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Zhu Z, Chen D, Sun M, Xiao M, Huang P, Ren D, Yang Y, Zhang Z, Zhao Q, Li R. Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of lignan biosynthesis in Herpetospermum pedunculosum (Cucurbitaceae). BMC Genomics 2024; 25:421. [PMID: 38684979 PMCID: PMC11059704 DOI: 10.1186/s12864-024-10306-1] [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: 01/08/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Herpetospermum pedunculosum (Ser.) C. B. Clarke is a traditional Chinese herbal medicine that heavily relies on the lignans found in its dried ripe seeds (Herpetospermum caudigerum), which have antioxidant and hepatoprotective functions. However, little is known regarding the lignan biosynthesis in H. pedunculosum. In this study, we used metabolomic (non-targeted UHPLC-MS/MS) and transcriptome (RNA-Seq) analyses to identify key metabolites and genes (both structural and regulatory) associated with lignan production during the green mature (GM) and yellow mature (YM) stages of H. pedunculosum. RESULTS The contents of 26 lignan-related metabolites and the expression of 30 genes involved in the lignan pathway differed considerably between the GM and YM stages; most of them were more highly expressed in YM than in GM. UPLC-Q-TOF/MS confirmed that three Herpetospermum-specific lignans (including herpetrione, herpetotriol, and herpetin) were found in YM, but were not detected in GM. In addition, we proposed a lignan biosynthesis pathway for H. pedunculosum based on the fundamental principles of chemistry and biosynthesis. An integrated study of the transcriptome and metabolome identified several transcription factors, including HpGAF1, HpHSFB3, and HpWOX1, that were highly correlated with the metabolism of lignan compounds during seed ripening. Furthermore, functional validation assays revealed that the enzyme 4-Coumarate: CoA ligase (4CL) catalyzes the synthesis of hydroxycinnamate CoA esters. CONCLUSION These results will deepen our understanding of seed lignan biosynthesis and establish a theoretical basis for molecular breeding of H. pedunculosum.
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Affiliation(s)
- Ziwei Zhu
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Daihan Chen
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China
| | - Min Sun
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- Institute for Advanced Study, Chengdu University, 610106, Chengdu, China
| | - Maotao Xiao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Peng Huang
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Dongsheng Ren
- Tibet Rhodiola Pharmaceutical Holding Company, 850000, Lhasa, China
| | - Yixi Yang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Zhen Zhang
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China
| | - Qi Zhao
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, 611137, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
| | - Rui Li
- Engineering Research Center of Sichuan-Tibet Traditional Medicinal Plant, Chengdu University, 610106, Chengdu, China.
- School of Food and Biological Engineering, Chengdu University, 610106, Chengdu, China.
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Su Y, Huang J, Guo Q, Shi H, Wei M, Wang C, Zhao K, Bao T. Combined metabolomic and transcriptomic analysis reveals the characteristics of the lignan in Isatis indigotica Fortune. Gene 2023; 888:147752. [PMID: 37661029 DOI: 10.1016/j.gene.2023.147752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Isatis indigotica Fortune is a plant species containing lignan compounds of significant economic value. Its root plays a crucial role in treating viruses and exhibits antitumor, anti-inflammatory, antibacterial, and other biological activities. Now, I. indigotica has been included in Isatis tinctoria Linnaeus. In this study, the roots of diploid I. indigotica, tetraploid I. indigotica, and Isatis tinctoria Linnaeus were analyzed using metabolome and transcriptome analysis. The metabolomic analysis detected 48 lignan metabolites, including Lirioresinol A, Vladinol A, Syringaresinol, Arctigenin, Acanthoside B, and Sesamin as characteristic compounds, without significant variations among the remaining metabolites. The transcriptomic analysis identified 41 differentially expressed phenylpropanoid synthase genes, which were further analyzed for variations in lignan transcriptome profiles across different samples. RT-qPCR analysis also revealed differential genes expression related to lignan biosynthesis pathway among the three sample groups. The analysis of transcription factors showed that the AP2-EREBP family (Iin24319), MYB family (Iin24843), and WRKY family (Iin08158) displayed expression patterns similar to Iin14549. Phylogenetic analyses also indicate that Iin14549 may play a role in lignan synthesis. These transcription factor families exhibited high expression in tetraploid I. indigotica, moderate expression in diploid I. indigotica, and low expression in I. tinctoria. The findings of this study can serve as a reference for improving the quality of I. indigotica and developing germplasms with high lignan content. Additionally, these results lay a foundation for the functional characterization of UGTs in lignan biosynthesis pathway.
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Affiliation(s)
- Yong Su
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
| | - Jiabin Huang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
| | - Qiaosheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China.
| | - Hongzhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
| | - Min Wei
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China; China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, Guangdong Province 518000, PR China
| | - Chengxiang Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
| | - Kun Zhao
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
| | - Tao Bao
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, Jiangsu Province 210095, PR China
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Tang Q, Xu Y, Gao F, Xu Y, Cheng C, Deng C, Chen J, Yuan X, Zhang X, Su J. Transcriptomic and metabolomic analyses reveal the differential accumulation of phenylpropanoids and terpenoids in hemp autotetraploid and its diploid progenitor. BMC PLANT BIOLOGY 2023; 23:616. [PMID: 38049730 PMCID: PMC10696708 DOI: 10.1186/s12870-023-04630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023]
Abstract
BACKGROUND Cannabis sativa, a dioecious plant that has been cultivated worldwide for thousands of years, is known for its secondary metabolites, especially cannabinoids, which possess several medicinal effects. In this study, we investigated the autopolyploidization effects on the biosynthesis and accumulation of these metabolites, transcriptomic and metabolomic analyses were performed to explore the gene expression and metabolic variations in industrial hemp autotetraploids and their diploid progenitors. RESULTS Through these analyses, we obtained 1,663 differentially expressed metabolites and 1,103 differentially expressed genes. Integrative analysis revealed that phenylpropanoid and terpenoid biosynthesis were regulated by polyploidization. No substantial differences were found in the cannabidiol or tetrahydrocannabinol content between tetraploids and diploids. Following polyploidization, some transcription factors, including nine bHLH and eight MYB transcription factors, affected the metabolic biosynthesis as regulators. Additionally, several pivotal catalytic genes, such as flavonol synthase/flavanone 3-hydroxylase, related to the phenylpropanoid metabolic pathway, were identified as being modulated by polyploidization. CONCLUSIONS This study enhances the overall understanding of the impact of autopolyploidization in C. sativa and the findings may encourage the application of polyploid breeding for increasing the content of important secondary metabolites in industrial hemp.
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Affiliation(s)
- Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Feng Gao
- Yunnan Academy of Industrial Hemp, Kunming, 650214, Yunnan, China
| | - Ying Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Chaohua Cheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Canhui Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jiquan Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoge Yuan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Xiaoyu Zhang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
- Center for Industrial Hemp Science and Technology Innovation, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, Hunan, China.
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Zixuan Z, Rongping D, Yingying Z, Yueyue L, Jiajing Z, Yue J, Tan M, Zengxu X. The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108025. [PMID: 37722282 DOI: 10.1016/j.plaphy.2023.108025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 08/07/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".
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Affiliation(s)
- Zhang Zixuan
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Ding Rongping
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Zhang Yingying
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Liao Yueyue
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Zhao Jiajing
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Jia Yue
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Mingpu Tan
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
| | - Xiang Zengxu
- College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, Jiangsu, China.
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Su Y, Zhang M, Guo Q, Wei M, Shi H, Wang T, Han Z, Liu H, Liu C, Huang J. Classification of Isatis indigotica Fortune and Isatis tinctoria Linnaeus via comparative analysis of chloroplast genomes. BMC Genomics 2023; 24:465. [PMID: 37596543 PMCID: PMC10436401 DOI: 10.1186/s12864-023-09534-8] [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: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Isatis tinctoria Linnaeus and Isatis indigotica Fortune are very inconsistent in their morphological characteristics, but the Flora of China treats them as the same species. In this work, a new technology that differs from conventional barcodes is developed to prove that they are different species and to clarify their classification. RESULTS AND METHODS I. indigotica was indistinguishable from I. tinctoria when using ITS2. CPGAVAS2 was used to construct the chloroplast genomes. MAFFT and DnaSP were used to calculate nucleotide polymorphism, the chloroplast genomes of the two have high diversity in the rpl32 ~ trnL-UAG short region. When using this region as a mini barcode, it was found that there are obvious differences in the base numbers of I. tinctoria and different ploidy I. indigotica were found, but diploid and tetraploid I. indigotica had the same number of bases. Moreover, the reconstruction of the maximum likelihood (ML) tree, utilizing the mini-barcode, demonstrated that I. tinctoria and both diploid and tetraploid I. indigotica are located on distinct branches. The genome size of tetraploid I. indigotica was approximately 643.773 MB, the heterozygosity rate was approximately 0.98%, and the repeat sequence content was approximately 90.43%. This species has a highly heterozygous, extremely repetitive genome. CONCLUSION A new method was established to differentiate between I. indigotica and I. tinctoria. Furthermore, this approach provides a reference and basis for the directional breeding of Isatis.
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Grants
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
- JATS|[2022]461,JATS[2022]291 Jiangsu Modern Agricultural Industrial Technology System Construction Project
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Affiliation(s)
- Yong Su
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Man Zhang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Qiaosheng Guo
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China.
| | - Min Wei
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Hongzhuan Shi
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Tao Wang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Zhengzhou Han
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Huihui Liu
- China Resources Sanjiu Medical & Pharmaceutical Co., Ltd, Shenzhen City, 518000, PR China
| | - Chang Liu
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
| | - Jianmin Huang
- Institute of Chinese Medicinal Materials, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, PR China
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Kadsura coccinea Lignan Metabolism Based on Metabolome and Transcriptome Analysis. JOURNAL OF ONCOLOGY 2022; 2022:3152155. [PMID: 35957804 PMCID: PMC9359851 DOI: 10.1155/2022/3152155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/16/2022] [Accepted: 06/18/2022] [Indexed: 11/18/2022]
Abstract
Kadsura coccinea is an important resource of traditional Chinese medicine. We find out the gene information of enzymes related to lignan biosynthesis and metabolism of Kadsura coccinea, so as to provide a scientific basis for the breeding of new varieties of Kadsura coccinea. In this paper, 2-year-old Kadsura coccinea from Hunan Kadsura coccinea provincial germplasm resource bank was used as the material and its root, stem, and leaf were analyzed by extensive targeted metabolomics combined with transcriptome sequencing. The results showed the following: (1) 51 lignans were detected by metabolome analysis, and the content of lignans in roots was higher than that in stems and leaves. The high content of lignans in roots, stems, and leaves includes ring-opening isolarch phenol-4-o-glucoside, narrow leaf schisandrin E, and schisandrin B. (2) After transcriptome sequencing, 13 classes of 137 Unigenes related to lignan biosynthesis pathway were retrieved. The analysis of differential genes in different parts showed that the overall expression amount and species of Kadsura coccinea lignan synthase gene in stems and leaves were closer than those in roots. CCoAOMT, C3H, and SIDR gene families are mainly expressed in roots and stems. (3) Metabolome combined with transcriptome analysis further screened these genes and obtained 11 genes of enzyme gene families such as HCT, DIR, COMT, CAD, SIDR, and PLR, which are highly correlated in lignan synthesis. Therefore, there are many lignans and their synthase-related genes in Kadsura coccinea roots, stems, and leaves, but the content and expression of different lignans and their synthase-related genes are quite different in each part. In this study, the gene information of the Kadsura coccinea lignan biosynthesis enzyme was obtained for the first time, which laid a good foundation for the cloning and molecular breeding of the key enzyme gene of lignan biosynthesis.
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