1
|
Yu J, Xie J, Sun M, Xiong S, Xu C, Zhang Z, Li M, Li C, Lin L. Plant-Derived Caffeic Acid and Its Derivatives: An Overview of Their NMR Data and Biosynthetic Pathways. Molecules 2024; 29:1625. [PMID: 38611904 PMCID: PMC11013677 DOI: 10.3390/molecules29071625] [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: 02/24/2024] [Revised: 03/31/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
In recent years, caffeic acid and its derivatives have received increasing attention due to their obvious physiological activities and wide distribution in nature. In this paper, to clarify the status of research on plant-derived caffeic acid and its derivatives, nuclear magnetic resonance spectroscopy data and possible biosynthetic pathways of these compounds were collected from scientific databases (SciFinder, PubMed and China Knowledge). According to different types of substituents, 17 caffeic acid and its derivatives can be divided into the following classes: caffeoyl ester derivatives, caffeyltartaric acid, caffeic acid amide derivatives, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl danshens and caffeoyl glycoside. Generalization of their 13C-NMR and 1H-NMR data revealed that acylation with caffeic acid to form esters involves acylation shifts, which increase the chemical shift values of the corresponding carbons and decrease the chemical shift values of the corresponding carbons of caffeoyl. Once the hydroxyl group is ester, the hydrogen signal connected to the same carbon shifts to the low field (1.1~1.6). The biosynthetic pathways were summarized, and it was found that caffeic acid and its derivatives are first synthesized in plants through the shikimic acid pathway, in which phenylalanine is deaminated to cinnamic acid and then transformed into caffeic acid and its derivatives. The purpose of this review is to provide a reference for further research on the rapid structural identification and biofabrication of caffeic acid and its derivatives.
Collapse
Affiliation(s)
- Jiahui Yu
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Jingchen Xie
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Miao Sun
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Suhui Xiong
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Chunfang Xu
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Zhimin Zhang
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Minjie Li
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| | - Chun Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Limei Lin
- Key Laboratory for Quality Evaluation of Bulk Herbs of Human Province, School of Pharmacy, Human University of Chinese Medicine, Changsha 410208, China; (J.Y.); (J.X.); (M.S.); (S.X.); (C.X.); (Z.Z.); (M.L.)
| |
Collapse
|
2
|
Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
Collapse
Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| |
Collapse
|
3
|
Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
Collapse
Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | | |
Collapse
|
4
|
Gao L, Xu W, Xin T, Song J. Application of third-generation sequencing to herbal genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1124536. [PMID: 36959935 PMCID: PMC10027759 DOI: 10.3389/fpls.2023.1124536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
There is a long history of traditional medicine use. However, little genetic information is available for the plants used in traditional medicine, which limits the exploitation of these natural resources. Third-generation sequencing (TGS) techniques have made it possible to gather invaluable genetic information and develop herbal genomics. In this review, we introduce two main TGS techniques, PacBio SMRT technology and Oxford Nanopore technology, and compare the two techniques against Illumina, the predominant next-generation sequencing technique. In addition, we summarize the nuclear and organelle genome assemblies of commonly used medicinal plants, choose several examples from genomics, transcriptomics, and molecular identification studies to dissect the specific processes and summarize the advantages and disadvantages of the two TGS techniques when applied to medicinal organisms. Finally, we describe how we expect that TGS techniques will be widely utilized to assemble telomere-to-telomere (T2T) genomes and in epigenomics research involving medicinal plants.
Collapse
|
5
|
Xin R, Feng X, Zhang H, Wang Y, Duan M, Xie T, Dong L, Yu Q, Huang L, Zhou F. Seven non-differentially expressed 'dark biomarkers' show transcriptional dysregulation in chronic lymphocytic leukemia. Per Med 2023. [PMID: 36705049 DOI: 10.2217/pme-2022-0123] [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] [Indexed: 01/28/2023]
Abstract
Aim: Transcriptional regulation is actively involved in the onset and progression of various diseases. This study used the feature-engineering approach model-based quantitative transcription regulation to quantitatively measure the correlation between mRNA and transcription factors in a reference dataset of chronic lymphocytic leukemia (CLL) transcriptomes. Methods: A comprehensive investigation of transcriptional regulation changes in CLL was conducted using 973 samples in six independent datasets. Results & conclusion: Seven mRNAs were detected to have significantly differential model-based quantitative transcription regulation values but no differential expression between CLL patients and controls. We called these genes 'dark biomarkers' because their original expression levels did not show differential changes in the CLL patients. The overlapping lncRNAs might have contributed their transcripts to the expression miscalculations of these dark biomarkers.
Collapse
Affiliation(s)
- Ruihao Xin
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China.,College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Xin Feng
- School of Science, Jilin Institute of Chemical Technology, Jilin,132000, China.,Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Hang Zhang
- College of Information & Control Engineering, Jilin Institute of Chemical Technology, Jilin, 132000, China
| | - Yueying Wang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Tunyang Xie
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Lin Dong
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Qiong Yu
- Department of Epidemiology & Biostatistics, School of Public Health, Jilin University, Changchun, 130012, China
| | - Lan Huang
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology & Key Laboratory of Symbolic Computation & Knowledge Engineering of Ministry of Education, Jilin University, Changchun, Jilin, 130012, China
| |
Collapse
|
6
|
Yang QQ, Hua WP, Zou HL, Yang JX, Wang XZ, Zhang T, Wang DH, Zhu XJ, Cao XY. Overexpression of SmLAC25 promotes lignin accumulation and decreases salvianolic acid content in Salvia miltiorrhiza. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111462. [PMID: 36126879 DOI: 10.1016/j.plantsci.2022.111462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Laccase (LAC) is a blue multicopper oxidase that contains four copper ions, which is involved in lignin polymerization and flavonoid biosynthesis in plants. Although dozens of LAC genes have been identified in Salvia miltiorrhiza Bunge (a model medicinal plant), most have not been functionally characterized. Here, we explored the expression patterns and the functionality of SmLAC25 in S. miltiorrhiza. SmLAC25 has a higher expression level in roots and responds to methyl jasmonate, auxin, abscisic acid, and gibberellin stimuli. The SmLAC25 protein is localized in the cytoplasm and chloroplasts. Recombinant SmLAC25 protein could oxidize coniferyl alcohol and sinapyl alcohol, two monomers of G-lignin and S-lignin. To investigate its function, we generated SmLAC25-overexpressed S. miltiorrhiza plantlets and hairy roots. The lignin content increased significantly in all SmLAC25-overexpressed plantlets and hairy roots, compared with the controls. However, the concentrations of rosmarinic acid and salvianolic acid B decreased significantly in all the SmLAC25-overexpressed lines. Further studies revealed that the transcription levels of some key enzyme genes in the lignin synthesis pathway (e.g., SmCCR and SmCOMT) were significantly improved in the SmLAC25-overexpressed lines, while the expression levels of multiple enzyme genes in the salvianolic acid biosynthesis pathway were inhibited. We speculated that the overexpression of SmLAC25 promoted the metabolic flux of lignin synthesis, which resulted in a decreased metabolic flux to the salvianolic acid biosynthesis pathway.
Collapse
Affiliation(s)
- Qian-Qian Yang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Wen-Ping Hua
- College of Life Science and Food Engineering, Shaanxi Xueqian Normal University, Xi'an 710100, China
| | - Hao-Lan Zou
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Jia-Xin Yang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Xiang-Zeng Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Tong Zhang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Dong-Hao Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China
| | - Xiao-Jia Zhu
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China.
| | - Xiao-Yan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China.
| |
Collapse
|
7
|
Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biol 2022; 23:149. [PMID: 35799267 PMCID: PMC9264592 DOI: 10.1186/s13059-022-02711-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 06/15/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. RESULTS We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts-twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. CONCLUSIONS AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.
Collapse
Affiliation(s)
- Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK.
| | - Richard Kuo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Max Coulter
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Present address: Institute of Biosciences, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Yamile Marquez
- Centre for Genomic Regulation, C/ Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Linda Milne
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Stefan Riegler
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Present address: Institute of Science and Technology Austria, Am Campus 1, 3400, Klosterneuburg, Austria
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Sarah Harvey
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Yubang Gao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Theresa Wießner-Kroh
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
| | - Alejandro Paniagua
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Martin Crespi
- French National Centre for Scientific Research | CNRS INRAE-Universities of Paris Saclay and Paris, Institute of Plant Sciences Paris Saclay IPS2, Rue de Noetzlin, 91192, Gif sur Yvette, France
| | - Katherine Denby
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York Wentworth Way, York, YO10 5DD, UK
| | - Asa Ben Hur
- Department of Computer Science, Colorado State University, 1873 Campus Delivery, Fort Collins, CO, 80523-1873, USA
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, 100 East 24th St., Austin, TX, 78712-1095, USA
| | - Michael Jantsch
- Department of Cell and Developmental Biology, Center for Anatomy and Cell Biology, Medical University of Vienna, Schwarzspanierstrasse 17 A-1090, Vienna, Austria
| | - Artur Jarmolowski
- Department of Gene Expression, Adam Mickiewicz University, Poznań, Poland
| | - Tino Koester
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Sascha Laubinger
- Institut für Biologie und Umweltwissenschaften (IBU), Carl von Ossietzky Universität Oldenburg, Carl von Ossietzky-Str. 9-11, 26111, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Qingshun Quinn Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Lianfeng Gu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty for Biology, Bielefeld University, Universitaetsstrasse 25, 33615, Bielefeld, Germany
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA
| | | | - Shih-Long Tu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Andreas Wachter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, 72076, Tübingen, Germany
- Present address: Institute for Molecular Physiology, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Liming Xiong
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiao-Ning Zhang
- Biology Department, School of Arts and Sciences, St. Bonaventure University, 3261 West State Road, St. Bonaventure, NY, 14778, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology (CSIC-UV), Spanish National Research Council, Paterna, Valencia, Spain
| | - Anireddy S N Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Center of Medical Biochemistry, Dr.-Bohr-Gasse 9/3, A-1030, Vienna, Austria
| | - Maria Kalyna
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| |
Collapse
|
8
|
Li Y, Di P, Tan J, Chen W, Chen J, Chen W. Alternative Splicing Dynamics During the Lifecycle of Salvia miltiorrhiza Root Revealed the Fine Tuning in Root Development and Ingredients Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 12:797697. [PMID: 35126423 PMCID: PMC8813970 DOI: 10.3389/fpls.2021.797697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
Alternative splicing (AS) is an essential post-transcriptional process that enhances the coding and regulatory potential of the genome, thereby strongly influencing multiple plant physiology processes, such as metabolic biosynthesis. To explore how AS affects the root development and synthesis of tanshinones and phenolic acid pathways in Salvia miltiorrhiza roots, we investigated the dynamic landscape of AS events in S. miltiorrhiza roots during an annual life history. Temporal profiling represented a distinct temporal variation of AS during the entire development stages, showing the most abundant AS events at the early seedling stage (ES stage) and troughs in 45 days after germination (DAG) and 120 DAG. Gene ontology (GO) analysis indicated that physiological and molecular events, such as lateral root formation, gravity response, RNA splicing regulation, and mitogen-activated protein kinase (MAPK) cascade, were greatly affected by AS at the ES stage. AS events were identified in the tanshinones and phenolic acids pathways as well, especially for the genes for the branch points of the pathways as SmRAS and SmKSL1. Fifteen Ser/Arg-rich (SR) proteins and eight phosphokinases (PKs) were identified with high transcription levels at the ES stage, showing their regulatory roles for the high frequency of AS in this stage. Simultaneously, a co-expression network that includes 521 highly expressed AS genes, SRs, and PKs, provides deeper insight into the mechanism for the variable programming of AS.
Collapse
Affiliation(s)
- Yajing Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
| | - Jingfu Tan
- Shangyao Huayu (Linyi) Traditional Chinese Resources Co. Ltd., Linyi, China
| | - Weixu Chen
- Shangyao Huayu (Linyi) Traditional Chinese Resources Co. Ltd., Linyi, China
| | - Junfeng Chen
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
- Center of Chinese Traditional Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
9
|
Pan Y, Zhao X, Wang Y, Tan J, Chen DX. Metabolomics integrated with transcriptomics reveals the distribution of iridoid and crocin metabolic flux in Gardenia jasminoides Ellis. PLoS One 2021; 16:e0256802. [PMID: 34506519 PMCID: PMC8432746 DOI: 10.1371/journal.pone.0256802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/16/2021] [Indexed: 11/18/2022] Open
Abstract
Gardenia jasminoides Ellis (G. jasminoides) fruits are used as a resource for obtaining natural colorants and in traditional Chinese herbal medicine. However, G. jasminoides presents a relatively long flowering period and different ripening periods, so there are significant differences in the accumulation of metabolites in fruits of different colors. In addition, the complete metabolic pathways of iridoidsand crocins, which are used as medicinal composition of G. jasminoides, are poorly understood at present. In this research, we comprehensively compared the transcriptome and metabolites profiles of the developmental stages and locations of iridoid and crocin biosynthesis. A large number of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were detected in four groups of samples, and clear variation in the pattern of metabolite abundance and gene expression were observed among different fruit colors and parts. Geniposide and gardenoside mainly accumulated in the sarcocarp of green fruit (GFS) and the sarcocarp of red fruit (FS), respectively. Crocin mainly accumulated in the peel and sarcocarp of red fruits. In the iridoid pathway, we hypothesized that there was a transport mechanism from the sarcocarp to the peel of G. jasminoides because of the inconsistent expression of G8O, 10-HGO and IS associated with differences in fruit ripening. UGTs play an important role in the biosynthesis of the active components of G. jasminoides. Combined transcriptome and metabonomics analysis showed a negative correlation between the biosynthesis of geniposide and crocin. The redirection of the metabolic flux and the regulation of key enzymes may be the main reasons for the changes in the biosynthesis of iridoid and crocin in G. jasminoides fruit. Our study expended valuable information for functional genomic library and provided new insights for metabolic engineering of secondary metabolite in G. Jasminoides.
Collapse
Affiliation(s)
- Yuan Pan
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Xiao Zhao
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Yu Wang
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Jun Tan
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
| | - Da-xia Chen
- Chongqing Academy of Chinese Materia Medica, Chongqing, China
- Chongqing Engineering Research Center for Fine Variety Breeding Techniques of Chinese Materia Medica, Chongqing, China
- Chongqing Subcenter of National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Science, Chongqing, China
- * E-mail:
| |
Collapse
|
10
|
Chen R, Cao Y, Wang W, Li Y, Wang D, Wang S, Cao X. Transcription factor SmSPL7 promotes anthocyanin accumulation and negatively regulates phenolic acid biosynthesis in Salvia miltiorrhiza. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110993. [PMID: 34315580 DOI: 10.1016/j.plantsci.2021.110993] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 05/24/2023]
Abstract
Plant-specific SQUAMOSA promoter-binding protein-like (SPL) transcription factors play critical regulatory roles during plant growth and development. However, the functions of SPLs in Salvia miltiorrhiza (SmSPLs; a model medicinal plant) have not been reported. Here, the expression patterns and functions of SmSPL7 were characterized in S. miltiorrhiza. SmSPL7 was expressed in all parts of S. miltiorrhiza, with the highest expression level in the leaves, and could be inhibited by multiple hormones, including methyl jasmonate, auxin, abscisic acid, and gibberellin. SmSPL7 is localized within the nucleus and exhibits robust transcriptional activation activity. Transgenic lines overexpressing SmSPL7 demonstrated pronounced growth inhibition, accompanied by increased anthocyanin accumulation via the genetic activation of the anthocyanin biosynthesis pathway. However, SmSPL7 overexpression significantly decreased salvianolic acid B (SalB) production by inhibiting the transcripts of genes implicated in its biosynthesis pathway. Further analysis indicated that SmSPL7 directly binds to SmTAT1 and Sm4CL9 promoters and blocks their expression to inhibit the biosynthesis of SalB. Taken together, these results indicate that SmSPL7 is a negative regulator of SalB biosynthesis but positively regulates anthocyanin accumulation in S. miltiorrhiza. These findings provide new insights into the functionality of the SPL family while establishing an important foundation for further uncovering the crucial roles of SmSPL7 in the growth of S. miltiorrhiza.
Collapse
Affiliation(s)
- Rui Chen
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Yao Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Wentao Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Yonghui Li
- College of Life Science, Luoyang Normal University, Luoyang 471934, China
| | - Donghao Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Shiqiang Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China
| | - Xiaoyan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi'an 710062, China.
| |
Collapse
|
11
|
Zhang C, Ren H, Yao X, Wang K, Chang J. Full-length transcriptome analysis of pecan ( Carya illinoinensis) kernels. G3 GENES|GENOMES|GENETICS 2021; 11:6288450. [PMID: 34849807 PMCID: PMC8496322 DOI: 10.1093/g3journal/jkab182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 11/12/2022]
Abstract
Abstract
Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.
Collapse
Affiliation(s)
- Chengcai Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Huadong Ren
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xiaohua Yao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Kailiang Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Jun Chang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| |
Collapse
|
12
|
SmSPL6 Induces Phenolic Acid Biosynthesis and Affects Root Development in Salvia miltiorrhiza. Int J Mol Sci 2021; 22:ijms22157895. [PMID: 34360660 PMCID: PMC8348295 DOI: 10.3390/ijms22157895] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 02/06/2023] Open
Abstract
Salvia miltiorrhiza is a renowned model medicinal plant species for which 15 SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) family genes have been identified; however, the specific functions of SmSPLs have not been well characterized as of yet. For this study, the expression patterns of SmSPL6 were determined through its responses to treatments of exogenous hormones, including indole acetic acid (IAA), gibberellic acid (GA3), methyl jasmonic acid (MeJA), and abscisic acid (ABA). To characterize its functionality, we obtained SmSPL6-ovexpressed transgenic S. miltiorrhiza plants and found that overexpressed SmSPL6 promoted the accumulation of phenolic acids and repressed the biosynthesis of anthocyanin. Meanwhile, the root lengths of the SmSPL6-overexpressed lines were significantly longer than the control; however, both the fresh weights and lateral root numbers decreased. Further investigations indicated that SmSPL6 regulated the biosynthesis of phenolic acid by directly binding to the promoter regions of the enzyme genes Sm4CL9 and SmCYP98A14 and activated their expression. We concluded that SmSPL6 regulates not only the biosynthesis of phenolic acids, but also the development of roots in S. miltiorrhiza.
Collapse
|
13
|
Zheng X, Chen D, Chen B, Liang L, Huang Z, Fan W, Chen J, He W, Chen H, Huang L, Chen Y, Zhu J, Xue T. Insights into salvianolic acid B biosynthesis from chromosome-scale assembly of the Salvia bowleyana genome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1309-1323. [PMID: 33634943 DOI: 10.1111/jipb.13085] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/26/2021] [Indexed: 05/21/2023]
Abstract
Salvia bowleyana is a traditional Chinese medicinal plant that is a source of nutritional supplements rich in salvianolic acid B and a potential experimental system for the exploration of salvianolic acid B biosynthesis in the Labiatae. Here, we report a high-quality chromosome-scale genome assembly of S. bowleyana covering 462.44 Mb, with a scaffold N50 value of 57.96 Mb and 44,044 annotated protein-coding genes. Evolutionary analysis revealed an estimated divergence time between S. bowleyana and its close relative S. miltiorrhiza of ~3.94 million years. We also observed evidence of a whole-genome duplication in the S. bowleyana genome. Transcriptome analysis showed that SbPAL1 (PHENYLALANINE AMMONIA-LYASE1) is highly expressed in roots relative to stem and leaves, paralleling the location of salvianolic acid B accumulation. The laccase gene family in S. bowleyana outnumbered their counterparts in both S. miltiorrhiza and Arabidopsis thaliana, suggesting that the gene family has undergone expansion in S. bowleyana. Several laccase genes were also highly expressed in roots, where their encoded proteins may catalyze the oxidative reaction from rosmarinic acid to salvianolic acid B. These findings provide an invaluable genomic resource for understanding salvianolic acid B biosynthesis and its regulation, and will be useful for exploring the evolution of the Labiatae.
Collapse
Affiliation(s)
- Xuehai Zheng
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Duo Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Binghua Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Limin Liang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Wenfang Fan
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Jiannan Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Wenjin He
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Huibin Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Luqiang Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Jinmao Zhu
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| | - Ting Xue
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Products of the State Oceanic Administration, Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, Southern Institute of Oceanography, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China
| |
Collapse
|
14
|
Yin M, Chu S, Shan T, Zha L, Peng H. Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge. PLANT METHODS 2021; 17:61. [PMID: 34130711 PMCID: PMC8207730 DOI: 10.1186/s13007-021-00762-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 06/07/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Astragalus mongholicus Bunge is an important medicinal plant used in traditional Chinese medicine. It is rich in isoflavonoids and triterpenoid saponins. Although these active constituents of A. mongholicus have been discovered for a long time, the genetic basis of isoflavonoid and triterpenoid saponin biosynthesis in this plant is virtually unknown because of the lack of a reference genome. Here, we used a combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to identify genes involved in the biosynthetic pathway of secondary metabolites in A. mongholicus. RESULTS In this study, NGS, SMRT sequencing, and targeted compound analysis were combined to investigate the association between isoflavonoid and triterpenoid saponin content, and specific gene expression in the root, stem, and leaves of A. mongholicus. Overall, 643,812 CCS reads were generated, yielding 121,107 non-redundant transcript isoforms with an N50 value of 2124 bp. Based on these highly accurate transcripts, 104,756 (86.50%) transcripts were successfully annotated by any of the seven databases (NR, NT, Swissprot, KEGG, KOG, Pfam and GO). Levels of four isoflavonoids and four astragalosides (triterpenoid saponins) were determined. Forty-four differentially expressed genes (DEGs) involved in isoflavonoid biosynthesis and 44 DEGs from 16 gene families that encode enzymes involved in triterpenoid saponin biosynthesis were identified. Transcription factors (TFs) associated with isoflavonoid and triterpenoid saponin biosynthesis, including 72 MYBs, 53 bHLHs, 64 AP2-EREBPs, and 11 bZIPs, were also identified. The above transcripts showed different expression trends in different plant organs. CONCLUSIONS This study provides important genetic information on the A. mongholicus genes that are essential for isoflavonoid and triterpenoid saponin biosynthesis, and provides a basis for developing the medicinal value of this plant.
Collapse
Affiliation(s)
- Minzhen Yin
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Research Unit of DAO-DI Herbs, Chinese Academy of Medical Sciences, 2019RU57, Beijing, 100700, China
| | - Shanshan Chu
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, 230012, China
| | - Tingyu Shan
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Liangping Zha
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Conservation and Development of Traditional Chinese Medicine Resources, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, 230012, China.
- State Key Laboratory of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Research Unit of DAO-DI Herbs, Chinese Academy of Medical Sciences, 2019RU57, Beijing, 100700, China.
| |
Collapse
|
15
|
Jiang M, Chen H, Liu J, Du Q, Lu S, Liu C. Genome-wide identification and functional characterization of natural antisense transcripts in Salvia miltiorrhiza. Sci Rep 2021; 11:4769. [PMID: 33637790 PMCID: PMC7910453 DOI: 10.1038/s41598-021-83520-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/29/2021] [Indexed: 01/01/2023] Open
Abstract
Salvia miltiorrhiza is one of the most widely used traditional medicines. Natural antisense transcripts (NATs) are a class of long noncoding RNAs that can regulate gene expression. Here, we identified 812 NATs, including 168 cis-NATs and 644 trans-NATs from twelve root, flower, and leaf samples of S. miltiorrhiza using RNA-seq. The expression profiles for 41 of 50 NATs and their sense transcripts (STs) obtained from RNA-Seq were validated using qRT-PCR. The expression profiles of 17 NATs positively correlated with their STs. GO and KEGG pathway analyses mapped the STs for cis-NATs to pathways for biosynthesis of secondary metabolites. We characterized four NATs in detail, including NAT0001, NAT0002, NAT0004, and NAT00023. Their STs are kaurene synthase-like 1 and the homologs of UDP-glucose flavonoid 3-O-glucosyltransferase 6, UDP-glycosyltransferase 90A1, and beta-glucosidase 40, respectively. The first gene is involved in the biosynthesis of bioactive tanshinones, the next two are involved in anthocyanin biosynthesis, whereas the last is involved in phenylpropanoid biosynthesis. Besides, we found seven STs that are potential targets of miRNAs. And we found two miRNAs including miR156a and miR7208, might originate from NATs, NAT0112 and NAT0086. The results suggest that S. miltiorrhiza NATs might interact with STs, produce miRNAs, and be regulated by miRNAs. They potentially play significant regulatory roles in the biosynthesis of bioactive compounds.
Collapse
Affiliation(s)
- Mei Jiang
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Haimei Chen
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Jingting Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Qing Du
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,College of Pharmacy, Key Laboratory of Plant Resources of Qinghai-Tibet Plateau in Chemical Research, Qinghai Nationalities University, Xining, 810007, Qinghai, People's Republic of China
| | - Shanfa Lu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
| | - Chang Liu
- Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine From Ministry of Education, Engineering Research Center of Chinese Medicine Resources From Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
| |
Collapse
|
16
|
Chen C, Shi X, Zhou T, Li W, Li S, Bai G. Full-length transcriptome analysis and identification of genes involved in asarinin and aristolochic acid biosynthesis in medicinal plant Asarum sieboldii. Genome 2020; 64:639-653. [PMID: 33320770 DOI: 10.1139/gen-2020-0095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Asarum sieboldii, a well-known traditional Chinese medicinal herb, is used for curing inflammation and ache. It contains both the bioactive ingredient asarinin and the toxic compound aristolochic acid. To address further breeding demand, genes involved in the biosynthetic pathways of asarinin and aristolochic acid should be explored. Therefore, the full-length transcriptome of A. sieboldii was sequenced using PacBio Iso-Seq to determine the candidate transcripts that encode the biosynthetic enzymes of asarinin and aristolochic acid. In this study, 63 023 full-length transcripts were generated with an average length of 1371 bp from roots, stems, and leaves, of which 49 593 transcripts (78.69%) were annotated against public databases. Furthermore, 555 alternative splicing (AS) events, 10 869 long noncoding RNAs (lncRNAs) as well as their 11 291 target genes, and 17 909 simple sequence repeats (SSRs) were identified. The data also revealed 97 candidate transcripts related to asarinin metabolism, of which six novel genes that encoded enzymes involved in asarinin biosynthesis were initially reported. In addition, 56 transcripts related to aristolochic acid biosynthesis were also identified, including CYP81B. In summary, these transcriptome data provide a useful resource to study gene function and genetic engineering in A. sieboldii.
Collapse
Affiliation(s)
- Chen Chen
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Xinwei Shi
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Tao Zhou
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76 Yanta West Road, 710061, Xi'an City, Shaanxi Province, China
| | - Weimin Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Sifeng Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, No. 17 Cuihua South Road, 710061, Xi'an City, Shaanxi Province, China
| |
Collapse
|
17
|
Li W, Liu C, Liu J, Bai Z, Liang Z. Transcriptomic analysis reveals the GRAS family genes respond to gibberellin in Salvia miltiorrhiza hairy roots. BMC Genomics 2020; 21:727. [PMID: 33106159 PMCID: PMC7590604 DOI: 10.1186/s12864-020-07119-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salvia miltiorrhiza is one of the most important traditional Chinese medicinal plants with high medicinal value. Gibberellins are growth-promoting phytohormones that regulate numerous growth and developmental processes in plants. However, their role on the secondary metabolism regulation has not been investigated. RESULTS In this study, we found that gibberellic acid (GA) can promote hairy roots growth and increase the contents of tanshinones and phenolic acids. Transcriptomic sequencing revealed that many genes involved in the secondary metabolism pathway were the GA-responsive. After further analysis of GA signaling pathway genes, which their expression profiles have significantly changed, it was found that the GRAS transcription factor family had a significant response to GA. We identified 35 SmGRAS genes in S. miltiorrhiza, which can be divided into 10 subfamilies. Thereafter, members of the same subfamily showed similar conserved motifs and gene structures, suggesting possible conserved functions. CONCLUSIONS Most SmGRAS genes were significantly responsive to GA, indicating that they may play an important role in the GA signaling pathway, also participating in the GA regulation of root growth and secondary metabolism in S. miltiorrhiza.
Collapse
Affiliation(s)
- Wenrui Li
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China.,School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Chuangfeng Liu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Jingling Liu
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Zhenqing Bai
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Zongsuo Liang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, 712100, China. .,College of Life Sciences and Medicine, The Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| |
Collapse
|
18
|
Zheng X, Li H, Chen M, Zhang J, Tan R, Zhao S, Wang Z. smi-miR396b targeted SmGRFs, SmHDT1, and SmMYB37/4 synergistically regulates cell growth and active ingredient accumulation in Salvia miltiorrhiza hairy roots. PLANT CELL REPORTS 2020; 39:1263-1283. [PMID: 32607753 DOI: 10.1007/s00299-020-02562-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/19/2020] [Indexed: 06/11/2023]
Abstract
MIR396b had been cloned and overexpressed in Salvia miltiorrhiza hairy roots. MiR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to regulate cell growth and secondary metabolism in S. miltiorrhiza hairy roots. Danshen (Salvia miltiorrhiza Bunge) is a valuable medicinal herb with two kinds of clinically used natural products, salvianolic acids and tanshinones. miR396 is a conserved microRNA and plays extensive roles in plants. However, it is still unclear how miR396 works in S. miltiorrhiza. In this study, an smi-MIR396b has been cloned from S. miltiorrhiza. Overexpression of miR396b in danshen hairy roots inhibited hairy root growth, reduced salvianolic acid concentration, but enhanced tanshinone accumulation, resulting in the biomass and total salvianolic acids respectively reduced to 55.5 and 72.1% of the control and total tanshinones increased up to 1.91-fold of the control. Applied degradome sequencing, 5'RLM-RACE, and qRT-PCR, 13 targets for miR396b were identified including seven conserved SmGRF1-7 and six novel ones. Comparative transcriptomics and microRNomics analysis together with qRT-PCR results confirmed that miR396b targets SmGRFs, SmHDT1, and SmMYB37/4 to mediate the phytohormone, especially gibberellin signaling pathways and consequentially resulted in the phenotype variation of miR396b-OE hairy roots. Furthermore, miR396b could be activated by methyl jasmonate, abscisic acid, gibberellin, salt, and drought stresses. The findings in this study indicated that smi-miR396b acts as an upstream and central regulator in cell growth and the biosynthesis of tanshinones and salvianolic acids, shedding light on the coordinated regulation of plant growth and biosynthesis of active ingredients in S. miltiorrhiza.
Collapse
Affiliation(s)
- Xiaoyu Zheng
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Hang Li
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Min Chen
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Jinjia Zhang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Ronghui Tan
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China
| | - Shujuan Zhao
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
| | - Zhengtao Wang
- The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and Shanghai Key Laboratory of Compound Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong New District, Shanghai, 201203, People's Republic of China.
| |
Collapse
|
19
|
Zhou Y, Feng J, Li Q, Huang D, Chen X, Du Z, Lv Z, Xiao Y, Han Y, Chen J, Chen W. SmMYC2b Enhances Tanshinone Accumulation in Salvia miltiorrhiza by Activating Pathway Genes and Promoting Lateral Root Development. FRONTIERS IN PLANT SCIENCE 2020; 11:559438. [PMID: 33042182 PMCID: PMC7517298 DOI: 10.3389/fpls.2020.559438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Salvia miltiorrhiza Bunge (Lamiaceae) is an economically important medicinal plant as well as an emerging model plant. Our previous studies indicate that SmMYC2b is a positive transcription factor that can affect the biosynthesis of phenolic acids and tanshinones in S. miltiorrhiza. Moreover, MYC2s are well known to induce the development of lateral roots. As tanshinones are mainly distributed in the periderm, the promotion of lateral root development probably leads to increased accumulation of tanshinones. In this paper, we firstly discovered that SmMYC2b played a dual regulatory role in effectively enhancing the tanshinone accumulation by activating tanshinone biosynthetic pathway and promoting lateral root development. The expression levels of the previously studied pathway genes SmCPS1, SmKSL1, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 dramatically increased. In addition, SmMYC2b was proved to exhibit a similar function as other homologs in promoting lateral root development, which increased the tanshinone produced tissue and further enhanced the biosynthesis of tanshinones. RNA-seq assays revealed that SmMYC2b-regulated genes comprised 30.6% (1,901 of 6,210) of JA-responsive genes, confirming that SmMYC2b played a crucial role in transcriptional regulation of JA-regulated genes. Overall, we concluded that SmMYC2b could enhance tanshinone accumulation by activating the tanshinone biosynthetic pathway and promoting lateral root development. Our study provides an effective approach to enhance the production of desired tanshinones and enriches our knowledge of the related regulatory network.
Collapse
Affiliation(s)
- Yangyun Zhou
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Jingxian Feng
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Li
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Doudou Huang
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiao Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zenan Du
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zongyou Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yonglong Han
- Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai, China
| | - Junfeng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| |
Collapse
|
20
|
Li W, Bai Z, Pei T, Yang D, Mao R, Zhang B, Liu C, Liang Z. SmGRAS1 and SmGRAS2 Regulate the Biosynthesis of Tanshinones and Phenolic Acids in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2019; 10:1367. [PMID: 31737003 PMCID: PMC6831727 DOI: 10.3389/fpls.2019.01367] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 10/04/2019] [Indexed: 05/24/2023]
Abstract
Salvia miltiorrhiza is one of the most widely used traditional Chinese medicinal plants because of its excellent performance in treating heart diseases. Tanshinones and phenolic acids are two important classes of effective metabolites, and their biosynthesis has attracted widespread interest. Here, we functionally characterized SmGRAS1 and SmGRAS2, two GRAS family transcription factors from S. miltiorrhiza. SmGRAS1/2 were highly expressed in the root periderm, where tanshinones mainly accumulated in S. miltiorrhiza. Overexpression of SmGRAS1/2 upregulated tanshinones accumulation and downregulated GA, phenolic acids contents, and root biomass. However, antisense expression of SmGRAS1/2 reduced the tanshinones accumulation and increased the GA, phenolic acids contents, and root biomass. The expression patterns of biosynthesis genes were consistent with the changes in compounds accumulation. GA treatment increased tanshinones, phenolic acids, and GA contents in the overexpression lines, and restored the root growth inhibited by overexpressing SmGRAS1/2. Subsequently, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays (EMSA) showed SmGRAS1 promoted tanshinones biosynthesis by directly binding to the GARE motif in the SmKSL1 promoter and activating its expression. Yeast two-hybrid assays showed SmGRAS1 interacted physically with SmGRAS2. Taken together, the results revealed that SmGRAS1/2 acted as repressors in root growth and phenolic acids biosynthesis but as positive regulators in tanshinones biosynthesis. Overall, our findings revealed the potential value of SmGRAS1/2 in genetically engineering changes in secondary metabolism.
Collapse
Affiliation(s)
- Wenrui Li
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhenqing Bai
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Tianlin Pei
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Dongfeng Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Renjun Mao
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Bingxue Zhang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chuangfeng Liu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Zongsuo Liang
- Institute of Soil and Water Conservation, Chinese Academy of Sciences and Ministry of Water Resources, Yangling, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| |
Collapse
|
21
|
Liu X, Jin M, Zhang M, Li T, Sun S, Zhang J, Dai J, Wang Y. The application of combined 1H NMR-based metabolomics and transcriptomics techniques to explore phenolic acid biosynthesis in Salvia miltiorrhiza Bunge. J Pharm Biomed Anal 2019; 172:126-138. [PMID: 31035094 DOI: 10.1016/j.jpba.2019.04.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022]
Abstract
Salvia miltiorrhiza Bunge is a traditional Chinese medicine, and its water-soluble phenolic acid active compounds have very important medicinal value; however, the synthesis pathways of the main active ingredients remain unknown. Here, we employed nuclear magnetic resonance (NMR)-based metabolomics and transcriptomics techniques to study the biosynthesis mechanism of salvianolic acids. High-performance liquid chromatography (HPLC) combined with NMR showed an improvement over traditional techniques, and 54 metabolites were detected. The results of the multivariate statistical analysis showed that salvianolic acid B (SAB), rosmarinic acid (RA), caffeic acid, succinate, and citrate were among the multiple compounds that were increased in the methyl jasmonate (MeJA)-elicited group; the levels of sucrose, fructose, glutamine, and tyrosine were decreased. Combined with the differentially expressed genes (DEGs) found by transcriptome sequencing, we speculate that the synthesis of RA after MeJA treatment mostly occurred through caffeic acid and bypassed 4-hydroxyphenyllactic acid. This provides useful information for the study of salvianolic acids synthesis.
Collapse
Affiliation(s)
- Xia Liu
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Mengxia Jin
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Min Zhang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Tianqi Li
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Shanshan Sun
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Jinyue Zhang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Jungui Dai
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China
| | - Yinghong Wang
- State Key Laboratory for Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, No.1 Xiannongtan Street, Beijing, BJ, China.
| |
Collapse
|
22
|
Huang P, Lin F, Li B, Zheng Y. Hybrid-Transcriptome Sequencing and Associated Metabolite Analysis Reveal Putative Genes Involved in Flower Color Difference in Rose Mutants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E267. [PMID: 31387222 PMCID: PMC6724100 DOI: 10.3390/plants8080267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/21/2019] [Accepted: 07/29/2019] [Indexed: 02/04/2023]
Abstract
Gene mutation is a common phenomenon in nature that often leads to phenotype differences, such as the variations in flower color that frequently occur in roses. With the aim of revealing the genomic information and inner mechanisms, the differences in the levels of both transcription and secondary metabolism between a pair of natural rose mutants were investigated by using hybrid RNA-sequencing and metabolite analysis. Metabolite analysis showed that glycosylated derivatives of pelargonidin, e.g., pelargonidin 3,5 diglucoside and pelargonidin 3-glucoside, which were not detected in white flowers (Rosa 'Whilte Mrago Koster'), constituted the major pigments in pink flowers. Conversely, the flavonol contents of petal, such as kaempferol-3-glucoside, quercetin 3-glucoside, and rutin, were higher in white flowers. Hybrid RNA-sequencing obtained a total of 107,280 full-length transcripts in rose petal which were annotated in major databases. Differentially expressed gene (DEG) analysis showed that the expression of genes involved in the flavonoid biosynthesis pathway was significantly different, e.g., CHS, FLS, DFR, LDOX, which was verified by qRT-PCR during flowering. Additionally, two MYB transcription factors were found and named RmMYBAN2 and RmMYBPA1, and their expression patterns during flowering were also analyzed. These findings indicate that these genes may be involved in the flower color difference in the rose mutants, and competition between anthocyanin and flavonol biosynthesis is a primary cause of flower color variation, with its regulation reflected by transcriptional and secondary metabolite levels.
Collapse
Affiliation(s)
- Ping Huang
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Furong Lin
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Bin Li
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yongqi Zheng
- State Key Laboratory of Tree Genetics and Breeding, Laboratory of Forest Silviculture and Tree Cultivation, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| |
Collapse
|
23
|
Guodong R, Jianguo Z, Xiaoxia L, Ying L. Identification of putative genes for polyphenol biosynthesis in olive fruits and leaves using full-length transcriptome sequencing. Food Chem 2019; 300:125246. [PMID: 31357017 DOI: 10.1016/j.foodchem.2019.125246] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
Olive (Olea europaea) is a rich source of valuable bioactive polyphenols, which has attracted widespread interest. In this study, we combined targeted metabolome, Pacbio ISOseq transcriptome, and Illumina RNA-seq transcriptome to investigate the association between polyphenols and gene expression in the developing olive fruits and leaves. A total of 12 main polyphenols were measured, and 122 transcripts of 17 gene families, 101 transcripts of 9 gene families, and 106 transcripts of 6 gene families that encode for enzymes involved in flavonoid, oleuropein, and hydroxytyrosol biosynthesis were separately identified. Additionally, 232 alternative splicing events of 18 genes related to polyphenol synthesis were analyzed. This is the first time that the third generations of full-length transcriptome technology were used to study the gene expression pattern of olive fruits and leaves. The results of transcriptome combined with targeted metabolome can help us better understand the polyphenol biosynthesis pathways in the olive.
Collapse
Affiliation(s)
- Rao Guodong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Zhang Jianguo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Liu Xiaoxia
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Luo Ying
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| |
Collapse
|
24
|
Li Q, Feng J, Chen L, Xu Z, Zhu Y, Wang Y, Xiao Y, Chen J, Zhou Y, Tan H, Zhang L, Chen W. Genome-Wide Identification and Characterization of Salvia miltiorrhiza Laccases Reveal Potential Targets for Salvianolic Acid B Biosynthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:435. [PMID: 31024599 PMCID: PMC6463009 DOI: 10.3389/fpls.2019.00435] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/22/2019] [Indexed: 05/29/2023]
Abstract
Laccases are widely distributed in plant kingdom catalyzing the polymerization of lignin monolignols. Rosmarinic acid (RA) has a lignin monolignol-like structure and is converted into salvianolic acid B (SAB), which is a representatively effective hydrophilic compound of a well-known medicinal plant Salvia miltiorrhiza and also the final compound of phenolic acids metabolism pathway in the plant. But the roles of laccases in the biosynthesis of SAB are poorly understood. This work systematically characterizes S. miltiorrhiza laccase (SmLAC) gene family and identifies the SAB-specific candidates. Totally, 29 laccase candidates (SmLAC1-SmLAC29) are found to contain three signature Cu-oxidase domains. They present relatively low sequence identity and diverse intron-exon patterns. The phylogenetic clustering of laccases from S. miltiorrhiza and other ten plants indicates that the 29 SmLACs can be divided into seven groups, revealing potential distinct functions. Existence of diverse cis regulatory elements in the SmLACs promoters suggests putative interactions with transcription factors. Seven SmLACs are found to be potential targets of miR397. Putative glycosylation sites and phosphorylation sites are identified in SmLAC amino acid sequences. Moreover, the expression profile of SmLACs in different organs and tissues deciphers that 5 SmLACs (SmLAC7/8/20/27/28) are expressed preferentially in roots, adding the evidence that they may be involved in the phenylpropanoid metabolic pathway. Besides, silencing of SmLAC7, SmLAC20 and SmLAC28, and overexpression of SmLAC7 and SmLAC20 in the hairy roots of S. miltiorrhiza result in diversification of SAB, signifying that SmLAC7 and SmLAC20 take roles in SAB biosynthesis. The results of this study lay a foundation for further elucidation of laccase functions in S. miltiorrhiza, and add to the knowledge for SAB biosynthesis in S. miltiorrhiza.
Collapse
Affiliation(s)
- Qing Li
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jingxian Feng
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Liang Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yingjie Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yun Wang
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ying Xiao
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junfeng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yangyun Zhou
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Hexin Tan
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Second Military Medical University, Shanghai, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Hangzhou, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| |
Collapse
|
25
|
Apollo: Democratizing genome annotation. PLoS Comput Biol 2019; 15:e1006790. [PMID: 30726205 PMCID: PMC6380598 DOI: 10.1371/journal.pcbi.1006790] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 01/10/2019] [Indexed: 12/05/2022] Open
Abstract
Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo’s newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.
Collapse
|
26
|
Wang J, Xu J, Gong X, Yang M, Zhang C, Li M. Biosynthesis, Chemistry, and Pharmacology of Polyphenols from Chinese Salvia Species: A Review. Molecules 2019; 24:E155. [PMID: 30609767 PMCID: PMC6337547 DOI: 10.3390/molecules24010155] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/27/2018] [Accepted: 12/29/2018] [Indexed: 12/30/2022] Open
Abstract
Salvia species find widespread application in food and pharmaceutical products owing to their large polyphenol content. The main polyphenols in Chinese Salvia species are phenolic acids and flavonoids, which exhibit anti-oxygenation, anti-ischemia-reperfusion injury, anti-thrombosis, anti-tumour, and other therapeutic effects. However, there are few peer-reviewed studies on polyphenols in Chinese Salvia species, especially flavonoids. This review is a systematic, comprehensive collation of available information on the biosynthesis, chemistry, and pharmacology of Chinese Salvia species. We believe that our study makes a significant contribution to the literature because this review provides a detailed literary resource on the currently available information on various polyphenolic components of Chinese Salvia species, including their bioactivities and structures. In addition, the study provides information that would encourage further investigation of this plant material as a natural resource with potential for a broad range of applications in various industries, such as the food and pharmaceutical industries.
Collapse
Affiliation(s)
- Jie Wang
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
| | - Jianping Xu
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
| | - Xue Gong
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
| | - Min Yang
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
| | - Chunhong Zhang
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
| | - Minhui Li
- Inner Mongolia Research Center of Characteristic Medicinal Plants Cultivation and Protection Engineering Technology, Baotou Medical College, Baotou 014060, Inner Mongolia, China.
- Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot 010020, Inner Mongolia, China.
| |
Collapse
|
27
|
Clark S, Yu F, Gu L, Min XJ. Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato. FRONTIERS IN PLANT SCIENCE 2019; 10:689. [PMID: 31191588 PMCID: PMC6546887 DOI: 10.3389/fpls.2019.00689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/08/2019] [Indexed: 05/17/2023]
Abstract
Tomato (Solanum lycopersicum) is an important vegetable and fruit crop. Its genome was completely sequenced and there are also a large amount of available expressed sequence tags (ESTs) and short reads generated by RNA sequencing (RNA-seq) technologies. Mapping transcripts including mRNA sequences, ESTs, and RNA-seq reads to the genome allows identifying pre-mRNA alternative splicing (AS), a post-transcriptional process generating two or more RNA isoforms from one pre-mRNA transcript. We comprehensively analyzed the AS landscape in tomato by integrating genome mapping information of all available mRNA and ESTs with mapping information of RNA-seq reads which were collected from 27 published projects. A total of 369,911 AS events were identified from 34,419 genomic loci involving 161,913 transcripts. Within the basic AS events, intron retention is the prevalent type (18.9%), followed by alternative acceptor site (12.9%) and alternative donor site (7.3%), with exon skipping as the least type (6.0%). Complex AS types having two or more basic event accounted for 54.9% of total AS events. Within 35,768 annotated protein-coding gene models, 23,233 gene models were found having pre-mRNAs generating AS isoform transcripts. Thus the estimated AS rate was 65.0% in tomato. The list of identified AS genes with their corresponding transcript isoforms serves as a catalog for further detailed examination of gene functions in tomato biology. The post-transcriptional information is also expected to be useful in improving the predicted gene models in tomato. The sequence and annotation information can be accessed at plant alternative splicing database (http://proteomics.ysu.edu/altsplice).
Collapse
Affiliation(s)
- Sarah Clark
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
| | - Feng Yu
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiang Jia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, United States
- *Correspondence: Xiang Jia Min,
| |
Collapse
|
28
|
Molecular Regulation of Catalpol and Acteoside Accumulation in Radial Striation and non-Radial Striation of Rehmannia glutinosa Tuberous Root. Int J Mol Sci 2018; 19:ijms19123751. [PMID: 30486279 PMCID: PMC6321003 DOI: 10.3390/ijms19123751] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/08/2018] [Accepted: 11/22/2018] [Indexed: 12/19/2022] Open
Abstract
Rehmannia glutinosa L., a perennial plant of Scrophulariaceae, is one of the most commonly used herbs in traditional Chinese medicine (TCM) that have been widely cultivated in China. However, to date, the biosynthetic pathway of its two quality-control components, catalpol and acteoside, are only partially elucidated and the mechanism for their tissue-specific accumulation remains unknown. To facilitate the basic understanding of the key genes and transcriptional regulators involved in the biosynthesis of catalpol and acteoside, transcriptome sequencing of radial striation (RS) and non-radial striation (nRS) from four R. glutinosa cultivars was performed. A total of 715,158,202 (~107.27 Gb) high quality reads obtained using paired-end Illumina sequencing were de novo assembled into 150,405 transcripts. Functional annotation with multiple public databases identified 155 and 223 unigenes involved in catalpol and acteoside biosynthesis, together with 325 UGTs, and important transcription factor (TF) families. Comparative analysis of the transcriptomes identified 362 unigenes, found to be differentially expressed in all RS vs. nRS comparisons, with 143 upregulated unigenes, including those encoding enzymes of the catalpol and acteoside biosynthetic pathway, such as geranyl diphosphate synthase (RgGPPS), geraniol 8-hydroxylase (RgG10H), and phenylalanine ammonia-lyase (RgPAL). Other differentially expressed unigenes predicted to be related to catalpol and acteoside biosynthesis fall into UDP-dependent glycosyltransferases (UGTs), as well as transcription factors. In addition, 16 differentially expressed genes were selectively confirmed by real-time PCR. In conclusion, a large unigene dataset of R. glutinosa generated in the current study will serve as a resource for the identification of potential candidate genes for investigation of the tuberous root development and biosynthesis of active components.
Collapse
|
29
|
Full-length transcriptome sequences and the identification of putative genes for flavonoid biosynthesis in safflower. BMC Genomics 2018; 19:548. [PMID: 30041604 PMCID: PMC6057038 DOI: 10.1186/s12864-018-4946-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/19/2018] [Indexed: 12/20/2022] Open
Abstract
Background The flower of the safflower (Carthamus tinctorius L.) has been widely used in traditional Chinese medicine for the ability to improve cerebral blood flow. Flavonoids are the primary bioactive components in safflower, and their biosynthesis has attracted widespread interest. Previous studies mostly used second-generation sequencing platforms to survey the putative flavonoid biosynthesis genes. For a better understanding of transcription data and the putative genes involved in flavonoid biosynthesis in safflower, we carry our study. Results High-quality RNA was extracted from six types of safflower tissue. The RNAs of different tissues were mixed equally and used for multiple size-fractionated libraries (1–2, 2–3 and 3-6 k) library construction. Five cells were carried (2 cells for 1–2 and for 2-3 k libraries and 1 cell for 3-6 k libraries). 10.43Gb clean data and 38,302 de-redundant sequences were captured. 44 unique isoforms were annotated as encoding enzymes involved in flavonoid biosynthesis. The full length flavonoid genes were characterized and their evolutional relationship and expressional pattern were analyzed. They can be divided into eight families, with a large differences in the tissue expression. The temporal expressions under MeJA treatment were also measured, 9 genes are significantly up-regulated and 2 genes are significantly down-regulated. The genes involved in flavonoid synthesis in safflower were predicted in our study. Besides, the SSR and lncRNA are also analyzed in our study. Conclusions Full-length transcriptome sequences were used in our study. The genes involved in flavonoid synthesis in safflower were predicted in our study. Combined the determination of flavonoids, CtC4H2, CtCHS3, CtCHI3, CtF3H3, CtF3H1 are mainly participated in MeJA promoting the synthesis of flavonoids. Our results also provide a valuable resource for further study on safflower. Electronic supplementary material The online version of this article (10.1186/s12864-018-4946-9) contains supplementary material, which is available to authorized users.
Collapse
|
30
|
Diverse specialized metabolism and their responses to lactalbumin hydrolysate in hairy root cultures of Salvia miltiorrhiza Bunge and Salvia castanea Diels f. t omentosa Stib. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2017.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
31
|
Zhang Y, Xu Z, Ji A, Luo H, Song J. Genomic survey of bZIP transcription factor genes related to tanshinone biosynthesis in Salvia miltiorrhiza. Acta Pharm Sin B 2018; 8:295-305. [PMID: 29719790 PMCID: PMC5925414 DOI: 10.1016/j.apsb.2017.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 07/24/2017] [Accepted: 08/06/2017] [Indexed: 01/06/2023] Open
Abstract
Tanshinones are a class of bioactive components in the traditional Chinese medicine Salvia miltiorrhiza, and their biosynthesis and regulation have been widely studied. Current studies show that basic leucine zipper (bZIP) proteins regulate plant secondary metabolism, growth and developmental processes. However, the bZIP transcription factors involved in tanshinone biosynthesis are unknown. Here, we conducted the first genome-wide survey of the bZIP gene family and analyzed the phylogeny, gene structure, additional conserved motifs and alternative splicing events in S. miltiorrhiza. A total of 70 SmbZIP transcription factors were identified and categorized into 11 subgroups based on their phylogenetic relationships with those in Arabidopsis. Moreover, seventeen SmbZIP genes underwent alternative splicing events. According to the transcriptomic data, the SmbZIP genes that were highly expressed in the Danshen root and periderm were selected. Based on the prediction of bZIP binding sites in the promoters and the co-expression analysis and co-induction patterns in response to Ag+ treatment via quantitative real-time polymerase chain reaction (qRT-PCR), we concluded that SmbZIP7 and SmbZIP20 potentially participate in the regulation of tanshinone biosynthesis. These results provide a foundation for further functional characterization of the candidate SmbZIP genes, which have the potential to increase tanshinone production.
Collapse
|
32
|
Yang N, Zhou W, Su J, Wang X, Li L, Wang L, Cao X, Wang Z. Overexpression of SmMYC2 Increases the Production of Phenolic Acids in Salvia miltiorrhiza. FRONTIERS IN PLANT SCIENCE 2017; 8:1804. [PMID: 29230228 PMCID: PMC5708653 DOI: 10.3389/fpls.2017.01804] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/04/2017] [Indexed: 05/20/2023]
Abstract
MYC2 is a core transcription factor in the plant response to jasmonates. It also functions in secondary metabolism and various processes for growth and development. However, the knowledge about its role in Salvia miltiorrhiza is still very limited. We determined that the biosynthesis of salvianolic acid B (Sal B) was strongly induced in 2-month-old transgenic plants that over-expressed SmMYC2. In the roots of transgenic line 12 that over-expressed SmMYC2 (OEM-12), the Sal B concentration was as high as 5.95 ± 0.07 mg g-1, a level that was 1.88-fold higher than that in control plants that had been transformed with an empty vector. Neither tanshinone IIA nor cryptotanshinone was detected by high-performance liquid chromatography in any of the genotypes. Global transcriptomic analysis using RNA sequencing revealed that most enzyme-encoding genes for the phenylpropanoid biosynthesis pathway were up-regulated in the overexpression lines. Furthermore, both the phenylalanine and tyrosine biosynthesis pathways were activated in those transgenics. Our data demonstrate that overexpression of SmMYC2 promotes the production of phenolic acids by simultaneously activating both primary and secondary pathways for metabolism in S. miltiorrhiza.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Xiaoyan Cao
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an, China
| | - Zhezhi Wang
- Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, Shaanxi Normal University, Xi’an, China
| |
Collapse
|
33
|
Xin J, Zhang RC, Wang L, Zhang YQ. Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2017; 2017:7521363. [PMID: 28900463 PMCID: PMC5576426 DOI: 10.1155/2017/7521363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/21/2017] [Accepted: 05/16/2017] [Indexed: 12/12/2022]
Abstract
Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers.
Collapse
Affiliation(s)
- Jie Xin
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Rong-chao Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Lei Wang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yong-qing Zhang
- School of Pharmacy, Shan Dong University of Traditional Chinese Medicine, Jinan 250355, China
| |
Collapse
|
34
|
Liu Y, Sun G, Zhong Z, Ji L, Zhang Y, Zhou J, Zheng X, Deng K. Overexpression of AtEDT1 promotes root elongation and affects medicinal secondary metabolite biosynthesis in roots of transgenic Salvia miltiorrhiza. PROTOPLASMA 2017; 254:1617-1625. [PMID: 27915455 DOI: 10.1007/s00709-016-1045-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/07/2016] [Indexed: 05/13/2023]
Abstract
Medicinal secondary metabolites (salvianolic acids and tanshinones) are valuable natural bioactive compounds in Salvia miltiorrhiza and have widespread applications. Improvement of medicinal secondary metabolite accumulation through biotechnology is necessary and urgent to satisfy their increasing demand. Herein, it was demonstrated that the overexpression of the transcription factor Arabidopsis thaliana-enhanced drought tolerance 1 (AtEDT1) could affect medicinal secondary metabolite accumulation. In this study, we observed that the transgenic lines significantly conferred drought tolerance phenotype. Meanwhile, we found that the overexpression of AtEDT1 promoted root elongation in S. miltiorrhiza. Interestingly, we also found that the overexpression of AtEDT1 determined the accumulation of salvianolic acids, such as rosmarinic acid, lithospermic acid, salvianolic acid B, and total salvianolic acids due to the induction of the expression levels of salvianolic acid biosynthetic genes. Conversely, S. miltiorrhiza plants overexpressing the AtEDT1 transgene showed a decrease in tanshinone synthesis. Our results demonstrated that the overexpression of AtEDT1 significantly increased the accumulation of salvianolic acids in S. miltiorrhiza. Further studies are required to better elucidate the functional role of AtEDT1 in the regulation of phytochemical compound synthesis.
Collapse
Affiliation(s)
- Yu Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Geng Sun
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zhaohui Zhong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Linyi Ji
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yong Zhang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Jianping Zhou
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xuelian Zheng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| | - Kejun Deng
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.
| |
Collapse
|
35
|
Li H, Fu Y, Sun H, Zhang Y, Lan X. Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum. Sci Rep 2017; 7:74. [PMID: 28250432 PMCID: PMC5428373 DOI: 10.1038/s41598-017-00078-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 01/30/2017] [Indexed: 11/23/2022] Open
Abstract
Dracocephalum tanguticum Maxim, a Lamiaceae species endemic to the Qinghai-Tibetan Plateau and adjacent regions, is an important ornamental, medicinal and aromatic herb. In this study, a comprehensive transcriptome of 18 libraries from six organs namely, roots, stems, leaves, sepals, flowers and seeds of D. tanguticum were generated. More than 100 Gb of sequence data were obtained and assembled de novo into 187,447 transcripts, including 151,463 unigenes, among which the six organs shared 17.7% (26,841). In addition, all unigenes were assigned to 362 pathways, in which 'biosynthesis of secondary metabolites' is the second enriched pathway. Furthermore, rosmarinic acid (RA) is one of the multifunctional phenolic bioactive compounds produced in some Lamiaceae species. The six organs of D. tanguticum were confirmed to produce RA. A total of 22 predicted biosynthetic genes related to RA from the transcriptome were further isolated. Two of these genes were identified as candidates by evaluating the correlation coefficient between the RA contents and the expression of the predicted biosynthetic genes in the six organs. The new sequence information will improve the knowledge of D. tanguticum, as well as provide a reference tool for future studies of biosynthetic genes related to RA in this species.
Collapse
Affiliation(s)
- Huie Li
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
- College of Agriculture, Guizhou University, Guiyang, 550025, China
| | - Yaru Fu
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Hao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Yanfu Zhang
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China
| | - Xiaozhong Lan
- Medicinal Plants Research Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China.
- TAAHC-SWU Medicinal Plants Joint Research and Development Centre, Tibet Agricultural and Animal Husbandry College, Nyingchi, 860000, China.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Ji A, Jia J, Xu Z, Li Y, Bi W, Ren F, He C, Liu J, Hu K, Song J. Transcriptome-Guided Mining of Genes Involved in Crocin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:518. [PMID: 28443112 PMCID: PMC5387100 DOI: 10.3389/fpls.2017.00518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/23/2017] [Indexed: 05/11/2023]
Abstract
Gardenia jasminoides is used in traditional Chinese medicine and has drawn attention as a rich source of crocin, a compound with reported activity against various cancers, depression and cardiovascular disease. However, genetic information on the crocin biosynthetic pathway of G. jasminoides is scarce. In this study, we performed a transcriptome analysis of the leaves, green fruits, and red fruits of G. jasminoides to identify and predict the genes that encode key enzymes responsible for crocin production, compared with Crocus sativus. Twenty-seven putative pathway genes were specifically expressed in the fruits, consistent with the distribution of crocin in G. jasminoides. Twenty-four of these genes were reported for the first time, and a novel CCD4a gene was predicted that encodes carotenoid cleavage dioxygenase leading to crocin synthesis, in contrast to CCD2 of C. sativus. In addition, 6 other candidate genes (ALDH12, ALDH14, UGT94U1, UGT86D1, UGT71H4, and UGT85K18) were predicted to be involved in crocin biosynthesis following phylogenetic analysis and different gene expression profiles. Identifying the genes that encode key enzymes should help elucidate the crocin biosynthesis pathway.
Collapse
Affiliation(s)
- Aijia Ji
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Jing Jia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Zhichao Xu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Ying Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Wu Bi
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Fengming Ren
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
- Chongqing Institute of Medicinal Plant CultivationChongqing, China
| | - Chunnian He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
| | - Jie Liu
- Chongqing Institute of Medicinal Plant CultivationChongqing, China
| | - Kaizhi Hu
- Chongqing Institute of Medicinal Plant CultivationChongqing, China
- *Correspondence: Kaizhi Hu
| | - Jingyuan Song
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing, China
- Chongqing Institute of Medicinal Plant CultivationChongqing, China
- Jingyuan Song
| |
Collapse
|
38
|
Xu Q, Zhu J, Zhao S, Hou Y, Li F, Tai Y, Wan X, Wei C. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis. FRONTIERS IN PLANT SCIENCE 2017; 8:1205. [PMID: 28744294 PMCID: PMC5504172 DOI: 10.3389/fpls.2017.01205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/26/2017] [Indexed: 05/22/2023]
Abstract
Characteristic secondary metabolites, including flavonoids, theanine and caffeine, are important components of Camellia sinensis, and their biosynthesis has attracted widespread interest. Previous studies on the biosynthesis of these major secondary metabolites using next-generation sequencing technologies limited the accurately prediction of full-length (FL) splice isoforms. Herein, we applied single-molecule sequencing to pooled tea plant tissues, to provide a more complete transcriptome of C. sinensis. Moreover, we identified 94 FL transcripts and four alternative splicing events for enzyme-coding genes involved in the biosynthesis of flavonoids, theanine and caffeine. According to the comparison between long-read isoforms and assemble transcripts, we improved the quality and accuracy of genes sequenced by short-read next-generation sequencing technology. The resulting FL transcripts, together with the improved assembled transcripts and identified alternative splicing events, enhance our understanding of genes involved in the biosynthesis of characteristic secondary metabolites in C. sinensis.
Collapse
|