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Gao S, Peng J, Rong M, Liu Y, Xu Y, Wei J. Screening and validation of reference genes in Dracaena cochinchinensis using quantitative real-time PCR. Sci Rep 2024; 14:6165. [PMID: 38486003 PMCID: PMC10940652 DOI: 10.1038/s41598-024-52754-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/23/2024] [Indexed: 03/18/2024] Open
Abstract
Dragon's blood, the red resin derived from the wounded Dracaena, is a precious traditional medicine used by different culture. Dracaena cochinchinensis is one of the main species of Dracaena, and is the endangered medicinal plants in China. The vulnerable status severely limits the medicinal value and wide application of dragon's blood. Therefore, it's essential to analyze the mechanisms that form dragon's blood in order to increase artificial production. To clarify the mechanisms forming dragon's blood, understanding gene expression in the flavonoid biosynthesis pathway is the foundation. However, reference genes of D. cochinchinensis haven't been analyzed. In this study, expression profiles of seven commonly used housekeeping genes (Actin, α-EF, UBC, β-tubulin, 18S, GAPDH, His) were evaluated by using quantitative real-time PCR combined with the algorithms geNorm, NormFinder, BestKeeper, and RefFinder. On the basis of overall stability ranking, the best reference genes were the combinations β-tubulin +UBC for wounded stems and α-EF +18S + Actin for different organs. Reliability of the recommended reference genes was validated by normalizing relative expression of two key enzyme genes PAL1 and CHI1 in the flavonoid biosynthesis pathway. The results provide a foundation to study gene expression in future research on D. cochinchinensis or other Dracaena.
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Affiliation(s)
- Shixi Gao
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junxiang Peng
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mei Rong
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Liu
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanhong Xu
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jianhe Wei
- Key Laboratory of Bioactive Substances and Rescoures Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Hainan Procincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Hainan, China.
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Liao G, Mi C, Yang L, Zhang H, Ding X, Cai M, Wang H, Mei W, Dai H, Tang X. p-Quinone Methide-Mediated Nonenzymatic Formation of Chalcane-Containing Dimers in Dragon's Blood. Org Lett 2022; 24:9275-9280. [PMID: 36512336 DOI: 10.1021/acs.orglett.2c03850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Chalcane-containing dimers are major compounds identified from dragon's blood, the red resin that accumulates in Dracaena trees after injury. The key step for the formation of these dimers was a p-quinone methide (p-QM, 3) mediated nonenzymatic Michael addition. Compound 3 is derived from the spontaneous dehydration of chalcane alcohol-M274 (2). Two dihydroflavonol-4-reductases, discovered in D. cambodiana, reduce dihydrochalcone-M272 (7) to 2. Moreover, the application potential of p-QMs was demonstrated using a 3-like p-QM to synthesize diverse dimeric derivatives.
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Affiliation(s)
- Ge Liao
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.,Institute of Molecular Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Chengneng Mi
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.,College of Pharmacy, Xiangnan University, Chenzhou 423000, China
| | - Li Yang
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haili Zhang
- Institute of Molecular Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Xupo Ding
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Mingwei Cai
- Institute of Molecular Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hao Wang
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Wenli Mei
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haofu Dai
- Hainan Key Laboratory for Research and Development of Natural Products from Li Folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xiaoyu Tang
- Institute of Molecular Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
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Transcriptomics and Metabolomics Analyses Reveal Defensive Responses and Flavonoid Biosynthesis of Dracaena cochinchinensis (Lour.) S. C. Chen under Wound Stress in Natural Conditions. Molecules 2022; 27:molecules27144514. [PMID: 35889387 PMCID: PMC9320494 DOI: 10.3390/molecules27144514] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/09/2022] [Accepted: 07/09/2022] [Indexed: 12/27/2022] Open
Abstract
Dracaena cochinchinensis has special defensive reactions against wound stress. Under wound stress, D. cochinchinensis generates a resin that is an important medicine known as dragon’s blood. However, the molecular mechanism underlying the defensive reactions is unclear. Metabolomics and transcriptomics analyses were performed on stems of D. cochinchinensis at different timepoints from the short term to the long term after wounding. According to the 378 identified compounds, wound-induced secondary metabolic processes exhibited three-phase characteristics: short term (0–5 days), middle term (10 days–3 months), and long term (6–17 months). The wound-induced transcriptome profile exhibited characteristics of four stages: within 24 h, 1–5 days, 10–30 days, and long term. The metabolic regulation in response to wound stress mainly involved the TCA cycle, glycolysis, starch and sucrose metabolism, phenylalanine biosynthesis, and flavonoid biosynthesis, along with some signal transduction pathways, which were all well connected. Flavonoid biosynthesis and modification were the main reactions against wound stress, mainly comprising 109 flavonoid metabolites and 93 wound-induced genes. A group of 21 genes encoding CHS, CHI, DFR, PPO, OMT, LAR, GST, and MYBs were closely related to loureirin B and loureirin C. Wound-induced responses at the metabolome and transcriptome level exhibited phase characteristics. Complex responses containing primary metabolism and flavonoid biosynthesis are involved in the defense mechanism against wound stress in natural conditions, and flavonoid biosynthesis and modification are the main strategies of D. cochinchinensis in the long-term responses to wound stress.
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Ahmad S, Gao J, Wei Y, Lu C, Zhu G, Yang F. The Transcriptome Profiling of Flavonoids and Bibenzyls Reveals Medicinal Importance of Rare Orchid Arundina graminifolia. FRONTIERS IN PLANT SCIENCE 2022; 13:923000. [PMID: 35812923 PMCID: PMC9260279 DOI: 10.3389/fpls.2022.923000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Orchids are very important flowering plants that spend long juvenile phases before flowering. Along with aesthetic importance, they are rich sources of medicinal components. However, their long reproductive cycle is the major hurdle to study the medicinal efficacy. Arundina graminifolia is a rare orchid that grows fast, unlike other orchids, and this characteristic makes it an ideal plant to study the medicinal enrichment of orchids. Therefore, this study presents the identification of important medicinal components in various parts of A. graminifolia. Transcriptome analysis was performed for five stages (FD1-FD5) of flower development and four tissue types (mature flower, silique, root, and leaf) to ascertain genetic regulators of flavonoids and bibenzyls. Most of the genes showed the highest expression in roots as compared with other tissues. Weighted gene coexpression network analysis (WGCNA) was performed to identify the coexpression modules and the candidate genes involving biosynthesis pathways of these chemicals. MEyellow module contained the highly coexpressed genes. Moreover, the concentrations of phenylpropanoid, bibenzyls, and flavone were ascertained through high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Phenylpropanoid and bibenzyl were comparatively high in the leaf, while flavone showed a high concentration in the stem. The selected candidate genes [bibenzyl biosynthesis (BIBSY212), CYP84A1, CYP73A4, 4CLL7, UGT88B1, UGT73C3, anthocyanin synthase (ANS), phenylalanine ammonia-lyase (PAL), flavanone synthase FLS, and CHS8] were validated through quantitative real-time PCR (qRT-PCR). Most of these genes showed high expression in leaf and root as compared with other tissue. Therefore, the presence of bibenzyls and flavonoids in different parts of A. graminifolia and their molecular regulators can provide a quick source to decipher the medicinal efficacy of orchids.
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Affiliation(s)
- Sagheer Ahmad
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jie Gao
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yonglu Wei
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chuqiao Lu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Genfa Zhu
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Fengxi Yang
- Guangdong Key Laboratory of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Gichuki DK, Li Q, Hou Y, Liu Y, Ma M, Zhou H, Xu C, Zhu Z, Wang L, Musila FM, Wang Q, Xin H. Characterization of Flavonoids and Transcripts Involved in Their Biosynthesis in Different Organs of Cissus rotundifolia Lam. Metabolites 2021; 11:metabo11110741. [PMID: 34822399 PMCID: PMC8621200 DOI: 10.3390/metabo11110741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Cissus rotundifolia Lam. is used as a medicinal herb and vegetable. Flavonoids are the major components for the therapeutic effects. However, flavonoids constituents and expression profiles of related genes in C. rotundifolia organs are unknown. Colorimetric assay showed the highest flavonoid concentration in roots compared to the stem and leaf. Widely target-based metabolome analysis allowed tentative identification of 199 compounds in three organs. Flavonols and flavones were the dominant flavonoids subclasses. Among the metabolites, 171 were common in the three organs. Unique accumulation profile was observed in the root while the stem and leaf exhibited relatively similar patterns. In the root, six unique compounds (jaceosidin, licoagrochalcone D, 8-prenylkaempferol, hesperetin 7-O-(6″malonyl) glucoside, aureusidin, apigenin-4′-O-rhamnoside) that are used for medicinal purposes were detected. In total, 18,427 expressed genes were identified from transcriptome of the three organs covering about 60% of annotated genes in C. rotundifolia genome. Fourteen gene families, including 52 members involved in the main pathway of flavonoids biosynthesis, were identified. Their expression could be found in at least one organ. Most of the genes were highly expressed in roots compared to other organs, coinciding with the metabolites profile. The findings provide fundamental data for exploration of metabolites biosynthesis in C. rotundifolia and diversification of parts used for medicinal purposes.
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Affiliation(s)
- Duncan Kiragu Gichuki
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyun Li
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujun Hou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanshuang Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengxue Ma
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Huimin Zhou
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Xu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhenfei Zhu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Wang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Fredrick Mutie Musila
- School of Biological and Life Sciences, Technical University of Kenya, Nairobi 52428-00200, Kenya;
| | - Qingfeng Wang
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Haiping Xin
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; (D.K.G.); (Q.L.); (Y.H.); (Y.L.); (M.M.); (H.Z.); (C.X.); (Z.Z.); (L.W.); (Q.W.)
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- Correspondence: ; Tel.: +86-27-87700880
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Sun HF, Song MF, Zhang Y, Zhang ZL. Transcriptome profiling reveals candidate flavonoid-related genes during formation of dragon's blood from Dracaena cochinchinensis (Lour.) S.C.Chen under conditions of wounding stress. JOURNAL OF ETHNOPHARMACOLOGY 2021; 273:113987. [PMID: 33667570 DOI: 10.1016/j.jep.2021.113987] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Dragon's Blood (Resina Draconis) is a red resin that has been used in traditional medicine to promote blood circulation, regenerate muscles, reduce swelling and pain, stop bleeding, etc., and its main chemical constituents are flavonoids. Dracaena cochinchinensis (Lour.) S.C.Chen is the only plant defined by the Pharmacopoeia of the People's Republic of China as a source of dragon's blood. AIM OF THE STUDY We aimed to reveal genes involved in the biosynthesis and accumulation of flavonoids of D. cochinchinensis which is under wounding stress by performing a de novo transcriptome analysis. MATERIALS AND METHODS D. cochinchinensis samples were collected for transcriptome sequencing and bioinformatics analysis at 0 days (0 d), 3 days (3 d), 6 days (6 d), and 10 days (10 d) after induction wounding stress, and tissues were microscopically observed after wounding stress. RESULTS A total of 63,244 unigenes were obtained through bioinformatics analysis, and genes associated with the biosynthesis of flavonoids were identified. Through the analysis of DEGs after wounding stress in D. cochinchinensis, based on gene expression consistent with flavonoid accumulation levels, 20 genes in connection with the flavonoid synthesis pathway and 56 genes that may be responsible for flavonoid modification and transport, and also revealed TFs (MYB, bHLH) that may be responsible for flavonoid biosynthesis. Analysis of DEGs between the four periods revealed that after wounding stress, the greatest number of significant DEGs were enriched during the first 3 days, while fewer DEGs were enriched after day 3, which corresponding to only about 1/10 (353/3883) the number of DEGs during the first 3 days. In addition, putative unigenes involved in lignin biosynthesis, such as CSE, HCT, CCR, F5H, and CAD, were significantly down-regulation after D. cochinchinensis wounding stress, but the putative unigenes responsible for flavonoid biosynthesis, such as CHS, CHI, DFR, F3'5'H, F3H, ANR, FLS, and ANS were significantly up-regulation. CONCLUSION We performed de novo transcriptome analysis of D.cochinchinensis under wounding stress, candidate genes and TFs involved in the biosynthesis and accumulation of flavonoids were identified, which is the first report on the transcript variants in flavonoid form accumulation in D. cochinchinensis under wounding stress. According to the results of DEGs analysis, wounding stress attenuated lignin biosynthesis meanwhile promoted flavonoid biosynthesis. In addition, we also compared the transcriptomics of the two different original plants (D.cochinchinensis and D.cambodiana) that form dragon's blood in order to provide further understanding of the formation of dragon's blood.
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Affiliation(s)
- Hui-Fang Sun
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Mei-Fang Song
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Yue Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China
| | - Zhong-Lian Zhang
- Yunnan Branch of Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Yunnan Key Laboratory of Southern Medicinal Utilization, Jinghong 666100, China.
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Yuan L, Pan K, Li Y, Yi B, Gao B. Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes. BMC Genom Data 2021; 22:19. [PMID: 34090339 PMCID: PMC8180045 DOI: 10.1186/s12863-021-00973-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. RESULTS In all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves. CONCLUSION The DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.
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Affiliation(s)
- Lin Yuan
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Kun Pan
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Yonghui Li
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China
| | - Bo Yi
- Department of Pharmacy, 928th Hospital of PLA Joint Logistics Support Force, Haikou, 571159, China.
| | - Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of the Ministry of Education, Hainan Key Laboratory for Research and Development of Tropical Herbs, Hainan Medical University, Haikou, 571199, China.
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Transcriptomic Analyses Shed Light on Critical Genes Associated with Bibenzyl Biosynthesis in Dendrobium officinale. PLANTS 2021; 10:plants10040633. [PMID: 33810588 PMCID: PMC8065740 DOI: 10.3390/plants10040633] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
The Dendrobium plants (members of the Orchidaceae family) are used as traditional Chinese medicinal herbs. Bibenzyl, one of the active compounds in Dendrobium officinale, occurs in low amounts among different tissues. However, market demands require a higher content of thes compounds to meet the threshold for drug production. There is, therefore, an immediate need to dissect the physiological and molecular mechanisms underlying how bibenzyl compounds are biosynthesized in D. officinale tissues. In this study, the accumulation of erianin and gigantol in tissues were studied as representative compounds of bibenzyl. Exogenous application of Methyl-Jasmonate (MeJA) promotes the biosynthesis of bibenzyl compounds; therefore, transcriptomic analyses were conducted between D. officinale-treated root tissues and a control. Our results show that the root tissues contained the highest content of bibenzyl (erianin and gigantol). We identified 1342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes in our transcriptome dataset. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. We also identified two candidate cytochrome P450 genes and nine other enzymatic genes functionally involved in bibenzyl biosynthesis. Our study provides insights on the identification of critical genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, paving the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as guide genetic engineering for the improvement of Dendrobium varieties through increasing bibenzyl content for drug production and industrialization.
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Zhu J, Zhao W, Li R, Guo D, Li H, Wang Y, Mei W, Peng S. Identification and Characterization of Chalcone Isomerase Genes Involved in Flavonoid Production in Dracaena cambodiana. FRONTIERS IN PLANT SCIENCE 2021; 12:616396. [PMID: 33719287 PMCID: PMC7947852 DOI: 10.3389/fpls.2021.616396] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/29/2021] [Indexed: 05/20/2023]
Abstract
Dragon's blood is a traditional medicine in which flavonoids are the main bioactive compounds; however, the underlying formation mechanism of dragon's blood remains largely poorly understood. Chalcone isomerase (CHI) is the key enzyme in the flavonoid biosynthesis pathway. However, CHI family genes are not well understood in Dracaena cambodiana Pierre ex Gagnep, an important source plant of dragon's blood. In this study, 11 CHI family genes were identified from D. cambodiana, and they were classified into three types. Evolutionary and transcriptional profiling analysis revealed that DcCHI1 and DcCHI4 might be involved in flavonoid production. Both DcCHI1 and DcCHI4 displayed low expression levels in stem under normal growth conditions and were induced by methyl jasmonate (MeJA), 6-benzyl aminopurine (6-BA, synthetic cytokinin), ultraviolet-B (UV-B), and wounding. The recombinant proteins DcCHI1 and DcCHI4 were expressed in Escherichia coli and purified by His-Bind resin chromatography. Enzyme activity assay indicated that DcCHI1 catalyzed the formation of naringenin from naringenin chalcone, while DcCHI4 lacked this catalytic activity. Overexpression of DcCHI1 or DcCHI4 enhanced the flavonoid production in D. cambodiana and tobacco. These findings implied that DcCHI1 and DcCHI4 play important roles in flavonoid production. Thus, our study will not only contribute to better understand the function and expression regulation of CHI family genes involved in flavonoid production in D. cambodiana but also lay the foundation for developing the effective inducer of dragon's blood.
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Affiliation(s)
- Jiahong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wan Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Rongshuang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Huiliang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wenli Mei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Wenli Mei,
| | - Shiqing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Shiqing Peng,
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Dragon’s Blood from Dracaena cambodiana in China: Applied History and Induction Techniques toward Formation Mechanism. FORESTS 2020. [DOI: 10.3390/f11040372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Dragon’s blood that is extracted from Dracaena plants has been widely used as traditional medicine in various ancient cultures. The application of dragon’s blood has a cherished history in China, even though the original plants were not discovered for some period. Dracaena cochinchinensis and Dracaena cambodiana were successively discovered in southern China during the 1970s–1980s. In the last half of the century, Chinese scientists have extensively investigated the production of dragon’s blood from these two Dracaena species, whereas these results have not been previously systematically summarized, as in the present paper. Herein, we present the applied history in ancient China and artificially induced technologies for dragon’s blood development based on these two Dracaena species, in particular, using tissue cultures seedlings and tender plants of D. cambodiana. Big data research, including transcriptomic and genomic studies, has suggested that dragon’s blood might be a defense substance that is secreted by Dracaena plants in response to (a)biotic stimuli. This review represents an effort to highlight the progress and achievements from applied history as well as induction techniques that are used for the formation of dragon’s blood that have taken place in China. Such knowledge might aid in the global conservation of wild Dracaena species and contribute to understanding dragon blood formation mechanisms, eventually assisting in the efficient utilization of limited Dracaena plant resources for the sustainable production of dragon’s blood.
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11
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Yin YC, Zhang XD, Gao ZQ, Hu T, Liu Y. The Research Progress of Chalcone Isomerase (CHI) in Plants. Mol Biotechnol 2019; 61:32-52. [PMID: 30324542 DOI: 10.1007/s12033-018-0130-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Chalcone isomerase (CHI) is the second rate-limiting and the first reported enzyme involved in the biosynthetic pathway of flavonoids. It catalyzes the intramolecular cyclization reaction, converting the bicyclic chalcone into tricyclic (2S)-flavanone. In this paper, we obtained and analyzed 916 DNA sequences, 1310 mRNA sequences, and 2403 amino acid sequences of CHI registered in NCBI by Jan 2018. The full length of CHI DNA sequences ranges from 218 to 3758 bp, CHI mRNA sequences ranges from 265 to 1436 bp, and CHI amino acid sequences ranges from 35 to 465 amino acid residues. Forty representative species were selected from each family to construct the maximum likelihood tree and analyze the evolutionary relationship. According to the medicinal and agricultural use, 13 specific species were selected, and their physicochemical properties were analyzed. The molecular weight of CHI ranges from 23 to 26 kD, and the isoelectric point of CHI ranges from 4.93 to 5.85. All the half-life periods of CHI are 30 h in mammalian reticulocytes in vitro, 20 h in yeast, and 10 h in E. coli in vivo, theoretically. The consistency of the 13 CHI amino acid sequences is 63.55%. According to the similarity between each sequence, we selected four CHI sequences of Paeonia suffruticosa, Paeonia lactiflora, Taxus wallichiana, and Tradescantia hirsutiflora for secondary structure, three-dimensional protein models, conserved domains, transmembrane structure, and signal peptide prediction analysis. It was found that CHI sequences of Paeonia suffruticosa and Paeonia lactiflora owned a higher similarity; they both share the template 4doi.1.A. The four CHI all have no signal peptides, and they exert their activities in cytoplasm. Then, PubMed, Web of Science, Science Direct, and Research Gate were used as information sources through the search terms 'chalcone isomerase', 'biosynthesis', 'expression', and their combinations to get the latest and comprehensive information of CHI, mainly from the year 2010 to 2018. More than 300 papers were searched and 116 papers were reviewed in the present work. We summarized the classification of CHI, catalytic reaction mechanism of CHI, and progress of genetic engineering regarding CHI clone, expression, and exogenous stimulator regulation. This paper will lay a foundation for further studies of CHI and other functional genes involved in flavonoids biosynthetic pathway.
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Affiliation(s)
- Yan-Chao Yin
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Xiao-Dong Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Zhi-Qiang Gao
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Ting Hu
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China
| | - Ying Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Yangguang South Street, Fangshan District, Beijing, 102401, China.
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Comparative transcriptome among Euscaphis konishii Hayata tissues and analysis of genes involved in flavonoid biosynthesis and accumulation. BMC Genomics 2019; 20:24. [PMID: 30626333 PMCID: PMC6327468 DOI: 10.1186/s12864-018-5354-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 12/09/2018] [Indexed: 02/01/2023] Open
Abstract
BACHGROUND Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candidate genes involved in flavonoid biosynthesis and accumulation, we analyzed transcriptome data from three E. konishii tissues (leaf, branch and capsule) using Illumina Hiseq 2000 platform. RESULTS A total of 91.7, 100.3 and 100.1million clean reads were acquired for the leaf, branch and capsule, respectively; and 85,342 unigenes with a mean length of 893.60 bp and N50 length of 1307 nt were assembled using Trinity program. BLASTx analysis allowed to annotate 40,218 unigenes using public protein databases, including NR, KOG/COG/eggNOG, Swiss-Prot, KEGG and GO. A total of 14,291 (16.75%) unigenes were assigned to 128 KEGG pathways, and 900 unigenes were annotated into 22 KEGG secondary metabolites, including flavonoid biosynthesis. The structure enzymes involved in flavonoid biosynthesis, such as phenylalanine ammonia lyase, cinnamate 4-hydroxylase, 4-coumarate CoA ligase, shikimate O-hydroxycinnamoyltransferase, coumaroylquinate 3'-monooxygenase, caffeoyl-CoA O-methyltransferase, chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase, flavonolsynthese, dihydroflavonol 4-reductase, anthocyanidinreductase, leucoanthocyanidin dioxygenase, leucoanthocyanidin reductase, were identified in the transcriptome data, 40 UDP-glycosyltransferase (UGT), 122 Cytochrome P450 (CYP) and 25 O-methyltransferase (OMT) unigenes were also found. A total of 295 unigenes involved in flavonoid transport and 220 transcription factors (97 MYB, 84 bHLH and 39 WD40) were identified. Furthermore, their expression patterns among different tissues were analyzed by DESeq, the differentially expressed genes may play important roles in tissues-specific synthesis, accumulation and modification of flavonoids. CONCLUSION We present here the de novo transcriptome analysis of E. konishii and the identification of candidate genes involved in biosynthesis and accumulation of flavonoid. In general, these results are an important resource for further research on gene expression, genomic and functional genomics in E. konishii and other related species.
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Ding X, Mei W, Huang S, Wang H, Zhu J, Hu W, Ding Z, Tie W, Peng S, Dai H. Genome survey sequencing for the characterization of genetic background of Dracaena cambodiana and its defense response during dragon's blood formation. PLoS One 2018; 13:e0209258. [PMID: 30550595 PMCID: PMC6294377 DOI: 10.1371/journal.pone.0209258] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/03/2018] [Indexed: 11/26/2022] Open
Abstract
Dragon's blood collected from the genus Dracaena is used as a renowned traditional medicine in various cultures worldwide. However, the genetics of the genus Dracaena and the formation mechanism of dragon's blood remain poorly understood. Here, we generate the first draft genome reference assembly of an elite Chinese Dracaena species, Dracaena cambodiana, from next-generation sequencing data with 89.46× coverage. The reads were assembled into 2,640,704 contigs with an N50 length of 1.87 kb, and a 1.05 Gb assembly was finally assembled with 2,379,659 scaffolds. Furthermore, 97.75% of the 267,243 simple sequence repeats identified from these scaffolds were mononucleotide, dinucleotide, and trinucleotide repeats. Among all 53,700 predicted genes, 158 genes involved in cell wall and plant hormone synthesis and reactive oxygen species scavenging showed altered regulation during the formation of dragon's blood. This study provides a genomic characterization of D. cambodiana and improves understanding of the molecular mechanism of dragon's blood formation. This report represents the first genome-wide characterization of a Dracaena species in the Asparagaceae.
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Affiliation(s)
- Xupo Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
- Hainan Key Laboratory for Research and Development of Natural Products from Li folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Wenli Mei
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
- Hainan Key Laboratory for Research and Development of Natural Products from Li folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Shengzhuo Huang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
- Hainan Key Laboratory for Research and Development of Natural Products from Li folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Hui Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
- Hainan Key Laboratory for Research and Development of Natural Products from Li folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Jiahong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Shiqing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
| | - Haofu Dai
- Key Laboratory of Biology and Genetic Resources of Tropical Crops of Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
- Hainan Key Laboratory for Research and Development of Natural Products from Li folk Medicine, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, People’s Republic of China
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14
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Lin Y, Wang Y, Li B, Tan H, Li D, Li L, Liu X, Han J, Meng X. Comparative transcriptome analysis of genes involved in anthocyanin synthesis in blueberry. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:561-572. [PMID: 29727860 DOI: 10.1016/j.plaphy.2018.04.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/10/2018] [Accepted: 04/25/2018] [Indexed: 05/09/2023]
Abstract
Blueberry (Vaccinium, family Ericaceae) is well known for its strong antioxidant properties and abundant active ingredients including anthocyanins, flavonols, and proanthocyanidins. In this study, variations in anthocyanin and phenolic compounds content in Bluecrop and Northblue blueberry cultivar fruits were studied, and comparative transcriptome analysis was performed to analyze differences in the molecular mechanisms of anthocyanin biosynthesis. A total of 13 799 unique genes were identified by differential expression analysis, and further subjected to GO classification and pathway enrichment. Nine differentially expressed genes (DEGs), including CHI, DFR, F3'H, FLS, CHS, OMT, UGT, ANS and F3H, were selected to validate the differential expression data using quantitative real-time PCR. The obtained qRT-PCR expression results were consistent with the RNA-Seq results. The expression levels of 9 candidate genes involved in flavonoid biosynthesis and metabolism were concurrent with the anthocyanin content. The developmental stage appeared to affect the expression of genes related to flavonoid biosynthesis to a greater extent than the tissue or cultivar type. This study provides an abundant data resource that will further our understanding of the molecular mechanisms of anthocyanin biosynthesis in blueberries.
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Affiliation(s)
- Yang Lin
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuehua Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Bin Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hui Tan
- Faculty of Health Sciences, Hokkaido Universty, Sapporo, Japan
| | - Dongnan Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Li Li
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Xuan Liu
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Jichen Han
- Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd, Shanghai, China
| | - Xianjun Meng
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China.
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15
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Zhu JH, Li HL, Guo D, Wang Y, Dai HF, Mei WL, Peng SQ. Identification, characterization and expression analysis of genes involved in steroidal saponin biosynthesis in Dracaena cambodiana. JOURNAL OF PLANT RESEARCH 2018; 131:555-562. [PMID: 29234988 DOI: 10.1007/s10265-017-1004-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/22/2017] [Indexed: 05/24/2023]
Abstract
Dracaena cambodiana is a traditional medicinal plant used for producing dragon's blood. The plants and dragon's blood of D. cambodiana contain a rich variety of steroidal saponins. However, little is known about steroidal saponin biosynthesis and its regulation in D. cambodiana. Here, 122 genes encoding enzymes involved in steroidal saponin biosynthesis were identified based on transcriptome data, with 29 of them containing complete open reading frames (ORF). Transcript expression analysis revealed that several genes related to steroidal saponin biosynthesis showed distinct tissue-specific expression patterns; the expression levels of genes encoding the key enzymes involved in the biosynthesis and early modification of steroidal saponins were significantly down-regulated in the stems in response to the inducer of dragon's blood, exhibiting positive correlations with the content of steroidal saponins. These results provide insights on the steroidal saponins biosynthetic pathway and mechanisms underlying induced formation of dragon's blood in D. cambodiana.
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Affiliation(s)
- Jia-Hong Zhu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hui-Liang Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Dong Guo
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Ying Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Hao-Fu Dai
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Wen-Li Mei
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Shi-Qing Peng
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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16
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Lei Z, Zhou C, Ji X, Wei G, Huang Y, Yu W, Luo Y, Qiu Y. Transcriptome Analysis Reveals genes involved in flavonoid biosynthesis and accumulation in Dendrobium catenatum From Different Locations. Sci Rep 2018. [PMID: 29686299 DOI: 10.1038/s41598-018-24751-y/2045-2322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
In this study, we applied transcriptome and UHPLC-MS technologies to investigate the flavonoids and their biosynthesis- and accumulation-related genes in Dendrobium catenatum from three different locations. Eight flavonoid glycosides were identified using standard references or previously isolated substances with MS data analysis. The total flavonoid contents were determined by reagents, and all the data were analyzed. In total, 23139 unigenes were obtained using the Dendrobium catenatum genome data. Of these, 10398 were annotated in the Gene Ontology (GO) database, 4203 were annotated in the KEGG database, and 10917 were annotated in the EuKaryotic Orthologous Groups (KOG) database. Thirty-one of the unigenes annotated by the KEGG database were involved in flavonoid pathways. The genes involved in bio-modification, accumulation, transportation and the regulation of the flavonoid bio-synthesis process were investigated. In conclusion, the flavonoids in Dendrobium catenatum from three different locations were different in quantitative and qualitative which may contribute to the establishment of quality control method for this herbal plant. These differences were determined by flavonoids biosynthesis process and they were concluded by sorting out the expression level of certain biosynthesis related genes.
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Affiliation(s)
- Zhouxi Lei
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Chunhua Zhou
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Xiaoyu Ji
- Research Center of Chinese Herbal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Gang Wei
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China.
| | - Yuechun Huang
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Wenxia Yu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Yingyi Luo
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
| | - Yue Qiu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou city, 510006, China
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17
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Transcriptome Analysis Reveals genes involved in flavonoid biosynthesis and accumulation in Dendrobium catenatum From Different Locations. Sci Rep 2018; 8:6373. [PMID: 29686299 PMCID: PMC5913234 DOI: 10.1038/s41598-018-24751-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
In this study, we applied transcriptome and UHPLC-MS technologies to investigate the flavonoids and their biosynthesis- and accumulation-related genes in Dendrobium catenatum from three different locations. Eight flavonoid glycosides were identified using standard references or previously isolated substances with MS data analysis. The total flavonoid contents were determined by reagents, and all the data were analyzed. In total, 23139 unigenes were obtained using the Dendrobium catenatum genome data. Of these, 10398 were annotated in the Gene Ontology (GO) database, 4203 were annotated in the KEGG database, and 10917 were annotated in the EuKaryotic Orthologous Groups (KOG) database. Thirty-one of the unigenes annotated by the KEGG database were involved in flavonoid pathways. The genes involved in bio-modification, accumulation, transportation and the regulation of the flavonoid bio-synthesis process were investigated. In conclusion, the flavonoids in Dendrobium catenatum from three different locations were different in quantitative and qualitative which may contribute to the establishment of quality control method for this herbal plant. These differences were determined by flavonoids biosynthesis process and they were concluded by sorting out the expression level of certain biosynthesis related genes.
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18
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Dubrovina AS, Kiselev KV. Regulation of stilbene biosynthesis in plants. PLANTA 2017; 246:597-623. [PMID: 28685295 DOI: 10.1007/s00425-017-2730-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/28/2017] [Indexed: 05/18/2023]
Abstract
This review analyzes the advances in understanding the natural signaling pathways and environmental factors regulating stilbene biosynthesis. We also discuss the studies reporting on stilbene content and repertoire in plants. Stilbenes, including the most-studied stilbene resveratrol, are a family of phenolic plant secondary metabolites that have been the subject of intensive research due to their valuable pharmaceutical effects and contribution to plant disease resistance. Understanding the natural mechanisms regulating stilbene biosynthesis in plants could be useful for both the development of new plant protection strategies and for commercial stilbene production. In this review, we focus on the environmental factors and cell signaling pathways regulating stilbene biosynthesis in plants and make a comparison with the regulation of flavonoid biosynthesis. This review also analyzes the recent data on stilbene biosynthetic genes and summarizes the available studies reporting on both stilbene content and stilbene composition in different plant families.
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Affiliation(s)
- A S Dubrovina
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia.
| | - K V Kiselev
- Laboratory of Biotechnology, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia.
- Department of Biotechnology and Microbiology, The School of Natural Sciences, Far Eastern Federal University, Vladivostok, 690090, Russia.
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