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Wang J, Wang Z, Wang P, Wu J, Kong L, Ma L, Jiang S, Ren W, Liu W, Guo Y, Ma W, Liu X. Genome-wide identification of YABBY gene family and its expression pattern analysis in Astragalus mongholicus. PLANT SIGNALING & BEHAVIOR 2024; 19:2355740. [PMID: 38776425 PMCID: PMC11123558 DOI: 10.1080/15592324.2024.2355740] [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: 03/12/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
During plant growth and development, the YABBY gene plays a crucial role in the morphological structure, hormone signaling, stress resistance, crop breeding, and agricultural production of plant lateral organs, leaves, flowers, and fruits. Astragalus mongholicus is a perennial herbaceous plant in the legume family, widely used worldwide due to its high medicinal and edible value. However, there have been no reports of the YABBY gene family in A. mongholicus. This study used bioinformatics methods, combined with databases and analysis websites, to systematically analyze the AmYABBY gene family in the entire genome of A. mongholicus and verified its expression patterns in different tissues of A. mongholicus through transcriptome data and qRT-PCR experiments. A total of seven AmYABBY genes were identified, which can be divided into five subfamilies and distributed on three chromosomes. Two pairs of AmYABBY genes may be involved in fragment duplication on three chromosomes. All AmYABBY proteins have a zinc finger YABBY domain, and members of the same group have similar motif composition and intron - exon structure. In the promoter region of the genes, light-responsive and MeJa-response cis-elements are dominant. AmYABBY is highly expressed in stems and leaves, especially AmYABBY1, AmYABBY2, and AmYABBY3, which play important roles in the growth and development of stems and leaves. The AmYABBY gene family regulates the growth and development of A. mongholicus. In summary, this study provides a theoretical basis for in-depth research on the function of the AmYABBY gene and new insights into the molecular response mechanism of the growth and development of the traditional Chinese medicine A. mongholicus.
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Affiliation(s)
- Jiamei Wang
- Equipment Department, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Panpan Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jianhao Wu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lingyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lengleng Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shan Jiang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weili Liu
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yanli Guo
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Ma
- Pharmacy of College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, Jiamusi, China
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Li XL, Zhang JQ, Shen XJ, Zhang Y, Guo DA. Overview and limitations of database in global traditional medicines: A narrative review. Acta Pharmacol Sin 2024:10.1038/s41401-024-01353-1. [PMID: 39095509 DOI: 10.1038/s41401-024-01353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024] Open
Abstract
The study of traditional medicine has garnered significant interest, resulting in various research areas including chemical composition analysis, pharmacological research, clinical application, and quality control. The abundance of available data has made databases increasingly essential for researchers to manage the vast amount of information and explore new drugs. In this article we provide a comprehensive overview and summary of 182 databases that are relevant to traditional medicine research, including 73 databases for chemical component analysis, 70 for pharmacology research, and 39 for clinical application and quality control from published literature (2000-2023). The review categorizes the databases by functionality, offering detailed information on websites and capacities to facilitate easier access. Moreover, this article outlines the primary function of each database, supplemented by case studies to aid in database selection. A practical test was conducted on 68 frequently used databases using keywords and functionalities, resulting in the identification of highlighted databases. This review serves as a reference for traditional medicine researchers to choose appropriate databases and also provides insights and considerations for the function and content design of future databases.
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Affiliation(s)
- Xiao-Lan Li
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Qing Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xuan-Jing Shen
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zhang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Research Center of TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Jin Q, Yang K, Zhang Y, Zhang S, Liu Z, Guan Y, Zhang L, Zhang Y, Wang Q. Physiological and molecular mechanisms of silicon and potassium on mitigating iron-toxicity stress in Panax ginseng. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:108975. [PMID: 39084170 DOI: 10.1016/j.plaphy.2024.108975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 07/01/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024]
Abstract
Iron plays a crucial role in plant chlorophyll synthesis, respiration, and plant growth. However, excessive iron content can contribute to ginseng poisoning. We previously discovered that the application of silicon (Si) and potassium (K) can mitigate the iron toxicity on ginseng. To elucidate the molecular mechanism of how Si and K alleviate iron toxicity stress in ginseng. We investigated the physiological and transcriptional effects of exogenous Si and K on Panax ginseng. The results suggested that the leaves of ginseng with Si and K addition under iron stress increased antioxidant enzyme activity or secondary metabolite content, such as phenylalanine amino-lyase, polyphenol oxidase, ascorbate peroxidase, total phenols and lignin, by 6.21%-25.94%, 30.12%-309.19%, 32.26%-38.82%, 7.81%-23.66%, and 4.68%-48.42%, respectively. Moreover, Si and K increased the expression of differentially expressed genes (DEGs) associated with resistance to both biotic and abiotic stress, including WRKY (WRKY1, WRKY5, and WRKY65), bHLH (bHLH35, bHLH66, bHLH128, and bHLH149), EREBP, ERF10 and ZIP. Additionally, the amount of DEGs of ginseng by Si and K addition was enriched in metabolic processes, single-organism process pathways, signal transduction, metabolism, synthesis and disease resistance. In conclusion, the utilization of Si and K can potentially reduce the accumulation of iron in ginseng, regulate the expression of iron tolerance genes, and enhance the antioxidant enzyme activity and secondary metabolite production in both leaves and roots, thus alleviating the iron toxicity stress in ginseng.
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Affiliation(s)
- Qiao Jin
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Kexin Yang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Yayu Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China; College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610106, China
| | - Shuna Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Zhengbo Liu
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Yiming Guan
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Linlin Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Yue Zhang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China
| | - Qiuxia Wang
- Institute of Special Wild Economic Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, 130112, China; Jilin Provincial Key Laboratory of Traditional Chinese Medicinal Materials Cultivation and Propagation, Changchun, 130112, China.
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Wang P, Wang Z, Cao H, He J, Qin C, He L, Liu B, Wang J, Kong L, Ren W, Liu X, Ma W. Genome-wide identification and expression pattern analysis of the GRF transcription factor family in Astragalus mongholicus. Mol Biol Rep 2024; 51:618. [PMID: 38705956 DOI: 10.1007/s11033-024-09581-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Astragalus membranaceus is a plant of the Astragalus genus, which is used as a traditional Chinese herbal medicine with extremely high medicinal and edible value. Astragalus mongholicus, as one of the representative medicinal materials with the same origin of medicine and food, has a rising market demand for its raw materials, but the quality is different in different production areas. Growth-regulating factors (GRF) are transcription factors unique to plants that play important roles in plant growth and development. Up to now, there is no report about GRF in A. mongholicus. METHODS AND RESULTS This study conducted a genome-wide analysis of the AmGRF gene family, identifying a total of nine AmGRF genes that were classified into subfamily V based on phylogenetic relationships. In the promoter region of the AmGRF gene, we successfully predicted cis-elements that respond to abiotic stress, growth, development, and hormone production in plants. Based on transcriptomic data and real-time quantitative polymerase chain reaction (qPCR) validation, the results showed that AmGRFs were expressed in the roots, stems, and leaves, with overall higher expression in leaves, higher expression of AmGRF1 and AmGRF8 in roots, and high expression levels of AmGRF1 and AmGRF9 in stems. CONCLUSIONS The results of this study provide a theoretical basis for the further exploration of the functions of AmGRFs in plant growth and development.
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Affiliation(s)
- Panpan Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Zhen Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Huiyan Cao
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Jiajun He
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Chen Qin
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Lianqing He
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Bo Liu
- Library, Harbin Cambridge University, Harbin, 150069, China
| | - Jiamei Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
- Equipment department, Heilongjiang University of Chinese Medicine, Haerbin, 150040, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
| | - Xiubo Liu
- Jiamusi College, Heilongjiang University of Chinese Medicine, Jiamusi, 154007, China.
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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Ouyang P, Kang D, You W, Shen X, Mo X, Liu Y. Pogostemon cablin essential oil affects anxiety- and depressive-like behaviors and the gut microbiota in chronic unpredictable mild stress model rats. Front Nutr 2024; 11:1303002. [PMID: 38419848 PMCID: PMC10899464 DOI: 10.3389/fnut.2024.1303002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
The gut microbiota is thought to be an important factor that influences brain processes and behaviors through the gut-brain axis. Pogostemon cablin is used in traditional Chinese medicine (TCM) to treat gastrointestinal symptoms. Patchouli essential oil (PCO), the main active agent in P. cablin, is used in aromatherapy for stress relief. The aim of our study was to investigate the effects of orally administered PCO on anxiety- and depressive-like behaviors and the gut microbiota. We constructed a rat model of chronic unpredictable mild stress (CUMS) and explored the anxiolytic- and antidepressant-like effects of PCO using the open field test (OFT) and forced swim test (FST). Changes in the abundance of the gut microbiota, short-chain fatty acids (SCFAs), and other related molecules were assessed to determine the role of the gut microbiota. Our results showed that CUMS induced an anxiety-like phenotype in the OFT, which was reversed by PCO, and that PCO also significantly mitigated the depression-like behaviors caused by CUMS in the FST. Furthermore, we found that PCO increased the relative abundances of several probiotics, including Bacteroides and Blautia, and decreased the relative abundances of Ruminococcus_1 and Ruminococcus_2, which were increased by CUMS. Regarding SCFAs, the metabolites of the gut microbiota, PCO increased the concentration of propionic acid and decreased that of caproic acid. Finally, PCO restored the serotonin (5-hydroxytryptamine, 5-HT) level in the hippocampus, which had been decreased by CUMS. The results of this study suggested that PCO can improve stress-related anxiety- and depression-like behaviors and might exert its effects on the central nervous system through interactions with the gut microbiota.
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Affiliation(s)
- Puyue Ouyang
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Dali Kang
- School of Traditional Chinese Medicine, Shenyang Medical College, Shenyang, China
- College of Medical Technology, Ningbo College of Health Sciences, Ningbo, China
| | - Weijing You
- College of Medical Technology, Ningbo College of Health Sciences, Ningbo, China
| | - Xiaozhong Shen
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Xiaolu Mo
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Yao Liu
- College of Chinese Materia Medica, Guangdong Food and Drug Vocational College, Guangzhou, China
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6
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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: 2] [Impact Index Per Article: 2.0] [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.
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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.
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Chen J, Wu W, Ding X, Zhang D, Dai C, Pan H, Shi P, Wu C, Zhang J, Zhao J, Liao B, Qiu X, Huang Z. Genome-wide characterization of regulator of chromosome condensation 1 (RCC1) gene family in Artemisia annua L. revealed a conservation evolutionary pattern. BMC Genomics 2023; 24:692. [PMID: 37980503 PMCID: PMC10657572 DOI: 10.1186/s12864-023-09786-4] [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: 02/27/2023] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
BACKGROUND Artemisia annua is the major source for artemisinin production. The artemisinin content in A. annua is affected by different types of light especially the UV light. UVR8, a member of RCC1 gene family was found to be the UV-B receptor in plants. The gene structures, evolutionary history and expression profile of UVR8 or RCC1 genes remain undiscovered in A. annua. RESULTS Twenty-two RCC1 genes (AaRCC1) were identified in each haplotype genome of two diploid strains of A. annua, LQ-9 and HAN1. Varied gene structures and sequences among paralogs were observed. The divergence of most RCC1 genes occurred at 46.7 - 51 MYA which overlapped with species divergence of core Asteraceae during the Eocene, while no recent novel RCC1 members were found in A. annua genome. The number of RCC1 genes remained stable among eudicots and RCC1 genes underwent purifying selection. The expression profile of AaRCC1 is analogous to that of Arabidopsis thaliana (AtRCC1) when responding to environmental stress. CONCLUSIONS This study provided a comprehensive characterization of the AaRCC1 gene family and suggested that RCC1 genes were conserved in gene number, structures, constitution of amino acids and expression profiles among eudicots.
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Affiliation(s)
- Jieting Chen
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Wenguang Wu
- Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Danchun Zhang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Chunyan Dai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hengyu Pan
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Peiqi Shi
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | | | - Jun Zhang
- Sunribio Co.Ltd, Shenzhen, 518101, China
| | | | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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Kielich N, Mazur O, Musidlak O, Gracz-Bernaciak J, Nawrot R. Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research. Brief Funct Genomics 2023:elad050. [PMID: 37952099 DOI: 10.1093/bfgp/elad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 11/14/2023] Open
Abstract
Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.
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Affiliation(s)
- Natalia Kielich
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oliwia Mazur
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Oskar Musidlak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Gracz-Bernaciak
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
| | - Robert Nawrot
- Department of Molecular Virology, Institute of Experimental Biology, Adam Mickiewicz University, Poznań, Poland
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Su H, Ding X, Liao B, Zhang D, Huang J, Bai J, Xu S, Zhang J, Xu W, Qiu X, Gong L, Huang Z. Comparative chloroplast genomes provided insights into the evolution and species identification on the Datureae plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1270052. [PMID: 37941675 PMCID: PMC10628451 DOI: 10.3389/fpls.2023.1270052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Generally, chloroplast genomes of angiosperms are always highly conserved but carry a certain number of variation among species. In this study, chloroplast genomes of 13 species from Datureae tribe that are of importance both in ornamental gardening and medicinal usage were studied. In addition, seven chloroplast genomes from Datureae together with two from Solanaceae species retrieved from the National Center for Biotechnology Information (NCBI) were integrated into this study. The chloroplast genomes ranged in size from 154,686 to 155,979 and from 155,497 to 155,919 bp for species of Datura and Brugmansia, respectively. As to Datura and Brugmansia, a total of 128 and 132 genes were identified, in which 83 and 87 protein coding genes were identified, respectively; Furthermore, 37 tRNA genes and 8 rRNA genes were both identified in Datura and Brugmansia. Repeats analysis indicated that the number and type varied among species for Simple sequence repeat (SSR), long repeats, and tandem repeats ranged in number from 53 to 59, 98 to 99, and 22 to 30, respectively. Phylogenetic analysis based on the plastid genomes supported the monophyletic relationship among Datura and Brugmansia and Trompettia, and a refined phylogenic relationships among each individual was resolved. In addition, a species-specific marker was designed based on variation spot that resulted from a comparative analysis of chloroplast genomes and verified as effective maker for identification of D. stramonium and D. stramonium var. inermis. Interestingly, we found that 31 genes were likely to be under positive selection, including genes encoding ATP protein subunits, photosystem protein subunit, ribosome protein subunits, NAD(P)H dehydrogenase complex subunits, and clpP, petB, rbcL, rpoCl, ycf4, and cemA genes. These genes may function as key roles in the adaption to diverse environment during evolution. The diversification of Datureae members was dated back to the late Oligocene periods. These chloroplast genomes are useful genetic resources for taxonomy, phylogeny, and evolution for Datureae.
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Affiliation(s)
- He Su
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaoxia Ding
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baosheng Liao
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Danchun Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Juan Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Junqi Bai
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Subing Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jing Zhang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Wen Xu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xiaohui Qiu
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Lu Gong
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Zhihai Huang
- The Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
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10
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Liu Z, Du Y, Sun Z, Cheng B, Bi Z, Yao Z, Liang Y, Zhang H, Yao R, Kang S, Shi Y, Wan H, Qin D, Xiang L, Leng L, Chen S. Manual correction of genome annotation improved alternative splicing identification of Artemisia annua. PLANTA 2023; 258:83. [PMID: 37721598 DOI: 10.1007/s00425-023-04237-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/04/2023] [Indexed: 09/19/2023]
Abstract
Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic information, especially for species with complex genomes. Artemisia annua L. is the only commercial resource of artemisinin production though the content of artemisinin is still to be improved. Genome-based genetic modification and breeding are useful strategies to boost artemisinin content and therefore, ensure the supply of artemisinin and reduce costs, but better gene annotation is urgently needed. In this study, we manually corrected the newly released genome annotation of A. annua using second- and third-generation transcriptome data. We found that incorrect gene information may lead to differences in structural, functional, and expression levels compared to the original expectations. We also identified alternative splicing events and found that genome annotation information impacted identifying alternative splicing genes. We further demonstrated that genome annotation information and alternative splicing could affect gene expression estimation and gene function prediction. Finally, we provided a valuable version of A. annua genome annotation and demonstrated the importance of gene annotation in future research.
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Affiliation(s)
- Zhaoyu Liu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yupeng Du
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Zhihao Sun
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Bohan Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zenghao Bi
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Zhicheng Yao
- School of Information Engineering, Jingdezhen Ceramic University, Jingdezhen, 333403, China
| | - Yuting Liang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Huiling Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Run Yao
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shen Kang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Yuhua Shi
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huihua Wan
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Dou Qin
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi, 830000, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Prescription Laboratory of Xinjiang Traditional Uyghur Medicine, Xinjiang Institute of Traditional Uyghur Medicine, Urmuqi, 830000, China.
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Shilin Chen
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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11
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Liao X, Guo S, Liao B, Shen X, He W, Meng Y, Liang C, Pei J, Liu J, Zhang Y, Xu J, Chen S. Chromatin architecture of two different strains of Artemisia annua reveals the alterations in interaction and gene expression. PLANTA 2023; 258:74. [PMID: 37668722 DOI: 10.1007/s00425-023-04223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/02/2023] [Indexed: 09/06/2023]
Abstract
MAIN CONCLUSION The hierarchical architecture of chromatins affects the gene expression level of glandular secreting trichomes and the artemisinin biosynthetic pathway-related genes, consequently bringing on huge differences in the content of artemisinin and its derivatives of A. annua. The plant of traditional Chinese medicine "Qinghao" is called Artemisia annua L. in Chinese Pharmacopoeia. High content and the total amount of artemisinin is the main goal of A. annua breeding, nevertheless, the change of chromatin organization during the artemisinin synthesis process has not been discovered yet. This study intended to find the roles of chromatin structure in the production of artemisinin through bioinformatics and experimental validation. Chromosome conformation capture analysis was used to scrutinize the interactions among chromosomes and categorize various scales of chromatin during artemisinin synthesis in A. annua. To confirm the effect of the changes in chromatin structure, Hi-C and RNA-sequencing were performed on two different strains to find the correlation between chromatin structure and gene expression levels on artemisinin synthesis progress and regulation. Our results revealed that the frequency of intra-chromosomal interactions was higher in the inter-chromosomal interactions between the root and leaves on a high artemisinin production strain (HAP) compared to a low artemisinin production strain (LAP). We found that compartmental transition was connected with interactions among different chromatins. Interestingly, glandular secreting trichomes (GSTs) and the artemisinin biosynthetic pathway (ABP) related genes were enriched in the areas which have the compartmental transition, reflecting the regulation of artemisinin synthesis. Topologically associated domain boundaries were associated with various distributions of genes and expression levels. Genes associated with ABP and GST in the adjacent loop were highly expressed, suggesting that epigenetic regulation plays an important role during artemisinin synthesis and glandular secreting trichomes production process. Chromatin structure could show an important status in the mechanisms of artemisinin synthesis process in A. annua.
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Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wenrui He
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ying Meng
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Conglian Liang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, 100193, China
| | - Yongqing Zhang
- Pharmacy College, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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12
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Xie C, Zhan T, Huang J, Lan J, Shen L, Wang H, Zheng X. Functional characterization of nine critical genes encoding rate-limiting enzymes in the flavonoid biosynthesis of the medicinal herb Grona styracifolia. BMC PLANT BIOLOGY 2023; 23:299. [PMID: 37268882 DOI: 10.1186/s12870-023-04290-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/16/2023] [Indexed: 06/04/2023]
Abstract
Grona styracifolia is a photophilous legume that contains abundant flavonoids with multiple pharmacological activities, which is used to cure urethral and biliary calculus in China for thousands of years. The authentication of the rate-limiting enzymes involved in the flavonoids biosynthesis pathway enabled a better understanding of the molecular aspect of quality formation and modulation of this medicinal herb. In this study, the chemical distribution characteristics and content of flavonoids in different tissues of Grona styracifolia were analyzed using ultraperormance liquid chromatography coupled with Q-TOF mass spectrometry and showed that active flavonoids were primarily synthesized and stored in the leaves. Subsequently, RNA sequencing (RNA-seq)-based transcriptome profiling of the different tissues revealed that the flavonoids biosynthesis in the leaves was the most active. Meanwhile, 27 full-length transcripts inferred encoding vital enzymes involved in the flavonoids biosynthesis were preliminarily excavated. Finally, four CHSs, four CHIs, and one FNSII were successfully characterized by heterologous expression, which involved in three rate-limiting steps of the flavonoid biosynthetic pathway. In conclusion, these results laid a foundation for further investigation of the molecular mechanism of the biosynthesis and modulation of active flavonoids in Grona styracifolia.
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Affiliation(s)
- Chunzhu Xie
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Ting Zhan
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jinqin Huang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jun Lan
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Lingling Shen
- Guangzhou Analytical Applications Center, Shimadzu (China) Co., LTD, Guangzhou, 510010, China
| | - Hongbin Wang
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China.
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13
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Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
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Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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14
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Zhao D, Qin Y, Liu J, Tang K, Lu S, Liu Z, Lin Y, Zhang C, Huang F, Chang J, Li C, Tian M, Ma Y, Li X, Zhou C, Li X, Peng X, Jin N, Jiang C. Orally administered BZL-sRNA-20 oligonucleotide targeting TLR4 effectively ameliorates acute lung injury in mice. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2219-0. [PMID: 36808291 PMCID: PMC9938506 DOI: 10.1007/s11427-022-2219-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/22/2022] [Indexed: 02/21/2023]
Abstract
The global COVID-19 pandemic emerged at the end of December 2019. Acute respiratory distress syndrome (ARDS) and acute lung injury (ALI) are common lethal outcomes of bacterial lipopolysaccharide (LPS), avian influenza virus, and SARS-CoV-2. Toll-like receptor 4 (TLR4) is a key target in the pathological pathway of ARDS and ALI. Previous studies have reported that herbal small RNAs (sRNAs) are a functional medical component. BZL-sRNA-20 (Accession number: B59471456; Family ID: F2201.Q001979.B11) is a potent inhibitor of Toll-like receptor 4 (TLR4) and pro-inflammatory cytokines. Furthermore, BZL-sRNA-20 reduces intracellular levels of cytokines induced by lipoteichoic acid (LTA) and polyinosinic-polycytidylic acid (poly (I:C)). We found that BZL-sRNA-20 rescued the viability of cells infected with avian influenza H5N1, SARS-CoV-2, and several of its variants of concern (VOCs). Acute lung injury induced by LPS and SARS-CoV-2 in mice was significantly ameliorated by the oral medical decoctosome mimic (bencaosome; sphinganine (d22:0)+BZL-sRNA-20). Our findings suggest that BZL-sRNA-20 could be a pan-anti-ARDS ALI drug.
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Affiliation(s)
- Dandan Zhao
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Yuhao Qin
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Jiaqi Liu
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Kegong Tang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Shuaiyao Lu
- grid.506261.60000 0001 0706 7839Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650031 China
| | - Zirui Liu
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122 China
| | - Yexuan Lin
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Cong Zhang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China ,grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Fengming Huang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Jiahui Chang
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Chang Li
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122 China
| | - Mingyao Tian
- grid.410727.70000 0001 0526 1937Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122 China
| | - Yiming Ma
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Xiaoyun Li
- grid.506261.60000 0001 0706 7839State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005 China
| | - Congzhao Zhou
- grid.59053.3a0000000121679639Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027 China
| | - Xiao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medical Sciences, Kunming, 650031, China.
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, 130122, China.
| | - Chengyu Jiang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China.
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15
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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [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: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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16
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Oriola AO, Oyedeji AO. Essential Oils and Their Compounds as Potential Anti-Influenza Agents. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227797. [PMID: 36431899 PMCID: PMC9693178 DOI: 10.3390/molecules27227797] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]
Abstract
Essential oils (EOs) are chemical substances, mostly produced by aromatic plants in response to stress, that have a history of medicinal use for many diseases. In the last few decades, EOs have continued to gain more attention because of their proven therapeutic applications against the flu and other infectious diseases. Influenza (flu) is an infectious zoonotic disease that affects the lungs and their associated organs. It is a public health problem with a huge health burden, causing a seasonal outbreak every year. Occasionally, it comes as a disease pandemic with unprecedentedly high hospitalization and mortality. Currently, influenza is managed by vaccination and antiviral drugs such as Amantadine, Rimantadine, Oseltamivir, Peramivir, Zanamivir, and Baloxavir. However, the adverse side effects of these drugs, the rapid and unlimited variabilities of influenza viruses, and the emerging resistance of new virus strains to the currently used vaccines and drugs have necessitated the need to obtain more effective anti-influenza agents. In this review, essential oils are discussed in terms of their chemistry, ethnomedicinal values against flu-related illnesses, biological potential as anti-influenza agents, and mechanisms of action. In addition, the structure-activity relationships of lead anti-influenza EO compounds are also examined. This is all to identify leading agents that can be optimized as drug candidates for the management of influenza. Eucalyptol, germacrone, caryophyllene derivatives, eugenol, terpin-4-ol, bisabolene derivatives, and camphecene are among the promising EO compounds identified, based on their reported anti-influenza activities and plausible molecular actions, while nanotechnology may be a new strategy to achieve the efficient delivery of these therapeutically active EOs to the active virus site.
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17
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Gong L, Ding X, Guan W, Zhang D, Zhang J, Bai J, Xu W, Huang J, Qiu X, Zheng X, Zhang D, Li S, Huang Z, Su H. Comparative chloroplast genome analyses of Amomum: insights into evolutionary history and species identification. BMC PLANT BIOLOGY 2022; 22:520. [PMID: 36352400 PMCID: PMC9644571 DOI: 10.1186/s12870-022-03898-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Species in genus Amomum always have important medicinal and economic values. Classification of Amomum using morphological characters has long been a challenge because they exhibit high similarity. The main goals of this study were to mine genetic markers from cp genomes for Amomum species identification and discover their evolutionary history through comparative analysis. RESULTS Three species Amomum villosum, Amomum maximum and Amomum longipetiolatum were sequenced and annotated for the complete chloroplast (cp) genomes, and the cp genomes of A. longipetiolatum and A. maximum were the first reported. Three cp genomes exhibited typical quadripartite structures with 163,269-163,591 bp in length. Each genome encodes 130 functional genes including 79 protein-coding, 26 tRNAs and 3 rRNAs genes. 113-152 SSRs and 99 long repeats were identified in the three cp genomes. By designing specific primers, we amplified the highly variable loci and the mined genetic marker ccsA exhibited a relatively high species identification resolution in Amomum. The nonsynonymous and synonymous substitution ratios (Ka/Ks) in Amomum and Alpinia showed that most genes were subjected to a purifying selection. Phylogenetic analysis revealed the evolutionary relationships of Amomum and Alpinia species and proved that Amomum is paraphyletic. In addition, the sequenced sample of A. villosum was found to be a hybrid, becoming the first report of natural hybridization of this genus. Meanwhile, the high-throughput sequencing-based ITS2 analysis was proved to be an efficient tool for interspecific hybrid identification and with the help of the chloroplast genome, the hybrid parents can be also be determined. CONCLUSION The comparative analysis and mined genetic markers of cp genomes were conducive to species identification and evolutionary relationships of Amomum.
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Affiliation(s)
- Lu Gong
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaoxia Ding
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Wan Guan
- Luqiao Hospital, Taizhou Enze Medical Center (Group), Taizhou, Zhejiang, China
| | - Danchun Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
| | - Jing Zhang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Junqi Bai
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Wen Xu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Juan Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiaohui Qiu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Danyan Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Shijie Li
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Zhihai Huang
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
| | - He Su
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, Guangzhou, Guangdong, China.
- Guangzhou Key Laboratory of Chirality Research on Active Components of Traditional Chinese Medicine, Guangzhou, Guangdong, China.
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18
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Genomic, transcriptomic, and epigenomic analysis of a medicinal snake, Bungarus multicinctus, to provides insights into the origin of Elapidae neurotoxins. Acta Pharm Sin B 2022; 13:2234-2249. [DOI: 10.1016/j.apsb.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 11/11/2022] [Indexed: 11/19/2022] Open
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19
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Guo L, Yao H, Chen W, Wang X, Ye P, Xu Z, Zhang S, Wu H. Natural products of medicinal plants: biosynthesis and bioengineering in post-genomic era. HORTICULTURE RESEARCH 2022; 9:uhac223. [PMID: 36479585 PMCID: PMC9720450 DOI: 10.1093/hr/uhac223] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 09/22/2022] [Indexed: 06/01/2023]
Abstract
Globally, medicinal plant natural products (PNPs) are a major source of substances used in traditional and modern medicine. As we human race face the tremendous public health challenge posed by emerging infectious diseases, antibiotic resistance and surging drug prices etc., harnessing the healing power of medicinal plants gifted from mother nature is more urgent than ever in helping us survive future challenge in a sustainable way. PNP research efforts in the pre-genomic era focus on discovering bioactive molecules with pharmaceutical activities, and identifying individual genes responsible for biosynthesis. Critically, systemic biological, multi- and inter-disciplinary approaches integrating and interrogating all accessible data from genomics, metabolomics, structural biology, and chemical informatics are necessary to accelerate the full characterization of biosynthetic and regulatory circuitry for producing PNPs in medicinal plants. In this review, we attempt to provide a brief update on the current research of PNPs in medicinal plants by focusing on how different state-of-the-art biotechnologies facilitate their discovery, the molecular basis of their biosynthesis, as well as synthetic biology. Finally, we humbly provide a foresight of the research trend for understanding the biology of medicinal plants in the coming decades.
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Affiliation(s)
- Li Guo
- Corresponding authors. E-mails: ;
| | | | | | - Xumei Wang
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Peng Ye
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zhichao Xu
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Sisheng Zhang
- State Key laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory For Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hong Wu
- Corresponding authors. E-mails: ;
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20
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Emerging biotechnology applications in natural product and synthetic pharmaceutical analyses. Acta Pharm Sin B 2022; 12:4075-4097. [DOI: 10.1016/j.apsb.2022.08.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/15/2022] Open
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21
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Xu J, Liao B, Yuan L, Shen X, Liao X, Wang J, Hu H, Huang Z, Xiang L, Chen S. 50th anniversary of artemisinin: From the discovery to allele-aware genome assembly of Artemisia annua. MOLECULAR PLANT 2022; 15:1243-1246. [PMID: 35869631 DOI: 10.1016/j.molp.2022.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ling Yuan
- Kentucky Tobacco Research and Development Center, and Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Xuejiao Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jigang Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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22
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Liao B, Shen X, Xiang L, Guo S, Chen S, Meng Y, Liang Y, Ding D, Bai J, Zhang D, Czechowski T, Li Y, Yao H, Ma T, Howard C, Sun C, Liu H, Liu J, Pei J, Gao J, Wang J, Qiu X, Huang Z, Li H, Yuan L, Wei J, Graham I, Xu J, Zhang B, Chen S. Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield. MOLECULAR PLANT 2022; 15:1310-1328. [PMID: 35655434 DOI: 10.1016/j.molp.2022.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 03/25/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Artemisia annua is the major natural source of artemisinin, an anti-malarial medicine commonly used worldwide. Here, we present chromosome-level haploid maps for two A. annua strains with different artemisinin contents to explore the relationships between genomic organization and artemisinin production. High-fidelity sequencing, optical mapping, and chromatin conformation capture sequencing were used to assemble the heterogeneous and repetitive genome and resolve the haplotypes of A. annua. Approximately 50,000 genes were annotated for each haplotype genome, and a triplication event that occurred approximately 58.12 million years ago was examined for the first time in this species. A total of 3,903,467-5,193,414 variants (SNPs, indels, and structural variants) were identified in the 1.5-Gb genome during pairwise comparison between haplotypes, consistent with the high heterozygosity of this species. Genomic analyses revealed a correlation between artemisinin concents and the copy number of amorpha-4,11-diene synthase genes. This correlation was further confirmed by resequencing of 36 A. annua samples with varied artemisinin contents. Circular consensus sequencing of transcripts facilitated the detection of paralog expression. Collectively, our study provides chromosome-level allele-aware genome assemblies for two A. annua strains and new insights into the biosynthesis of artemisinin and its regulation, which will contribute to conquering malaria worldwide.
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Affiliation(s)
- Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shuai Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shiyu Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Ying Meng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yu Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Dandan Ding
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Junqi Bai
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Dong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Tomasz Czechowski
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Yi Li
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Tingyu Ma
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Caroline Howard
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1RQ, UK
| | - Chao Sun
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Haitao Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jihai Gao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jigang Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Artemisinin Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaohui Qiu
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Hongyi Li
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ling Yuan
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510520, China
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| | - Ian Graham
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Boli Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
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23
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Wang L, Ding X, Huang Q, Hu B, Liang L, Wang Q. Gllac7 Is Induced by Agricultural and Forestry Residues and Exhibits Allelic Expression Bias in Ganoderma lucidum. Front Microbiol 2022; 13:890686. [PMID: 35847055 PMCID: PMC9279560 DOI: 10.3389/fmicb.2022.890686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Ganoderma lucidum has a wide carbon spectrum, while the expression profile of key genes relevant to carbon metabolism on different carbon sources has been seldom studied. Here, the transcriptomes of G. lucidum mycelia cultured on each of 19 carbon sources were conducted. In comparison with glucose, 16 to 1,006 genes were upregulated and 7 to 1,865 genes were downregulated. Significant gene expression dynamics and induced activity were observed in laccase genes when using agricultural and forestry residues (AFRs) as solo carbon sources. Furthermore, study of laccase gene family in two haploids of G. lucidum GL0102 was conducted. Totally, 15 and 16 laccase genes were identified in GL0102_53 and GL0102_8, respectively, among which 15 pairs were allelic genes. Gene structures were conserved between allelic laccase genes, while sequence variations (most were SNPs) existed. Nine laccase genes rarely expressed on all the tested carbon sources, while the other seven genes showed high expression level on AFRs, especially Gllac2 and Gllac7, which showed 5- to 1,149-fold and 4- to 94-fold upregulation in mycelia cultured for 5 days, respectively. The expression of H53lac7 was consistently higher than that of H8lac7_1 on all the carbon sources except XM, exhibiting a case of allelic expression bias. A total of 47 SNPs and 3 insertions/deletions were observed between promoters of H53lac7 and H8lac7_1, which lead to differences in predicted binding sites of zinc fingers. These results provide scientific data for understanding the gene expression profile and regulatory role on different carbon sources and may support further functional research of laccase.
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Affiliation(s)
- Lining Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Xiaoxia Ding
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qinghua Huang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Biao Hu
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Lei Liang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingfu Wang
- Guangdong Engineering Laboratory of Biomass High-Value Utilization, Guangdong Plant Fiber Comprehensive Utilization Engineering Technology Research and Development Center, Guangzhou Key Laboratory of Biomass Comprehensive Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
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Wu HY, Shaw PC. Strategies for molecular authentication of herbal products: from experimental design to data analysis. Chin Med 2022; 17:38. [PMID: 35317843 PMCID: PMC8939074 DOI: 10.1186/s13020-022-00590-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/02/2022] [Indexed: 12/22/2022] Open
Abstract
Molecular herbal authentication has gained worldwide popularity in the past decade. DNA-based methods, including DNA barcoding and species-specific amplification, have been adopted for herbal identification by various pharmacopoeias. Development of next-generating sequencing (NGS) drastically increased the throughput of sequencing process and has sped up sequence collection and assembly of organelle genomes, making more and more reference sequences/genomes available. NGS allows simultaneous sequencing of multiple reads, opening up the opportunity of identifying multiple species from one sample in one go. Two major experimental approaches have been applied in recent publications of identification of herbal products by NGS, the PCR-dependent DNA metabarcoding and PCR-free genome skimming/shotgun metagenomics. This review provides a brief introduction of the use of DNA metabarcoding and genome skimming/shotgun metagenomics in authentication of herbal products and discusses some important considerations in experimental design for botanical identification by NGS, with a specific focus on quality control, reference sequence database and different taxon assignment programs. The potential of quantification or abundance estimation by NGS is discussed and new scientific findings that could potentially interfere with accurate taxon assignment and/or quantification is presented.
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Affiliation(s)
- Hoi-Yan Wu
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China. .,State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong) and Institute of Chinese Medicine, The Chinese University of Hong Kong, Hong Kong, China.
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25
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Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng). Arch Microbiol 2022; 204:208. [PMID: 35275265 DOI: 10.1007/s00203-022-02815-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/09/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023]
Abstract
Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.
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Meng Y, Liang Y, Liao B, He W, Liu Q, Shen X, Xu J, Chen S. Genome-Wide Identification, Characterization and Expression Analysis of Lipoxygenase Gene Family in Artemisia annua L. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050655. [PMID: 35270126 PMCID: PMC8912875 DOI: 10.3390/plants11050655] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/23/2022] [Accepted: 02/24/2022] [Indexed: 05/17/2023]
Abstract
Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without serious side effects. This study identified and analyzed LOX gene family members in the A. annua genome at the chromosomal level. Twenty LOX genes with various molecular weights, isoelectric points, and amino acid numbers were identified and named AaLOX, which were located in the cytoplasm or chloroplast. The average protein length of all AaLOX was 850 aa. Phylogenetic tree analysis revealed that the AaLOX was divided into two major groups, 9-LOX and 13-LOX. The exon numbers ranged from 1 to 12, indicating that different AaLOX genes have different functions. The secondary structure was mainly composed of alpha helix and random coil, and the tertiary structure was similar for most AaLOX. Upstream promoter region analysis revealed that a large number of cis-acting elements were closely related to plant growth and development, light response, hormone, and other stress responses. Transcriptome data analysis of different tissues suggested that the gene family was differently expressed in the roots, stems, leaves, and flowers of two A. annua strains HAN1 and LQ9. qRT-PCR confirmed that AaLOX5 and AaLOX17 had the highest expression in flowers and leaves. This study provides a theoretical basis for the further functional analysis of the AaLOX gene family.
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Affiliation(s)
- Ying Meng
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250000, China;
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Yu Liang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Wenrui He
- College of Pharmaceutical Science, Dali University, Dali 671000, China;
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 610000, China
| | - Qianwen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Xiaofeng Shen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100000, China; (Y.L.); (B.L.); (Q.L.); (X.S.)
- Correspondence: (J.X.); (S.C.)
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Meng F, Tang Q, Chu T, Li X, Lin Y, Song X, Chen W. TCMPG: an integrative database for traditional Chinese medicine plant genomes. HORTICULTURE RESEARCH 2022; 9:uhac060. [PMID: 35591924 PMCID: PMC9113410 DOI: 10.1093/hr/uhac060] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/25/2022] [Indexed: 05/12/2023]
Abstract
Because of their great therapeutic and economic value, medicinal plants have attracted increasing scientific attention. With the rapid development of high-throughput sequencing technology, the genomes of many medicinal plants have been sequenced. Storing and analyzing the increasing volume of genomic data has become an urgent task. To solve this challenge, we have proposed the Traditional Chinese Medicine Plant Genome database (TCMPG, http://cbcb.cdutcm.edu.cn/TCMPG/), an integrative database for storing the scattered genomes of medicinal plants. TCMPG currently includes 160 medicinal plants, 195 corresponding genomes, and 255 herbal medicines. Detailed information on plant species, genomes, and herbal medicines is also integrated into TCMPG. Popular genomic analysis tools are embedded in TCMPG to facilitate the systematic analysis of medicinal plants. These include BLAST for identifying orthologs from different plants, SSR Finder for identifying simple sequence repeats, JBrowse for browsing genomes, Synteny Viewer for displaying syntenic blocks between two genomes, and HmmSearch for identifying protein domains. TCMPG will be continuously updated by integrating new data and tools for comparative and functional genomic analysis.
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Affiliation(s)
- Fanbo Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, 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
| | - Qiang Tang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianzhe Chu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xianhai Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yue Lin
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
- Corresponding authors. E-mail: ,
| | - Wei Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, 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
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
- Corresponding authors. E-mail: ,
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Liu Q, Guo S, Zheng X, Shen X, Zhang T, Liao B, He W, Hu H, Cheng R, Xu J. Licorice Germplasm Resources Identification Using DNA Barcodes Inner-Variants. PLANTS (BASEL, SWITZERLAND) 2021; 10:2036. [PMID: 34685843 PMCID: PMC8541099 DOI: 10.3390/plants10102036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
Based on the gradual transformation from wild growth to artificial cultivation, the accurate authentication of licorice seeds contributes to the first committed step of its quality control and is pivotal to ensure the clinical efficacy of licorice. However, it is still challenging to obtain genetically stable licorice germplasm resources due to the multi-source, multi-heterozygous, polyploid, and hybrid characteristics of licorice seeds. Here, a new method for determining the heterozygosity of licorice seed mixture, based on the various sites, and finding the composition characteristics of licorice seed is preliminarily designed and proposed. Namely, high-throughput full-length multiple DNA barcodes(HFMD), based on ITS multi-copy variation exist, the full-length amplicons of ITS2, psbA-trnH and ITS are directly sequenced by rDNA through the next-generation sequence(NGS) and single-molecule real-time (SMRT) technologies. By comparing the three sequencing methods, our results proved that SMRT sequencing successfully identified the complete gradients of complex mixed samples with the best performance. Meanwhile, HFMD is a brilliant and feasible method for evaluating the heterozygosity of licorice seeds. It shows a perfect interpretation of DNA barcoding and can be applied in multi-base multi-heterozygous and polyploid species.
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Affiliation(s)
- Qianwen Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Shuai Guo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (S.G.); (W.H.)
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China;
| | - Xiaofeng Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China;
| | - Tianyi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Wenrui He
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (S.G.); (W.H.)
| | - Haoyu Hu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Ruiyang Cheng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (Q.L.); (T.Z.); (B.L.)
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Liao X, Guo S, Yin X, Liao B, Li M, Su H, Li Q, Pei J, Gao J, Lei J, Li X, Huang Z, Xu J, Chen S. Hierarchical chromatin features reveal the toxin production in Bungarus multicinctus. Chin Med 2021; 16:90. [PMID: 34535171 PMCID: PMC8447776 DOI: 10.1186/s13020-021-00502-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bungarus multicinctus, from which a classical Chinese medicine is produced, is known as the most venomous land snake in the world, but the chromatin organization and transcription factor activity during venom replenishment progress have not been explored yet. This study aimed to determine the roles of chromatin structure in toxin activity via bioinformatics and experimental validation. METHODS Chromosome conformation capture (Hi-C) analysis was used to examine interactions among chromosomes and identify different scales of chromatin during envenomation in B. multicinctus. Correlations between epigenetic modifications and chromatin structure were verified through ChIP-seq analysis. RNA-seq was used to validate the influence of variation in chromatin structure and gene expression levels on venom production and regulation. RESULTS Our results suggested that intra-chromosomal interactions are more intense than inter-chromosomal interactions among the control group, 3-day group of venom glands and muscles. Through this, we found that compartmental transition was correlated with chromatin interactions. Interestingly, the up-regulated genes in more compartmental switch regions reflect the function of toxin activity. Topologically associated domain (TAD) boundaries enriched with histone modifications are associated with different distributions of genes and the expression levels. Toxin-coding genes in the same loop are highly expressed, implying that the importance of epigenetic regulation during envenomination. On a smaller scale, the epigenetic markers affect transcriptional regulation by controlling the recruitment/inhibition of transcription initiation complexes. CONCLUSIONS Chromatin structure and epigenetic modifications could play a vital status role in the mechanisms of venom regulation in B. multicinctus.
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Affiliation(s)
- Xuejiao Liao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shuai Guo
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Xianmei Yin
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Mingqian Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - He Su
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Qiushi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jin Pei
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Jihai Gao
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Juan Lei
- College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhihai Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, 510006, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Wang L, Liao B, Gong L, Xiao S, Huang Z. Haploid Genome Analysis Reveals a Tandem Cluster of Four HSP20 Genes Involved in the High-Temperature Adaptation of Coriolopsis trogii. Microbiol Spectr 2021; 9:e0028721. [PMID: 34406871 PMCID: PMC8552761 DOI: 10.1128/spectrum.00287-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 01/16/2023] Open
Abstract
Coriolopsis trogii is a typical thermotolerant basidiomycete fungus, but its thermotolerance mechanisms are currently unknown. In this study, two monokaryons of C. trogii strain Ct001 were assembled: Ct001_29 had a genome assembly size of 38.85 Mb and encoded 13,113 genes, while Ct001_31 was 40.19 Mb in length and encoded 13,309 genes. Comparative intra- and interstrain genomic analysis revealed the rich genetic diversity of C. trogii, which included more than 315,194 single-nucleotide polymorphisms (SNPs), 30,387 insertion/deletions (indels), and 1,460 structural variations. Gene family analysis showed that the expanded families of C. trogii were functionally enriched in lignocellulose degradation activities. Furthermore, a total of 14 allelic pairs of heat shock protein 20 (HSP20) genes were identified in the C. trogii genome. The expression profile obtained from RNA sequencing (RNA-Seq) showed that four tandem-duplicated allelic pairs, HSP20.5 to HSP20.8, had more than 5-fold higher expression at 35°C than at 25°C. In particular, HSP20.5 and HSP20.8 were the most highly expressed HSP20 genes. Allelic expression bias was found for HSP20.5 and HSP20.8; the expression of Ct29HSP20.8 was at least 1.34-fold higher than that of Ct31HSP20.8, and that of Ct31HSP20.5 was at least 1.5-fold higher than that of Ct29HSP20.5. The unique structural and expression profiles of the HSP20 genes revealed by these haplotype-resolved genomes provide insight into the molecular mechanisms of high-temperature adaptation in C. trogii. IMPORTANCE Heat stress is one of the most frequently encountered environmental stresses for most mushroom-forming fungi. Currently available fungal genomes are mostly haploid because high heterozygosity hinders diploid genome assembly. Here, two haplotype genomes of C. trogii, a thermotolerant basidiomycete, were assembled separately. A conserved tandem cluster of four HSP20 genes showing allele-specific expression was found to be closely related to high-temperature adaptation in C. trogii. The obtained haploid genomes and their comparison offer a more thorough understanding of the genetic background of C. trogii. In addition, the responses of HSP20 genes at 35°C, which may contribute to the growth and survival of C. trogii at high temperatures, could inform the selection and breeding of elite strains in the future.
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Affiliation(s)
- Lining Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, People’s Republic of China
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Lu Gong
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
| | - Shuiming Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Zhihai Huang
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical Products Administration, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, People’s Republic of China
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Wang L, Lu C, Fan M, Liao B. Coriolopsis trogii hydrophobin genes favor a clustering distribution and are widely involved in mycelial growth and primordia formation. Gene 2021; 802:145863. [PMID: 34358628 DOI: 10.1016/j.gene.2021.145863] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/01/2022]
Abstract
Hydrophobins are small, secreted proteins with important physiological functions in mycelial growth and fungal development. Here, 1 nucleus-specific and 35 allelic hydrophobin genes were identified in the genome of a white rot fungus, Coriolopsis trogii. Among these, 22 were eight-cysteine class I hydrophobin genes and the other 14 were uncommon six-cysteine hydrophobin genes. The six-cysteine hydrophobins were speculated to have originated from a common ancestor. The hydrophobin genes favored a clustering distribution and two recent duplication pairs were identified. The genes had conserved gene structures with three exons and two introns. Cthyd18, Cthyd19, and Cthyd32 were constitutively highly expressed in all developmental stages. Cthyd20, Cthyd21, Cthyd22, Cthyd28, Cthyd30, Cthyd31, and Cthyd33 were highly expressed in mycelia, and Cthyd12 and Cthyd35 in the reproductive stages. Sixteen hydrophobin genes were regulated differently in the transition from mycelia to primordia; Cthyd35 showed maximal upregulation of 1922-fold, and Cthyd23 showed maximal downregulation of 552-fold. Most (32) hydrophobin genes showed significant differential expression between mycelia cultured in different media (potato dextrose agar or broth). Weighted gene co-expression network analysis and promoter analysis revealed that C2H2 zinc finger proteins may regulate hydrophobin genes. These results may support further research into the function and evolution of hydrophobins.
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Affiliation(s)
- Lining Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Chuanli Lu
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Min Fan
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou 510316, People's Republic of China
| | - Baosheng Liao
- Key Laboratory of Quality Evaluation of Chinese Medicine of the Guangdong Provincial Medical, the Second Clinical College, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China.
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