | - Yongtao Liu
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Zhao Zhang
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Qingyang Su
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Mengyuan Kong
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Chenyan Zhou
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
| | - Hong Ming
- Department of Biopharmaceutical Sciences, Synthetic Biology Engineering Lab of Henan Province, School of Life Science and Technology, Xinxiang Medical University, Xinxiang 453003, PR China.
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Zheng H, Zhang P, Qin J, Guo J, Deng J. High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca. Front Microbiol 2023; 13:1092552. [PMID: 36733772 PMCID: PMC9887035 DOI: 10.3389/fmicb.2022.1092552] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Gastrodia elata f.glauca (G. elata) is a commonly used Chinese Medicinal Materials with great medicinal value. The medicinal plant and its endophytic bacteria are a symbiotic whole, and the endophytic bacteria are rich in species, and their metabolites are a treasure trove of natural compounds. However, there is a relative lack of analysis on the diversity, flora composition and network interactions of the endophytic bacteria of G. elata. In this study, high-throughput sequencing technology based on the Illumina Miseq platform was used to reveal the core microbiota by examining the diversity and community structures of tuber endophytic bacteria in G. elata grown under different regions and exploring the effect of region on its endophytic bacteria. Here, 1,265 endophytic ASVs were found to coexist with G. elata tuber in Guizhou and Hubei. At the phylum level, the dominant phyla were Proteobacteria, Actinobacteria and Acdobacteriota. At the family level, the dominant family were Comamonadaceae, Nocardicaece, Xanthobacteraceae, and Burkholderiaceae. At the genus level, Delftia and Rhodococcus were represented the core microbiota in G. elata tuber, which served as the dominant genera that coexisted in all samples tested. Moreover, we found that the beta diversity of endophytic bacteria in G. elata tuber was higher level in the Guizhou region than Hubei region. Overall, this study results to provide a reference for screening active strains and interaction between plants and endophytic bacteria.
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Affiliation(s)
- Heng Zheng
- Emergency Department of Hubei Third People's Hospital Affiliated to Jianghan University, Wuhan, Hubei Province, China,School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, China
| | - Peng Zhang
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China
| | - Jing Qin
- Wuchang District Shouyilu Street Community Health Service Center, Wuhan, Hubei Province, China
| | - Jiani Guo
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China,*Correspondence: Jiani Guo, ; Jun Deng,
| | - Jun Deng
- Emergency Department of Hubei Third People's Hospital Affiliated to Jianghan University, Wuhan, Hubei Province, China,*Correspondence: Jiani Guo, ; Jun Deng,
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Koo H, Lee YS, Nguyen VB, Giang VNL, Koo HJ, Park HS, Mohanan P, Song YH, Ryu B, Kang KB, Sung SH, Yang TJ. Comparative transcriptome and metabolome analyses of four Panax species explore the dynamics of metabolite biosynthesis. J Ginseng Res 2023; 47:44-53. [PMID: 36644396 PMCID: PMC9834023 DOI: 10.1016/j.jgr.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/31/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
Background The genus Panax in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between Panax species has influenced their biosynthetic pathways is not fully understood. Methods Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species (Panax ginseng and P. quinquefolius) and two diploid species (P. notoginseng and P. vietnamensis) revealed the diversity of their metabolites and related gene expression profiles. Results The transcriptome analysis showed that 2,3-OXIDOSQUALENE CYCLASEs (OSCs) involved in phytosterol biosynthesis are upregulated in the diploid species, while the expression of OSCs contributing to ginsenoside biosynthesis is higher in the tetraploid species. In agreement with these results, the contents of dammarenediol-type ginsenosides were higher in the tetraploid species relative to the diploid species. Conclusion These results suggest that a whole-genome duplication event has influenced the triterpene biosynthesis pathway in tetraploid Panax species during their evolution or ecological adaptation. This study provides a basis for further efforts to explore the genetic variation of the Panax genus.
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Affiliation(s)
- Hyunjin Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yun Sun Lee
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Van Binh Nguyen
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Vo Ngoc Linh Giang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun Jo Koo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun-Seung Park
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Padmanaban Mohanan
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea,Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Hun Song
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Byeol Ryu
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Kyo Bin Kang
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Sang Hyun Sung
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea,Corresponding author. Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Yu E, Gao Y, Li Y, Zang P, Zhao Y, He Z. An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria. BMC PLANT BIOLOGY 2022; 22:621. [PMID: 36581798 PMCID: PMC9801631 DOI: 10.1186/s12870-022-04007-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Gastrodia elata Bl. f. glauca, a perennial herb of G.elata Bl. in Orchidaceae, is one of the most valuable traditional Chinese medicines. G. elata Bl. is a chlorophyll-free myco-heterotrophic plant, which must rely on the symbiotic growth of Armillaria, but not all Armillaria strains can play the symbiotic role. Additionally, Armillaria is easy to degenerate after multiple generations, and the compatibility between the strains from other areas and G. elata Bl. f. glauca in Changbai Mountain is unstable. Therefore, it is incredibly significant to isolate, identify and screen the symbiotic Armillaria suitable for the growth of G. elata Bl. f. glauca in Changbai Mountain, and to explore the mechanism by which Armillaria improves the production performance of G. elata Bl. f. glauca. RESULTS Firstly, G. elata Bl. f. glauca tubers, and rhizomorphs and fruiting bodies of Armillaria were used for the isolation and identification of Armillaria. Five Armillaria isolates were obtained in our laboratory and named: JMG, JMA, JMB, JMC and JMD. Secondly, Armillaria was selected based on the yield and the effective component content of G. elata Bl. f. glauca. It was concluded that the yield and quality of G. elata Bl. f. glauca co-planted with JMG is the highest. Finally, the mechanism of its high quality and yield was explored by investigating the effects of different Armillaria strains on the soil, its nutrition element contents and the soil microbial diversity around G. elata Bl. f. glauca in Changbai Mountain. CONCLUSIONS Compared with commercial strains, JMG significantly increased the content of Na, Al, Si, Mn, Fe, Zn, Rb and the absorption of C, Na, Mg, Ca, Cr, Cu, Zn and Rb in G. elata Bl. f. glauca; it improved the composition, diversity and metabolic functions of soil microbial communities around G. elata Bl. f. glauca at phylum, class and genus levels; it markedly increased the relative abundance of bacteria such as Chthoniobacter and Armillaria in the dominant populations, and enhanced such functions as Cell motility, amino acid metabolism and Lipid metabolism; it dramatically decreased the relative abundance of Bryobacter and other fungi in the dominant populations, and reduced such functions as microbial energy metabolism, translation and carbohydrate metabolism. This is the main reason why excellent Armillaria strains promote the high quality and yield of G. elata Bl. f. glauca in Changbai Mountain.
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Affiliation(s)
- En Yu
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Yugang Gao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China.
| | - Yaqi Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Pu Zang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Yan Zhao
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Zhongmei He
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
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Liu B, Chen J, Zhang W, Huang Y, Zhao Y, Juneidi S, Dekebo A, Wang M, Shi L, Hu X. The gastrodin biosynthetic pathway in Pholidota chinensis Lindl. revealed by transcriptome and metabolome profiling. FRONTIERS IN PLANT SCIENCE 2022; 13:1024239. [PMID: 36407583 PMCID: PMC9673822 DOI: 10.3389/fpls.2022.1024239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Pholidota chinensis Lindl. is an epiphytic or lithophytic perennial herb of Orchidaceae family used as a garden flower or medicinal plant to treat high blood pressure, dizziness and headache in traditional Chinese medicine. Gastrodin (GAS) is considered as a main bioactive ingredient of this herb but the biosynthetic pathway remains unclear in P. chinensis. To elucidate the GAS biosynthesis and identify the related genes in P. chinensis, a comprehensive analysis of transcriptome and metabolome of roots, rhizomes, pseudobulbs and leaves were performed by using PacBio SMART, Illumina Hiseq and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). A total of 1,156 metabolites were identified by UPLC-MS/MS, of which 345 differential metabolites were mainly enriched in phenylpropanoid/phenylalanine, flavone and flavonol biosynthesis. The pseudobulbs make up nearly half of the fresh weight of the whole plant, and the GAS content in the pseudobulbs was also the highest in four tissues. Up to 23,105 Unigenes were obtained and 22,029 transcripts were annotated in the transcriptome analysis. Compared to roots, 7,787, 8,376 and 9,146 differentially expressed genes (DEGs) were identified in rhizomes, pseudobulbs and leaves, respectively. And in total, 80 Unigenes encoding eight key enzymes for GAS biosynthesis, were identified. Particularly, glycosyltransferase, the key enzyme of the last step in the GAS biosynthetic pathway had 39 Unigenes candidates, of which, transcript28360/f2p0/1592, was putatively identified as the most likely candidate based on analysis of co-expression, phylogenetic analysis, and homologous searching. The metabolomics and transcriptomics of pseudobulbs versus roots showed that 8,376 DEGs and 345 DEMs had a substantial association based on the Pearson's correlation. This study notably enriched the metabolomic and transcriptomic data of P. chinensis, and it provides valuable information for GAS biosynthesis in the plant.
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Affiliation(s)
- Baocai Liu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jingying Chen
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Wujun Zhang
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yingzhen Huang
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yunqing Zhao
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Seifu Juneidi
- Department of Applied Biology, School of Natural Science, Adama Science and Technology University, Adama, Ethiopia
| | - Aman Dekebo
- Applied Chemistry Department, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Meijuan Wang
- Shengnongjia Academy of Forestry, Shengnongjia, Hubei, China
| | - Le Shi
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan, China
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10
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Bae EK, An C, Kang MJ, Lee SA, Lee SJ, Kim KT, Park EJ. Chromosome-level genome assembly of the fully mycoheterotrophic orchid Gastrodia elata. G3 (BETHESDA, MD.) 2022; 12:6511440. [PMID: 35100375 PMCID: PMC8896018 DOI: 10.1093/g3journal/jkab433] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/10/2021] [Indexed: 11/26/2022]
Abstract
Gastrodia elata, an obligate mycoheterotrophic orchid, requires complete carbon and mineral nutrient supplementation from mycorrhizal fungi during its entire life cycle. Although full mycoheterotrophy occurs most often in the Orchidaceae family, no chromosome-level reference genome from this group has been assembled to date. Here, we report a high-quality chromosome-level genome assembly of G. elata, using Illumina and PacBio sequencing methods with Hi-C technique. The assembled genome size was found to be 1045 Mb, with an N50 of 50.6 Mb and 488 scaffolds. A total of 935 complete (64.9%) matches to the 1440 embryophyte Benchmarking Universal Single-Copy Orthologs were identified in this genome assembly. Hi-C scaffolding of the assembled genome resulted in 18 pseudochromosomes, 1008 Mb in size and containing 96.5% of the scaffolds. A total of 18,844 protein-coding sequences (CDSs) were predicted in the G. elata genome, of which 15,619 CDSs (82.89%) were functionally annotated. In addition, 74.92% of the assembled genome was found to be composed of transposable elements. Phylogenetic analysis indicated a significant contraction of genes involved in various biosynthetic processes and cellular components and an expansion of genes for novel metabolic processes and mycorrhizal association. This result suggests an evolutionary adaptation of G. elata to a mycoheterotrophic lifestyle. In summary, the genomic resources generated in this study will provide a valuable reference genome for investigating the molecular mechanisms of G. elata biological functions. Furthermore, the complete G. elata genome will greatly improve our understanding of the genetics of Orchidaceae and its mycoheterotrophic evolution.
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Affiliation(s)
- Eun-Kyung Bae
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Chanhoon An
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Min-Jeong Kang
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Sang-A Lee
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
| | - Seung Jae Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon 57922, Korea
| | - Eung-Jun Park
- Forest Microbiology Division, National Institute of Forest Science, Suwon 16631, Korea
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11
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Xing YM, Li B, Liu L, Li Y, Yin SX, Yin SC, Chen J, Guo SX. Armillaria mellea Symbiosis Drives Metabolomic and Transcriptomic Changes in Polyporus umbellatus Sclerotia. Front Microbiol 2022; 12:792530. [PMID: 35185819 PMCID: PMC8851056 DOI: 10.3389/fmicb.2021.792530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Sclerotia, the medicinal part of Polyporus umbellatus, play important roles in diuresis and renal protection, with steroids and polysaccharides as the main active ingredients. The sclerotia grow and develop only after symbiosis with Armillaria sp. In this study, a systematic metabolomics based on non-targeted UPLC-MS method was carried out between the infected part of the separated cavity wall of the sclerotia (QR) and the uninfected part (the control group, CK) to find and identify differential metabolites. The biosynthetic pathway of characteristic steroids in sclerotia of P. umbellatus was deduced and the content of ergosterol, polyporusterone A and B in the QR and CK groups were detected with the High Performance Liquid Chromatography (HPLC). Furthermore, the expression patterns of putative genes associated with steroid biosynthesis pathway were also performed with quantitative real-time PCR. The results showed that a total of 258 metabolites originated from fungi with the fragmentation score more than 45 and high resolution mass were identified, based on UPLC-MS metabolomic analysis, and there were 118 differentially expressed metabolites (DEMs) between both groups. The metabolic pathways indicated that steroids, fatty acid and carbohydrate were active and enriched during P. umbellatus sclerotia infected by A. mellea. The content of ergosterol, polyporusterone A and B in the QR group increased by 32.2, 75.0, and 20.0%, in comparison to that of the control group. The qRT-PCR analysis showed that series of enzymes including C-8 sterol isomerase (ERG2), sterol C-24 methyltransferase (ERG6) and sterol 22-desaturase (ERG5), which played important roles in the final steps of ergosterol biosynthesis, all presented up-regulated patterns in the QR group in P. umbellatus. The comprehensive metabolomic and transcriptomic information will contribute to further study concerning the mechanisms of P. umbellatus sclerotial formation infected by A. mellea in the future.
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Affiliation(s)
- Yong-Mei Xing
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bing Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liu Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Li
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shu-Xue Yin
- Institute of Fungus Development of Liuba, Qinzheng Zhuling Development Co., Ltd., of Liuba, Hanzhong, China
| | - Shu-Chao Yin
- Institute of Fungus Development of Liuba, Qinzheng Zhuling Development Co., Ltd., of Liuba, Hanzhong, China
| | - Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shun-Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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12
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Sun H, Liu X, Pei J, Hao D, Li X, Chen D, Shen Y, Xu Z. Identification, characterisation and inhibition of
Geotrichum pseudocandidum
spoilage microbe in
Gastrodia elata
tuber. Int J Food Sci Technol 2021. [DOI: 10.1111/ijfs.15361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haiyan Sun
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Xiao Liu
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Jinjin Pei
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Danqing Hao
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Xinsheng Li
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Dejing Chen
- Key Laboratory of Life Resources of Shaanxi Province Shaanxi Key Laboratory of Resource Biology College of Biological Science and Engineering Shaanxi University of Technology Hanzhong China
| | - Yixiao Shen
- College of Food Science Shenyang Agricultural University Shenyang China
- School of Nutrition and Food Sciences Louisiana State University Baton Rouge LA USA
| | - Zhimin Xu
- School of Nutrition and Food Sciences Louisiana State University Baton Rouge LA USA
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13
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Shan T, Yin M, Wu J, Yu H, Liu M, Xu R, Wang J, Peng H, Zha L, Gui S. Comparative transcriptome analysis of tubers, stems, and flowers of Gastrodia elata Blume reveals potential genes involved in the biosynthesis of phenolics. Fitoterapia 2021; 153:104988. [PMID: 34246745 DOI: 10.1016/j.fitote.2021.104988] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
Orchidaceae, well known for its fascinating flowers, is one of the largest and most diverse families of flowering plants. There are many kinds of plants in this family; these are distributed practically globally and have high ornamental and medicinal values. Gastrodia elata Blume, a traditional Chinese medicinal herb, is a rootless and leafless achlorophyllous orchid. Phenolic compounds are considered to be the major bioactive constituents in G. elata, with antioxidant, antiangiogenic, neuroprotective, antidepressant, anxiolytic, and sedative activities. In this study, we determined the contents of six main phenolic components in tubers, stems and flowers from G. elata. Meanwhile, the transcriptomes of the tuber, stem and flower tissues of G. elata were obtained using the BGISEQ-500 platform. A total of 58.29 Gb of data and 113,067 unigenes were obtained, of which 74,820 unigenes were functionally annotated against seven public databases. Differentially expressed genes between tuber, stem and flower tissues were identified. A total of 76 DEGs encoding eight key enzymes were identified as candidate genes involved in the biosynthesis of phenolics in G. elata. For further validation, the expression levels of unigenes were measured using quantitative real-time PCR. Our results greatly enrich the transcriptomic data of G. elata and provide valuable information for the identification of candidate genes involved in the biosynthesis of secondary metabolites.
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Affiliation(s)
- Tingyu Shan
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Minzhen Yin
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Junxian Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Hanwen Yu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Mengli Liu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Rui Xu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Jutao Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Huasheng Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Chinese Academy of Medical Sciences Research Unit (No. 2019RU057), National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Liangping Zha
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China; Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei 230012, PR China; Institute of Traditional Chinese Medicine Resources, Anhui University of Chinese Medicine, Hefei 230012, China.
| | - Shuangying Gui
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei 230012, China.
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14
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Ren LY, Zhao H, Liu XL, Zong TK, Qiao M, Liu SY, Liu XY. Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata. Int J Mol Sci 2021; 22:6557. [PMID: 34207287 PMCID: PMC8235111 DOI: 10.3390/ijms22126557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 01/17/2023] Open
Abstract
Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.
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Affiliation(s)
- Li-Ying Ren
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
| | - Heng Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ling Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong-Kai Zong
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China;
| | - Min Qiao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
| | - Shu-Yan Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China;
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Xiao-Yong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (X.-L.L.)
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15
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Abstract
Species of Armillaria are distributed globally and include some of the most important pathogens of forest and ornamental trees. Some of them form large long-living clones that are considered as one of the largest organisms on earth and are capable of long-range spore-mediated transfer as well as vegetative spread by drought-resistant hyphal cords called rhizomorphs. However, the virus community infecting these species has remained unknown. In this study we used dsRNA screening and high-throughput sequencing to search for possible virus infections in a collection of Armillaria isolates representing three different species: Armillaria mellea from South Africa, A. borealis from Finland and Russia (Siberia) and A. cepistipes from Finland. Our analysis revealed the presence of both negative-sense RNA viruses and positive-sense RNA viruses, while no dsRNA viruses were detected. The viruses included putative new members of virus families Mymonaviridae, Botourmiaviridae and Virgaviridae and members of a recently discovered virus group tentatively named "ambiviruses" with ambisense bicistronic genomic organization. We demonstrated that Armillaria isolates can be cured of viruses by thermal treatment, which enables the examination of virus effects on host growth and phenotype using isogenic virus-infected and virus-free strains.
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16
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Ho LH, Lee YI, Hsieh SY, Lin IS, Wu YC, Ko HY, Klemens PA, Neuhaus HE, Chen YM, Huang TP, Yeh CH, Guo WJ. GeSUT4 mediates sucrose import at the symbiotic interface for carbon allocation of heterotrophic Gastrodia elata (Orchidaceae). PLANT, CELL & ENVIRONMENT 2021; 44:20-33. [PMID: 32583877 DOI: 10.1111/pce.13833] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
Gastrodia elata, a fully mycoheterotrophic orchid without photosynthetic ability, only grows symbiotically with the fungus Armillaria. The mechanism of carbon distribution in this mycoheterotrophy is unknown. We detected high sucrose concentrations in all stages of Gastrodia tubers, suggesting sucrose may be the major sugar transported between fungus and orchid. Thick symplasm-isolated wall interfaces in colonized and adjacent large cells implied involvement of sucrose importers. Two sucrose transporter (SUT)-like genes, GeSUT4 and GeSUT3, were identified that were highly expressed in young Armillaria-colonized tubers. Yeast complementation and isotope tracer experiments confirmed that GeSUT4 functioned as a high-affinity sucrose-specific proton-dependent importer. Plasma-membrane/tonoplast localization of GeSUT4-GFP fusions and high RNA expression of GeSUT4 in symbiotic and large cells indicated that GeSUT4 likely functions in active sucrose transport for intercellular allocation and intracellular homeostasis. Transgenic Arabidopsis overexpressing GeSUT4 had larger leaves but were sensitive to excess sucrose and roots were colonized with fewer mutualistic Bacillus, supporting the role of GeSUT4 in regulating sugar allocation. This is not only the first documented carbon import system in a mycoheterotrophic interaction but also highlights the evolutionary importance of sucrose transporters for regulation of carbon flow in all types of plant-microbe interactions.
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Affiliation(s)
- Li-Hsuan Ho
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Yung-I Lee
- Biology Department, National Museum of Natural Science, Taichung, Taiwan, Republic of China
| | - Shu-Ying Hsieh
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - I-Shiuan Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Yun-Chien Wu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Han-Yu Ko
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Patrick A Klemens
- Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Yi-Min Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
| | - Tzu-Pi Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan, Republic of China
| | - Chih-Hsin Yeh
- Taoyuan District Agricultural Research and Extension Station, Council of Agriculture, Taoyuan, Taiwan, Republic of China
| | - Woei-Jiun Guo
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, Taiwan, Republic of China
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17
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Yin H, Hu T, Zhuang Y, Liu T. Metabolic engineering of Saccharomyces cerevisiae for high-level production of gastrodin from glucose. Microb Cell Fact 2020; 19:218. [PMID: 33243241 PMCID: PMC7690157 DOI: 10.1186/s12934-020-01476-0] [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: 08/08/2020] [Accepted: 11/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The natural phenolic glycoside gastrodin is the major bioactive ingredient in the well-known Chinese herb Tianma and is widely used as a neuroprotective medicine in the clinic. Microbial production from sustainable resources is a promising method to replace plant extraction and chemical synthesis which were currently used in industrial gastrodin production. Saccharomyces cerevisiae is considered as an attractive host to produce natural plant products used in the food and pharmaceutical fields. In this work, we intended to explore the potential of S. cerevisiae as the host for high-level production of gastrodin from glucose. RESULTS Here, we first identified the plant-derived glucosyltransferase AsUGT to convert 4-hydroxybenzyl alcohol to gastrodin with high catalytic efficiency in yeast. Then, we engineered de novo production of gastrodin by overexpressing codon-optimized AsUGTsyn, the carboxylic acid reductase gene CARsyn from Nocardia species, the phosphopantetheinyl transferase gene PPTcg-1syn from Corynebacterium glutamicum, the chorismate pyruvate-lyase gene UbiCsyn from Escherichia coli, and the mutant ARO4K229L. Finally, we achieved an improved product titer by a chromosomal multiple-copy integration strategy and enhancement of metabolic flux toward the aglycon 4-hydroxybenzyl alcohol. The best optimized strain produced 2.1 g/L gastrodin in mineral medium with glucose as the sole carbon source by flask fermentation, which was 175 times higher than that of the original gastrodin-producing strain. CONCLUSIONS The de novo high-level production of gastrodin was first achieved. Instead of chemical synthesis or plants extraction, our work provides an alternative strategy for the industrial production of gastrodin by microbial fermentation from a sustainable resource.
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Affiliation(s)
- Hua Yin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tiandong Hu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yibin Zhuang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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18
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Yang J, Xiao Q, Xu J, Da L, Guo L, Huang L, Liu Y, Xu W, Su Z, Yang S, Pan Q, Jiang W, Zhou T. GelFAP: Gene Functional Analysis Platform for Gastrodia elata. FRONTIERS IN PLANT SCIENCE 2020; 11:563237. [PMID: 33193491 PMCID: PMC7642037 DOI: 10.3389/fpls.2020.563237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/16/2020] [Indexed: 06/11/2023]
Abstract
Gastrodia elata, also named Tianma, is a valuable traditional Chinese herbal medicine. It has numerous important pharmacological roles such as in sedation and lowering blood pressure and as anticonvulsant and anti-aging, and it also has effects on the immune and cardiovascular systems. The whole genome sequencing of G. elata has been completed in recent years, which provides a strong support for the construction of the G. elata gene functional analysis platform. Therefore, in our research, we collected and processed 39 transcriptome data of G. elata and constructed the G. elata gene co-expression networks, then we identified functional modules by the weighted correlation network analysis (WGCNA) package. Furthermore, gene families of G. elata were identified by tools including HMMER, iTAK, PfamScan, and InParanoid. Finally, we constructed a gene functional analysis platform for G. elata . In our platform, we introduced functional analysis tools such as BLAST, gene set enrichment analysis (GSEA), and cis-elements (motif) enrichment analysis tool. In addition, we analyzed the co-expression relationship of genes which might participate in the biosynthesis of gastrodin and predicted 19 mannose-binding lectin antifungal proteins of G. elata. We also introduced the usage of the G. elata gene function analysis platform (GelFAP) by analyzing CYP51G1 and GFAP4 genes. Our platform GelFAP may help researchers to explore the gene function of G. elata and make novel discoveries about key genes involved in the biological processes of gastrodin.
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Affiliation(s)
- Jiaotong Yang
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qiaoqiao Xiao
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jiao Xu
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Lingling Da
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yue Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Shiping Yang
- College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qi Pan
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Weike Jiang
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Tao Zhou
- Source Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
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19
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Wang Y, Shahid MQ, Ghouri F, Baloch FS. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 2020; 58:914-934. [DOI: 10.1007/s10528-020-09983-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
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20
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Draft genomic sequence of Armillaria gallica 012m: insights into its symbiotic relationship with Gastrodia elata. Braz J Microbiol 2020; 51:1539-1552. [PMID: 32572836 DOI: 10.1007/s42770-020-00317-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 06/09/2020] [Indexed: 10/24/2022] Open
Abstract
Armillaria species (Basidiomycota, Physalacriaceae) are well known as plant pathogens related to serious root rot disease on various trees in forests and plantations. Interestingly, some Armillaria species are essential symbionts of the rare Chinese medicinal herb Gastrodia elata, a rootless and leafless orchid used for over 2000 years. In this work, an 87.3-M draft genome of Armillaria gallica 012m strain, which was symbiotic with G. elata, was assembled. The genome includes approximately 23.6% repetitive sequences and encodes 26,261 predicted genes. In comparison with other four genomes of Armillaria, the following gene families related to pathogenicity/saprophytic phase, including cytochrome P450 monooxygenases, carbohydrate-active enzyme AA3, and hydrophobins, were significantly contracted in A. gallica 012m. These characteristics may be beneficial for G. elata to get less injuries. The genome-guided analysis of differential expression between rhizomorph (RH) and vegetative mycelium (VM) showed that a total of 2549 genes were differentially expressed, including 632 downregulated genes and 1917 upregulated genes. In the RH, most differentially expressed genes (DEGs) related to pathogenicity were significantly upregulated. To further elucidate gene function, Gene Ontology enrichment analysis showed that the upregulated DEGs significantly grouped into monooxygenase activity, hydrolase activity, glucosidase activity, extracellular region, fungal cell wall, response to xenobiotic stimulus, response to toxic substance, etc. These phenomena indicate that RH had better infection ability than VM. The infection ability of RH may be beneficial for G. elata to obtain nutrition, because the rhizomorph constantly infected the nutritional stems of G. elata and formed the hyphae that can be digested by G. elata. These results clarified the characteristics of A. gallica 012m and the reason why the strain 012m can establish a symbiotic relationship with G. elata in some extent from the perspective of genomics.
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21
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Ramya M, Jang S, An HR, Lee SY, Park PM, Park PH. Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation. Int J Mol Sci 2020; 21:ijms21031160. [PMID: 32050562 PMCID: PMC7037033 DOI: 10.3390/ijms21031160] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea;
| | - Hye-Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Su-Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pil-Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul 08826, Korea
- Correspondence: or ; Tel.: +82-10-4507-8321 or +82-63-238-6842; Fax: +82-63-238-6805
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22
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Shan C, Wang C, Zhang S, Shi Y, Ma K, Yang Q, Wu J. Transcriptome analysis of Clinopodium gracile (Benth.) Matsum and identification of genes related to Triterpenoid Saponin biosynthesis. BMC Genomics 2020; 21:49. [PMID: 31941462 PMCID: PMC6964110 DOI: 10.1186/s12864-020-6454-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/07/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Clinopodium gracile (Benth.) Matsum (C. gracile) is an annual herb with pharmacological properties effective in the treatment of various diseases, including hepatic carcinoma. Triterpenoid saponins are crucial bioactive compounds in C. gracile. However, the molecular understanding of the triterpenoid saponin biosynthesis pathway remains unclear. RESULTS In this study, we performed RNA sequencing (RNA-Seq) analysis of the flowers, leaves, roots, and stems of C. gracile plants using the BGISEQ-500 platform. The assembly of transcripts from all four types of tissues generated 128,856 unigenes, of which 99,020 were mapped to several public databases for functional annotation. Differentially expressed genes (DEGs) were identified via the comparison of gene expression levels between leaves and other tissues (flowers, roots, and stems). Multiple genes encoding pivotal enzymes, such as squalene synthase (SS), or transcription factors (TFs) related to triterpenoid saponin biosynthesis were identified and further analyzed. The expression levels of unigenes encoding important enzymes were verified by quantitative real-time PCR (qRT-PCR). Different chemical constituents of triterpenoid saponins were identified by Ultra-Performance Liquid Chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). CONCLUSIONS Our results greatly extend the public transcriptome dataset of C. gracile and provide valuable information for the identification of candidate genes involved in the biosynthesis of triterpenoid saponins and other important secondary metabolites.
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Affiliation(s)
- Chunmiao Shan
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Chenkai Wang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Shengxiang Zhang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Yuanyuan Shi
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China
| | - Kelong Ma
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China.,Clinical College of Integrated Traditional Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Qingshan Yang
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China
| | - Jiawen Wu
- Anhui University of Chinese Medicine and Anhui Academy of Chinese Medicine, Hefei, 230038, China. .,Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230038, China. .,Synergetic Innovation Center of Anhui Authentic Chinese Medicine Quality Improvement, Hefei, 230012, China.
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23
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Favre-Godal Q, Gourguillon L, Lordel-Madeleine S, Gindro K, Choisy P. Orchids and their mycorrhizal fungi: an insufficiently explored relationship. MYCORRHIZA 2020; 30:5-22. [PMID: 31982950 DOI: 10.1007/s00572-020-00934-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 01/17/2020] [Indexed: 05/03/2023]
Abstract
Orchids are associated with diverse fungal taxa, including nonmycorrhizal endophytic fungi as well as mycorrhizal fungi. The orchid mycorrhizal (OM) symbiosis is an excellent model for investigating the biological interactions between plants and fungi due to their high dependency on these symbionts for growth and survival. To capture the complexity of OM interactions, significant genomic, numerous transcriptomic, and proteomic studies have been performed, unraveling partly the role of each partner. On the other hand, several papers studied the bioactive metabolites from each partner but rarely interpreted their significance in this symbiotic relationship. In this review, we focus from a biochemical viewpoint on the OM dynamics and its molecular interactions. The ecological functions of OM in plant development and stress resistance are described first, summarizing recent literature. Secondly, because only few studies have specifically looked on OM molecular interactions, the signaling pathways and compounds allowing the establishment/maintenance of mycorrhizal association involved in arbuscular mycorrhiza (AM) are discussed in parallel with OM. Based on mechanistic similarities between OM and AM, and recent findings on orchids' endophytes, a putative model representing the different molecular strategies that OM fungi might employ to establish this association is proposed. It is hypothesized here that (i) orchids would excrete plant molecule signals such as strigolactones and flavonoids but also other secondary metabolites; (ii) in response, OM fungi would secrete mycorrhizal factors (Myc factors) or similar compounds to activate the common symbiosis genes (CSGs); (iii) overcome the defense mechanism by evasion of the pathogen-associated molecular patterns (PAMPs)-triggered immunity and by secretion of effectors such as small inhibitor proteins; and (iv) finally, secrete phytohormones to help the colonization or disrupt the crosstalk of plant defense phytohormones. To challenge this putative model, targeted and untargeted metabolomics studies with special attention to each partner's contribution are finally encouraged and some technical approaches are proposed.
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Affiliation(s)
- Quentin Favre-Godal
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France.
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France.
| | - Lorène Gourguillon
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
| | - Sonia Lordel-Madeleine
- CNRS, IPHC UMR 7178, Chimie analytique des molécules bioactives et pharmacognosie, Université de Strasbourg, F-67000, Strasbourg, France
| | - Katia Gindro
- Agroscope, Swiss Federal Research Station, Plant Protection, 60 Route de Duiller, PO Box, 1260, Nyon, Switzerland
| | - Patrick Choisy
- LVMH recherche, Innovation Matériaux Naturels et Développement Durable, 185 avenue de Verdun, 45800, St Jean de Braye, France
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24
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Wang Y, Shahid MQ, Ghouri F, Ercişli S, Baloch FS. Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. 3 Biotech 2019; 9:292. [PMID: 31321198 DOI: 10.1007/s13205-019-1823-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/23/2019] [Indexed: 01/28/2023] Open
Abstract
Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.
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25
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Luo C, Wang ZQ, Liu X, Zhao L, Zhou X, Xie Y. Identification and Analysis of Potential Genes Regulated by an Alphasatellite (TYLCCNA) that Contribute to Host Resistance against Tomato Yellow Leaf Curl China Virus and Its Betasatellite (TYLCCNV/TYLCCNB) Infection in Nicotiana benthamiana. Viruses 2019; 11:E442. [PMID: 31096636 PMCID: PMC6563268 DOI: 10.3390/v11050442] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 05/12/2019] [Accepted: 05/14/2019] [Indexed: 01/13/2023] Open
Abstract
Recently, begomovirus/betasatellite disease complexes were found to be associated with alphasatellites, and their presence modulated disease symptoms and/or viral DNA accumulation in infected plants. However, the biological functions of alphasatellites during begomovirus/betasatellite infections remain unclear. Tomato yellow leaf curl China virus (TYLCCNV) associated with a betasatellite (TYLCCNB) is a widespread monopartite begomovirus in China. In the Yunnan province of China, the TYLCCNV/TYLCCNB disease complex is found in association with an alphasatellite (TYLCCNA). In this study, in order to explain the mechanisms underlying TYLCCNV/TYLCCNB infection and reductions in viral DNA accumulation caused by TYLCCNA, we analyzed the transcriptome profiles of Nicotiana benthamiana seedlings challenged by TYLCCNV/TYLCCNB or TYLCCNV/TYLCCNB/TYLCCNA using RNA sequencing. In total, 2272 and 1207 differentially expressed genes (DEGs) were identified to respond to TYLCCNV/TYLCCNB and TYLCCNV/TYLCCNB/TYLCCNA infections, respectively. Compared with the DEGs in the TYLCCNV/TYLCCNB-infected N. benthamiana seedlings, the number of DEGs in plants co-infected with TYLCCNV/TYLCCNB + TYLCCNA was significantly reduced. Additionally, 36 DEGs were identified to be regulated by TYLCCNA, six of which were further analyzed using the virus-induced gene silencing (VIGS) approach. Silencing of these six TYLCCNA responsive DEGs caused more severe disease symptoms and higher viral DNA accumulation levels, suggesting that TYLCCNA responsive DEGs may attenuate TYLCCNV/TYLCCNB infection.
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Affiliation(s)
- Chaohu Luo
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Zhan Qi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China.
| | - Xianan Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Liling Zhao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
- Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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26
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Li HT, Zhou H, Duan RT, Li HY, Tang LH, Yang XQ, Yang YB, Ding ZT. Inducing Secondary Metabolite Production by Co-culture of the Endophytic Fungus Phoma sp. and the Symbiotic Fungus Armillaria sp. JOURNAL OF NATURAL PRODUCTS 2019; 82:1009-1013. [PMID: 30785282 DOI: 10.1021/acs.jnatprod.8b00685] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Co-culturing the endophytic fungus Phoma sp. YUD17001 from Gastrodia elata with Armillaria sp. in liquid nutrient medium resulted in the production of five new secondary metabolites, including two phenolic compounds, phexandiols A and B (1 and 2), three aliphatic ester derivatives, phomesters A-C (3-5), and a known fatty acid (6). The structures and absolute configurations of these compounds were elucidated by the interpretation of data from detailed spectroscopic analysis, Mosher's method, and electronic circular dichroism spectra, together with consideration of the biogenetic origins. None of the five new compounds were detected in single-strain cultures under identical fermentation conditions. The results of this work indicated that the production of 1-5 involved a complicated interaction process. None of the new compounds possessed significant cytotoxicity or antimicrobial activities.
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Affiliation(s)
- Hong-Tao Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Rong-Ting Duan
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Hong-Yu Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Lin-Huan Tang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Xue-Qiong Yang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Ya-Bin Yang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Zhong-Tao Ding
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
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27
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New Insights into the Symbiotic Relationship between Orchids and Fungi. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9030585] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mycorrhizas play an important role in plant growth and development. In mycorrhizal symbioses, fungi supply soil mineral nutrients, such as nitrogen and phosphorus, to their host plants in exchange for carbon resources. Plants gain as much as 80% of mineral nutrient requirements from mycorrhizal fungi, which form associations with the roots of over 90% of all plant species. Orchid seeds lack endosperms and contain very limited storage reserves. Therefore, the symbiosis with mycorrhizal fungi that form endomycorrhizas is essential for orchid seed germination and protocorm development under natural conditions. The rapid advancement of next-generation sequencing contributes to identifying the orchid and fungal genes involved in the orchid mycorrhizal symbiosis and unraveling the molecular mechanisms regulating the symbiosis. We aim to update and summarize the current understanding of the mechanisms on orchid-fungus symbiosis, and the main focus will be on the nutrient exchange between orchids and their fungal partners.
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28
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Chang CC, Cheng JJ, Lee IJ, Lu MK. Purification, structural elucidation, and anti-inflammatory activity of xylosyl galactofucan from Armillaria mellea. Int J Biol Macromol 2018; 114:584-591. [DOI: 10.1016/j.ijbiomac.2018.02.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/02/2018] [Accepted: 02/06/2018] [Indexed: 01/22/2023]
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29
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Yuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, Wang D, Lai C, Xu W, Huang J, Zha L, Liu D, Ma X, Wang L, Zhou M, Jiang Z, Meng H, Peng H, Liang Y, Li R, Jiang C, Zhao Y, Nan T, Jin Y, Zhan Z, Yang J, Jiang W, Huang L. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun 2018; 9:1615. [PMID: 29691383 PMCID: PMC5915607 DOI: 10.1038/s41467-018-03423-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 02/12/2018] [Indexed: 12/22/2022] Open
Abstract
We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.
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Affiliation(s)
- Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xin Wang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Deyi Wang
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Changjiangsheng Lai
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Jingwen Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Liangping Zha
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Dahui Liu
- Hubei University of Chinese Medicine, 430065, Wuhan, China
| | - Xiao Ma
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Li Wang
- Institute of Medicinal Botany, Yunnan Academy of Agricultural Sciences, 650223, Kunming, China
| | - Menyan Zhou
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Hubiao Meng
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huasheng Peng
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Yuting Liang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Tiegui Nan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yan Jin
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhilai Zhan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Jian Yang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
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30
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Yuan Y, Jin X, Liu J, Zhao X, Zhou J, Wang X, Wang D, Lai C, Xu W, Huang J, Zha L, Liu D, Ma X, Wang L, Zhou M, Jiang Z, Meng H, Peng H, Liang Y, Li R, Jiang C, Zhao Y, Nan T, Jin Y, Zhan Z, Yang J, Jiang W, Huang L. The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. Nat Commun 2018. [PMID: 29691383 DOI: 10.1038/s41467-018-03423-3425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
We present the 1.06 Gb sequenced genome of Gastrodia elata, an obligate mycoheterotrophic plant, which contains 18,969 protein-coding genes. Many genes conserved in other plant species have been deleted from the G. elata genome, including most of those for photosynthesis. Additional evidence of the influence of genome plasticity in the adaptation of this mycoheterotrophic lifestyle is evident in the large number of gene families that are expanded in G. elata, including glycoside hydrolases and urease that likely facilitate the digestion of hyphae are expanded, as are genes associated with strigolactone signaling, and ATPases that may contribute to the atypical energy metabolism. We also find that the plastid genome of G. elata is markedly smaller than that of green plant species while its mitochondrial genome is one of the largest observed to date. Our report establishes a foundation for studying adaptation to a mycoheterotrophic lifestyle.
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Affiliation(s)
- Yuan Yuan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
| | - Xiaohua Jin
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Junhui Zhou
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Xin Wang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Deyi Wang
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Changjiangsheng Lai
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wei Xu
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Jingwen Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Liangping Zha
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Dahui Liu
- Hubei University of Chinese Medicine, 430065, Wuhan, China
| | - Xiao Ma
- Institute of Botany, Chinese Academy of Sciences (IBCAS), 100093, Beijing, China
| | - Li Wang
- Institute of Medicinal Botany, Yunnan Academy of Agricultural Sciences, 650223, Kunming, China
| | - Menyan Zhou
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Hubiao Meng
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huasheng Peng
- Anhui University of Chinese Medicine, 230012, Hefei, China
| | - Yuting Liang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Ruiqiang Li
- Novogene Bioinformatics Institute, 100083, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yuyang Zhao
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Tiegui Nan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Yan Jin
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Zhilai Zhan
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Jian Yang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083, Beijing, China.
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, Chinese Academy of Chinese Medical Sciences, 100700, Beijing, China.
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Zeng X, Li Y, Ling H, Chen J, Guo S. Revealing proteins associated with symbiotic germination of Gastrodia elata by proteomic analysis. BOTANICAL STUDIES 2018; 59:8. [PMID: 29511914 PMCID: PMC5840113 DOI: 10.1186/s40529-018-0224-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 02/28/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Gastrodia elata, a mycoheterotrophic orchid, is a well-known medicinal herb. In nature, the seed germination of G. elata requires proper fungal association, because of the absence of endosperm. To germinate successfully, G. elata obtains nutrition from mycorrhizal fungi such as Mycena. However, Mycena is not able to supply nutrition for the further development and enlargement of protocorms into tubers, flowering and fruit setting of G. elata. To date, current genomic studies on this topic are limited. Here we used the proteomic approach to explore changes in G. elata at different stages of symbiotic germination. RESULTS Using mass spectrometry, 3787 unique proteins were identified, of which 599 were classified as differentially accumulated proteins. Most of these differentially accumulated proteins were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Among them, the defense genes (e.g., pathogenesis-/wound-related proteins, peroxidases, and serine/threonine-protein kinase) were highly expressed in late-stage protocorms, suggesting that fungal colonization triggered the significant defense responses of G. elata. CONCLUSIONS The present study indicated the metabolic change and defensive reaction could disrupt the balance between Mycena and G. elata during mycorrhizal symbiotic germination.
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Affiliation(s)
- Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Yuanyuan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Juan Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193 People’s Republic of China
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Tsai WC, Dievart A, Hsu CC, Hsiao YY, Chiou SY, Huang H, Chen HH. Post genomics era for orchid research. BOTANICAL STUDIES 2017; 58:61. [PMID: 29234904 PMCID: PMC5727007 DOI: 10.1186/s40529-017-0213-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/01/2017] [Indexed: 05/05/2023]
Abstract
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era. These include the orchid genome evolution, genome mapping (genome-wide association analysis, genetic map, physical map), comparative genomics (especially receptor-like kinase and terpene synthase), secondary metabolomics, and genome editing.
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Affiliation(s)
- Wen-Chieh Tsai
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Anne Dievart
- CIRAD, UMR AGAP, TA A 108/03, Avenue Agropolis, 34398 Montpellier, France
- Present Address: School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Life Sciences Building, Room 3-117, Shanghai, 200240 People’s Republic of China
| | - Chia-Chi Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Shang-Yi Chiou
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hsin Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Zeng X, Li Y, Ling H, Liu S, Liu M, Chen J, Guo S. Transcriptomic analyses reveal clathrin-mediated endocytosis involved in symbiotic seed germination of Gastrodia elata. BOTANICAL STUDIES 2017; 58:31. [PMID: 28741080 PMCID: PMC5524656 DOI: 10.1186/s40529-017-0185-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 07/10/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Gastrodia elata is a well-known medicinal orchid. In nature, the germination rate of G. elata is extremely poor, because there is no endosperm within the mature seed. It is crucial for G. elata to obtain nutrition from mycorrhizal fungi (Mycena) at the early-stage of germination. After germination, the seed gives rise to a protocorm. However, there are no "omic" studies on understanding the interaction between Gastrodia and Mycena. Here, we used transcriptomic approaches to explore changes in seed germination of G. elata. RESULTS Based on RNA-Seq, a total of ~221 million clean reads were assembled denovo into 139,756 unigenes, including 42,140 unigenes that were annotated in public databases. Meanwhile, 1750 unigenes were identified as differentially expressed genes. Most of these differentially expressed genes were putatively involved in energy metabolism, plant defense, molecular signaling, and secondary metabolism. Additionally, numerous genes involved in clathrin-mediated endocytosis were identified from our data. Most of these genes (e.g., clathrin, adaptor protein, dynamin, HSC70) were basally expressed in seeds and highly expressed in protocorms. CONCLUSIONS Our data suggested that clathrin-mediated endocytosis could play important roles in symbiotic seed germination of G. elata with Mycena infections.
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Affiliation(s)
- Xu Zeng
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Yuanyuan Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Hong Ling
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Sisi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Mengmeng Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Juan Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193 People’s Republic of China
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Chen J, Liu SS, Kohler A, Yan B, Luo HM, Chen XM, Guo SX. iTRAQ and RNA-Seq Analyses Provide New Insights into Regulation Mechanism of Symbiotic Germination of Dendrobium officinale Seeds (Orchidaceae). J Proteome Res 2017; 16:2174-2187. [DOI: 10.1021/acs.jproteome.6b00999] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Juan Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Si Si Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Annegret Kohler
- UMR
1136 INRA/Université de Lorraine, Interactions Arbres/Micro-organismes,
INRA, Institut National de la Recherche Agronomique, Centre INRA de Nancy, Champenoux 54280, France
| | - Bo Yan
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Hong Mei Luo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Xiao Mei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
| | - Shun Xing Guo
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, P. R. China
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Wang F, Zhi J, Zhang Z, Wang L, Suo Y, Xie C, Li M, Zhang B, Du J, Gu L, Sun H. Transcriptome Analysis of Salicylic Acid Treatment in Rehmannia glutinosa Hairy Roots Using RNA-seq Technique for Identification of Genes Involved in Acteoside Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:787. [PMID: 28567046 PMCID: PMC5434160 DOI: 10.3389/fpls.2017.00787] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/27/2017] [Indexed: 05/04/2023]
Abstract
Rehmannia glutinosa is a common bulk medicinal material that has been widely used in China due to its active ingredients. Acteoside, one of the ingredients, has antioxidant, antinephritic, anti-inflammatory, hepatoprotective, immunomodulatory, and neuroprotective effects, is usually selected as a quality-control component for R. glutinosa herb in the Chinese Pharmacopeia. The acteoside biosynthesis pathway in R. glutinosa has not yet been clearly established. Herein, we describe the establishment of a genetic transformation system for R. glutinosa mediated by Agrobacterium rhizogenes. We screened the optimal elicitors that markedly increased acteoside accumulation in R. glutinosa hairy roots. We found that acteoside accumulation dramatically increased with the addition of salicylic acid (SA); the optimal SA dose was 25 μmol/L for hairy roots. RNA-seq was applied to analyze the transcriptomic changes in hairy roots treated with SA for 24 h in comparison with an untreated control. A total of 3,716, 4,018, and 2,715 differentially expressed transcripts (DETs) were identified in 0 h-vs.-12 h, 0 h-vs.-24 h, and 12 h-vs.-24 h libraries, respectively. KEGG pathway-based analysis revealed that 127 DETs were enriched in "phenylpropanoid biosynthesis." Of 219 putative unigenes involved in acteoside biosynthesis, 54 were found to be up-regulated at at least one of the time points after SA treatment. Selected candidate genes were analyzed by quantitative real-time PCR (qRT-PCR) in hairy roots with SA, methyl jasmonate (MeJA), AgNO3 (Ag+), and putrescine (Put) treatment. All genes investigated were up-regulated by SA treatment, and most candidate genes were weakly increased by MeJA to some degree. Furthermore, transcription abundance of eight candidate genes in tuberous roots of the high-acteoside-content (HA) cultivar QH were higher than those of the low-acteoside-content (LA) cultivar Wen 85-5. These results will pave the way for understanding the molecular basis of acteoside biosynthesis in R. glutinosa, and can serve as a basis for future validation studies.
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Affiliation(s)
- Fengqing Wang
- College of Agronomy, Henan Agricultural UniversityZhengzhou, China
- *Correspondence: Fengqing Wang
| | - Jingyu Zhi
- College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Zhongyi Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lina Wang
- School of Medicine, Henan University of Traditional Chinese MedicineZhengzhou, China
| | - Yanfei Suo
- College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Caixia Xie
- School of Medicine, Henan University of Traditional Chinese MedicineZhengzhou, China
| | - Mingjie Li
- College of Crop Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Bao Zhang
- College of Crop Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jiafang Du
- College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Li Gu
- College of Crop Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Hongzheng Sun
- College of Agronomy, Henan Agricultural UniversityZhengzhou, China
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