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Wu T, Bafort Q, Mortier F, Almeida-Silva F, Natran A, de Peer YV. The immediate metabolomic effects of whole-genome duplication in the greater duckweed, Spirodela polyrhiza. AMERICAN JOURNAL OF BOTANY 2024; 111:e16383. [PMID: 39087852 PMCID: PMC7616399 DOI: 10.1002/ajb2.16383] [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: 10/30/2023] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 08/02/2024]
Abstract
PREMISE In plants, whole-genome duplication (WGD) is a common mutation with profound evolutionary potential. Given the costs associated with a superfluous genome copy, polyploid establishment is enigmatic. However, in the right environment, immediate phenotypic changes following WGD can facilitate establishment. Metabolite abundances are the direct output of the cell's regulatory network and determine much of the impact of environmental and genetic change on the phenotype. While it is well known that an increase in the bulk amount of genetic material can increase cell size, the impact of gene dosage multiplication on the metabolome remains largely unknown. METHODS We used untargeted metabolomics on four genetically distinct diploid-neoautotetraploid pairs of the greater duckweed, Spirodela polyrhiza, to investigate how WGD affects metabolite abundances per cell and per biomass. RESULTS Autopolyploidy increased metabolite levels per cell, but the response of individual metabolites varied considerably. However, the impact on metabolite level per biomass was restricted because the increased cell size reduced the metabolite concentration per cell. Nevertheless, we detected both quantitative and qualitative effects of WGD on the metabolome. Many effects were strain-specific, but some were shared by all four strains. CONCLUSIONS The nature and impact of metabolic changes after WGD depended strongly on the genotype. Dosage effects have the potential to alter the plant metabolome qualitatively and quantitatively, but were largely balanced out by the reduction in metabolite concentration due to an increase in cell size in this species.
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Affiliation(s)
- Tian Wu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent9000, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Quinten Bafort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent9000, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, 9000Ghent, Belgium
| | - Frederik Mortier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent9000, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- Department of Biology, Ghent University, 9000Ghent, Belgium
| | - Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent9000, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Annelore Natran
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent9000, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University Biochemistry, Nanjing210095, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria0028, South Africa
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Campos MT, Maia LF, Popović-Djordjević J, Edwards HG, de Oliveira LF. Ripening process in exocarps of scarlet eggplant ( Solanum aethiopicum) and banana ( Musa spp.) investigated by Raman spectroscopy. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100204. [PMID: 38659653 PMCID: PMC11039347 DOI: 10.1016/j.fochms.2024.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 04/13/2024] [Indexed: 04/26/2024]
Abstract
In this work, we used Raman spectroscopy to identify compounds present at different maturation stages of the exocarp of scarlet eggplant and two banana cultivars, 'prata' and 'nanica'. Raman spectral analyses of both fruits showed bands attributed to phenolic acids, flavonoids, carotenoids, and fatty acids. During the scarlet eggplant's maturation process, Raman spectral profile changes are mainly observed in the carotenoid content rather than flavonoids. Furthermore, it is suggested that naringenin chalcone together with β-carotene determines the orange-red color of the ripe stage. Variations in chemical composition among the maturation stages of bananas were observed predominantly in 'prata' when compared to 'nanica'. In contrast to scarlet eggplant changes in the spectral profile were more evident in the content of the flavonoid/phenolic acids. The in situ analysis was demonstrated to be useful as a guide in selecting bioactive compounds on demand from low-cost horticultural waste.
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Affiliation(s)
- Mariana T.C. Campos
- NEEM - Núcleo de Espectroscopia e Estrutura Molecular, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
| | - Lenize F. Maia
- NEEM - Núcleo de Espectroscopia e Estrutura Molecular, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
| | - Jelena Popović-Djordjević
- University of Belgrade, Faculty of Agriculture, Chair of Chemistry and Biochemistry, Nemanjina 6, 11080 Belgrade, Serbia
| | - Howell G.M. Edwards
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire BD7 1DP, United Kingdom
| | - Luiz F.C. de Oliveira
- NEEM - Núcleo de Espectroscopia e Estrutura Molecular, Departamento de Química, ICE, Universidade Federal de Juiz de Fora, Campus Universitário, Martelos, Juiz de Fora, MG 36036-330, Brazil
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3
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Wang Q, Shi J, Liu J, Zhang P, Li L, Xie H, Li H, Wang H, Liu C, Qin P. Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development. PLANT MOLECULAR BIOLOGY 2024; 114:10. [PMID: 38319430 DOI: 10.1007/s11103-023-01402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/15/2023] [Indexed: 02/07/2024]
Abstract
Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.
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Affiliation(s)
- Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jirong Shi
- Food Crop Research Institute, Zhaotong Academy of Agricultural Sciences, Zhaotong, 657000, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Chenghong Liu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences/Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai, 201106, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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4
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Shi H, Wu X, Zhu Y, Jiang T, Wang Z, Li X, Liu J, Zhang Y, Chen F, Gao J, Xu X, Zhang G, Xiao N, Feng X, Zhang P, Wu Y, Li A, Chen P, Li X. RefMetaPlant: a reference metabolome database for plants across five major phyla. Nucleic Acids Res 2024; 52:D1614-D1628. [PMID: 37953341 PMCID: PMC10767953 DOI: 10.1093/nar/gkad980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Plants are unique with tremendous chemical diversity and metabolic complexity, which is highlighted by estimates that green plants collectively produce metabolites numbering in the millions. Plant metabolites play crucial roles in all aspects of plant biology, like growth, development, stress responses, etc. However, the lack of a reference metabolome for plants, and paucity of high-quality standard compound spectral libraries and related analytical tools, have hindered the discovery and functional study of phytochemicals in plants. Here, by leveraging an advanced LC-MS platform, we generated untargeted mass spectral data from >150 plant species collected across the five major phyla. Using a self-developed computation protocol, we constructed reference metabolome for 153 plant species. A 'Reference Metabolome Database for Plants' (RefMetaPlant) was built to encompass the reference metabolome, integrated standard compound mass spectral libraries for annotation, and related query and analytical tools like 'LC-MS/MS Query', 'RefMetaBlast' and 'CompoundLibBlast' for searches and profiling of plant metabolome and metabolite identification. Analogous to a reference genome in genomic research, RefMetaPlant provides a powerful platform to support plant genome-scale metabolite analysis to promote knowledge/data sharing and collaboration in the field of metabolomics. RefMetaPlant is freely available at https://www.biosino.org/RefMetaDB/.
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Affiliation(s)
- Han Shi
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xueting Wu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tao Jiang
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | | | - Xuetong Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jianju Liu
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | | | - Feng Chen
- Agronomy College, Henan Agricultural University, Zhengzhou, China
| | - Jinshan Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiaoyan Xu
- Core Facility Center, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ning Xiao
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Peng Zhang
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yongrui Wu
- University of Chinese Academy of Sciences, Beijing, China
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Aihong Li
- Institute of Agricultural Sciences for Lixiahe Region in Jiangsu, Yangzhou, China
| | - Ping Chen
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
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5
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Hao DC, Xiao PG. An adventure from a work in progress: Challenges and opportunities of pharmacophylogeny in combat against COVID-19. Phytother Res 2023; 37:5421-5423. [PMID: 36706739 DOI: 10.1002/ptr.7736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023]
Affiliation(s)
- Da-Cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian, China
| | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
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6
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Tang H, Zhu X, Zhong Y, Li Y, Luo W, Liu H, Descombes P, Gange AC, Chu C. Global latitudinal patterns in leaf herbivory are related to variation in climate, rather than phytochemicals or mycorrhizal types. Natl Sci Rev 2023; 10:nwad236. [PMID: 37954199 PMCID: PMC10632796 DOI: 10.1093/nsr/nwad236] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/06/2023] [Indexed: 11/14/2023] Open
Affiliation(s)
- Hui Tang
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
| | - Xianhui Zhu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
| | - Yonglin Zhong
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, China
| | - Yuanzhi Li
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
| | - Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
| | - Hanlun Liu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
| | - Patrice Descombes
- Musée et Jardins botaniques cantonaux, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Switzerland
| | - Alan C Gange
- Department of Biological Sciences, Royal Holloway University of London, UK
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology/School of Life Sciences, Sun Yat-sen University, China
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7
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Li Y, Li Z, Zhang F, Li S, Gu Y, Tian W, Tian W, Wang J, Wen J, Li J. Integrated evolutionary pattern analyses reveal multiple origins of steroidal saponins in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:823-839. [PMID: 37522396 DOI: 10.1111/tpj.16411] [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: 09/05/2022] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/01/2023]
Abstract
Steroidal saponins are a class of specialized metabolites essential for plant's response to biotic and abiotic stresses. They are also important raw materials for the industrial production of steroid drugs. Steroidal saponins are present in some monocots, such as Dioscorea and Paris, but their distribution, origin, and evolution in plants remain poorly understood. By reconstructing the evolutionary history of the steroidal saponin-associated module (SSAM) in plants, we reveal that the steroidal saponin pathway has its origin in Asparagus and Dioscorea. Through evaluating the distribution and evolutionary pattern of steroidal saponins in angiosperms, we further show that steroidal saponins originated multiple times in angiosperms, and exist in early diverged lineages of certain monocot lineages including Asparagales, Dioscoreales, and Liliales. In these lineages, steroidal saponins are synthesized through the high copy and/or high expression mechanisms of key genes in SSAM. Together with shifts in gene evolutionary rates and amino acid usage, these molecular mechanisms shape the current distribution and diversity of steroidal saponins in plants. Consequently, our results provide new insights into the distribution, diversity and evolutionary history of steroidal saponins in plants, and enhance our understanding of plants' resistance to abiotic and biotic stresses. Additionally, fundamental understanding of the steroidal saponin biosynthesis will facilitate their industrial production and pharmacological applications.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zihao Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Furui Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Song Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongbing Gu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weijun Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Weirong Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20013-7012, DC, USA
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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8
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Zhao D, Zhang Y, Ren H, Shi Y, Dong D, Li Z, Cui G, Shen Y, Mou Z, Kennelly EJ, Huang L, Ruan J, Chen S, Yu D, Cun Y. Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2320-2335. [PMID: 37688324 DOI: 10.1111/jipb.13565] [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: 05/29/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Diterpenoid alkaloids (DAs) have been often utilized in clinical practice due to their analgesic and anti-inflammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown. In this study, we successfully assembled a high-quality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum (A. vilmorinianum) (5.76 Gb). An A. vilmorinianum-specific whole-genome duplication event was discovered using comparative genomic analysis, which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A. vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.
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Affiliation(s)
- Dake Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Ya Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Huanxing Ren
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yana Shi
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Ding Dong
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Zonghang Li
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Guanghong Cui
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yong Shen
- College of Agriculture and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Zongmin Mou
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Edward J Kennelly
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, 10468, New York, USA
- Graduate Center, City University of New York, Bronx, 10468, New York, USA
| | - Luqi Huang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jue Ruan
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Suiyun Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650500, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, 650500, China
| | - Yupeng Cun
- Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Domingo-Fernández D, Gadiya Y, Mubeen S, Bollerman TJ, Healy MD, Chanana S, Sadovsky RG, Healey D, Colluru V. Modern drug discovery using ethnobotany: A large-scale cross-cultural analysis of traditional medicine reveals common therapeutic uses. iScience 2023; 26:107729. [PMID: 37701812 PMCID: PMC10494464 DOI: 10.1016/j.isci.2023.107729] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023] Open
Abstract
For millennia, numerous cultures and civilizations have relied on traditional remedies derived from plants to treat a wide range of conditions and ailments. Here, we systematically analyzed ethnobotanical patterns across taxonomically related plants, demonstrating that congeneric medicinal plants are more likely to be used for treating similar indications. Next, we reconstructed the phytochemical space covered by medicinal plants to reveal that (i) taxonomically related medicinal plants cover a similar phytochemical space, and (ii) chemical similarity correlates with similar therapeutic usage. Lastly, we present several case scenarios illustrating how mining this information can be used for drug discovery applications, including: (i) investigating taxonomic hotspots around particular indications, (ii) exploring shared patterns of congeneric plants located in different geographic areas, but which have been used to treat the same indications, and (iii) showing the concordance between ethnobotanical patterns among non-taxonomically related plants and the presence of shared bioactive phytochemicals.
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Mukherjee A, Tikariha H, Bandla A, Pavagadhi S, Swarup S. Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes. mSystems 2023; 8:e0038723. [PMID: 37409823 PMCID: PMC10469690 DOI: 10.1128/msystems.00387-23] [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: 04/21/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
There are gaps in our understandings on how did the evolutionary relationships among members of the phytobiomes shape their ability to produce tremendously complex specialized metabolites under the influence of plant host. To determine these relationships, we investigated the phylogenetic conservation of biosynthetic gene clusters (BGCs) on a global collection of 4,519 high-quality and nonredundant (out of 12,181) bacterial isolates and metagenome-assembled genomes from 47 different plant hosts and soil, by adopting three independent phylogenomic approaches (D-test, Pagel's λ, and consenTRAIT). We report that the BGCs are phylogenetically conserved to varying strengths and depths in their different classes. We show that the ability to produce specialized metabolites qualifies as a complex trait, and the depth of conservation is equivalent to ecologically relevant complex microbial traits. Interestingly, terpene and aryl polyene BGCs had the strongest phylogenetic conservation in the phytobiomes, but not in the soil microbiomes. Furthermore, we showed that terpenes are largely uncharacterized in phytobiomes and pinpointed specific clades that harbor potentially novel terpenes. Taken together, this study sheds light on the evolution of specialized metabolites' biosynthesis potential in phytobiomes under the influence of plant hosts and presents strategies to rationally guide the discovery of potentially novel classes of metabolites. IMPORTANCE This study expands our understandings of the biosynthetic potential of phytobiomes by using such worldwide and extensive collection of microbiomes from plants and soil. Apart from providing such vital resource for the plant microbiome researchers, this study provides fundamental insights into the evolution of biosynthetic gene clusters (BGCs) in phytobiomes under the influence of plant host. Specifically, we report that the strength of phylogenetic conservation in microbiomes varies for different classes of BGCs and is influenced as a result of plant host association. Furthermore, our results indicate that biosynthetic potential of specialized metabolites is deeply conserved equivalent to other complex and ecologically relevant microbial traits. Finally, for the most conserved class of specialized metabolites (terpenes), we identified clades harboring potentially novel class of molecules. Future studies could focus on plant-microbe coevolution and interactions through specialized metabolites building upon these findings.
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Affiliation(s)
- Arijit Mukherjee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Hitesh Tikariha
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| | - Aditya Bandla
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Shruti Pavagadhi
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
| | - Sanjay Swarup
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
- NUS Environmental Research Institute, National University of Singapore, Singapore, Singapore
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Zhao ZY, Tong YP, Jiang W, Zang Y, Xiong J, Li J, Hu JF. Structurally Diverse Triterpene-26-oic Acids as Potential Dual ACL and ACC1 Inhibitors from the Vulnerable Conifer Keteleeria fortunei. JOURNAL OF NATURAL PRODUCTS 2023; 86:1487-1499. [PMID: 37291059 DOI: 10.1021/acs.jnatprod.3c00181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A preliminary phytochemical investigation on the 90% MeOH extract from the twigs and needles of the vulnerable conifer Keteleeria fortunei led to the isolation and characterization of 17 structurally diverse triterpen-26-oic acids, including nine previously undescribed ones (fortunefuroic acids A-I, 1-9) featuring a rare furoic acid moiety in the lateral chain. Among them, 1-5 are uncommon 9βH-lanostane-type triterpenoic acids. Friedo-rearranged triterpenoids 6 and 7 feature a unique 17,14-friedo-lanostane skeleton, whereas 9 possesses a rare 17,13-friedo-cycloartane-type framework. Their structures and absolute configurations were elucidated by extensive spectroscopic (e.g., detailed 2D NMR) and computational (NMR/ECD) calculations and the modified Mosher's method. In addition, the absolute structure of compound 1 was ascertained by single-crystal X-ray diffraction analyses. Fortunefuroic acids B (2), G (7), and I (9), along with isomangiferolic acid (12) and 3α,27-dihydroxycycloart-24E-en-26-oic acid (14), exhibited dual inhibitory effects against the adenosine triphosphate (ATP)-citrate lyase (ACL, IC50s: 5.7-11.4 μM) and acetyl-CoA carboxylase 1 (ACC1, IC50s: 7.5-10.5 μM), both of which are key enzymes for glycolipid metabolism. The interactions of the bioactive triterpenoids with both enzymes were examined by molecular docking studies. The above findings reveal the important role of protecting plant species diversity in support of chemical diversity and potential sources of new therapeutics for ACL-/ACC1-associated diseases.
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Affiliation(s)
- Ze-Yu Zhao
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Ying-Peng Tong
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
| | - Wei Jiang
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- School of Life Science and Technology, Wuhan Polytechnic University, Hubei 430023, People's Republic of China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Juan Xiong
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Science, Shanghai 201203, People's Republic of China
| | - Jin-Feng Hu
- Department of Natural Medicine, School of Pharmacy, Fudan University, Shanghai 201203, People's Republic of China
- Institute of Natural Medicine and Health Products, School of Pharmaceutical Sciences, Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, Zhejiang 318000, People's Republic of China
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12
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Mutie FM, Mbuni YM, Rono PC, Mkala EM, Nzei JM, Phumthum M, Hu GW, Wang QF. Important Medicinal and Food Taxa (Orders and Families) in Kenya, Based on Three Quantitative Approaches. PLANTS (BASEL, SWITZERLAND) 2023; 12:1145. [PMID: 36904005 PMCID: PMC10005506 DOI: 10.3390/plants12051145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Globally, food and medicinal plants have been documented, but their use patterns are poorly understood. Useful plants are non-random subsets of flora, prioritizing certain taxa. This study evaluates orders and families prioritized for medicine and food in Kenya, using three statistical models: Regression, Binomial, and Bayesian approaches. An extensive literature search was conducted to gather information on indigenous flora, medicinal and food plants. Regression residuals, obtained using LlNEST linear regression function, were used to quantify if taxa had unexpectedly high number of useful species relative to the overall proportion in the flora. Bayesian analysis, performed using BETA.INV function, was used to obtain superior and inferior 95% probability credible intervals for the whole flora and for all taxa. To test for the significance of individual taxa departure from the expected number, binomial analysis using BINOMDIST function was performed to obtain p-values for all taxa. The three models identified 14 positive outlier medicinal orders, all with significant values (p < 0.05). Fabales had the highest (66.16) regression residuals, while Sapindales had the highest (1.1605) R-value. Thirty-eight positive outlier medicinal families were identified; 34 were significant outliers (p < 0.05). Rutaceae (1.6808) had the highest R-value, while Fabaceae had the highest regression residuals (63.2). Sixteen positive outlier food orders were recovered; 13 were significant outliers (p < 0.05). Gentianales (45.27) had the highest regression residuals, while Sapindales (2.3654) had the highest R-value. Forty-two positive outlier food families were recovered by the three models; 30 were significant outliers (p < 0.05). Anacardiaceae (5.163) had the highest R-value, while Fabaceae had the highest (28.72) regression residuals. This study presents important medicinal and food taxa in Kenya, and adds useful data for global comparisons.
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Affiliation(s)
- Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - John Mulinge Nzei
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Methee Phumthum
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
| | - Guang-Wan Hu
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Dinan L, Lafont F, Lafont R. The Distribution of Phytoecdysteroids among Terrestrial Vascular Plants: A Comparison of Two Databases and Discussion of the Implications for Plant/Insect Interactions and Plant Protection. PLANTS (BASEL, SWITZERLAND) 2023; 12:776. [PMID: 36840124 PMCID: PMC9967490 DOI: 10.3390/plants12040776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Phytoecdysteroids are a class of plant secondary compounds which are present in a wide diversity of vascular plant species, where they contribute to a reduction in invertebrate predation. Over the past 55 years, a significant body of heterogeneous literature on the presence, identities and/or quantities of ecdysteroids in plant species has accumulated, resulting in the compilation of a first database, the Ecdybase Literature Survey (ELS; 4908 entries, covering 2842 species). A second extensive database on the distribution of ecdysteroids in vascular plants is available as the Exeter Survey (ES; 4540 entries, covering 4155 species), which used standardised extraction and analysis methods to survey seeds/spores. We compare the usefulness of these two databases to provide information on the occurrence of phytoecdysteroids at the order/family levels in relation to the recent molecular classifications of gymnosperms, pteridophytes/lycophytes and angiosperms. The study, in conjunction with the other published literature, provides insights into the distribution of phytoecdysteroids in the plant world, their role in plant protection in nature and their potential future contribution to crop protection. Furthermore, it will assist future investigations in the chemotaxonomy of phytoecdysteroids and other classes of plant secondary compounds.
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14
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Hu L, Xu Z, Fan R, Wang G, Wang F, Qin X, Yan L, Ji X, Meng M, Sim S, Chen W, Hao C, Wang Q, Zhu H, Zhu S, Xu P, Zhao H, Lindsey K, Daniell H, Wendel JF, Jin S. The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:78-96. [PMID: 36117410 PMCID: PMC9829393 DOI: 10.1111/pbi.13926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.
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Affiliation(s)
- Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Zhongping Xu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Minghui Meng
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Qinghuang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Huaguo Zhu
- College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggangHubeiChina
| | - Shu Zhu
- Jinjiaohong Spice Research InstituteJinjiaohong Agricultural Technology Group CorporationNanjingChina
| | - Pan Xu
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsHaikouChina
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
| | | | - Henry Daniell
- Department of Biochemistry, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jonathan F. Wendel
- Department Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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15
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Kremer D, Dunkić V, Radosavljević I, Bogunić F, Ivanova D, Ballian D, Stešević D, Matevski V, Ranđelović V, Eleftheriadou E, Šatović Z, Liber Z. Phytochemicals and Their Correlation with Molecular Data in Micromeria and Clinopodium (Lamiaceae) Taxa. PLANTS (BASEL, SWITZERLAND) 2022; 11:3407. [PMID: 36501446 PMCID: PMC9739532 DOI: 10.3390/plants11233407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
A study of the phytochemical and molecular characteristics of ten Micromeria and six Clinopodium taxa (family Lamiaceae) distributed in the Balkan Peninsula was carried out. The phytochemicals detected in essential oils by gas chromatography, mass spectrometry, and molecular data amplified fragment length polymorphism were used to study the taxonomic relationships among the taxa and the correlations between phytochemical and molecular data. STRUCTURE analysis revealed three genetic groups, while Bayesian Analysis of Population Structure grouped the studied taxa into 11 clusters nested in the groups obtained by STRUCTURE. Principal components analysis performed with the 21 most represented compounds in the essential oils yielded results that were partly consistent with those obtained by STRUCTURE and neighbour-joining analyses. However, their geographic distributions did not support the genetic grouping of the studied taxa and populations. The Mantel test showed a significant correlation between the phytochemical and genetic data (r = 0.421, p < 0.001). Genetic distance explained 17.8% of the phytochemical distance between populations. The current taxonomic position of several of the studied taxa is yet to be satisfactorily resolved, and further studies are needed. Such future research should include nuclear and plastid DNA sequences from a larger sample of populations and individuals.
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Affiliation(s)
- Dario Kremer
- Faculty of Pharmacy and Biochemistry, University of Zagreb, A. Kovačića 1, 10000 Zagreb, Croatia
| | - Valerija Dunkić
- Faculty of Science, University of Split, Rudera Boškovića 33, 21000 Split, Croatia
| | - Ivan Radosavljević
- Faculty of Science, University of Zagreb, Marulićev trg 9A, 10000 Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Faruk Bogunić
- Faculty of Forestry, University of Sarajevo, Zagrebačka 20, 71000 Sarajevo, Bosnia and Herzegovina
| | - Daniella Ivanova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., bl. 23, 1113 Sofia, Bulgaria
| | - Dalibor Ballian
- Faculty of Forestry, University of Sarajevo, Zagrebačka 20, 71000 Sarajevo, Bosnia and Herzegovina
- Slovenian Forestry Institute, Večna Pot 2, 1000 Ljubljana, Slovenia
| | - Danijela Stešević
- Faculty of Natural Sciences and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica, Montenegro
| | - Vlado Matevski
- Faculty of Natural Sciences and Mathematics, Ss. Cyril and Methodius University, Gazi Baba bb, 1000 Skopje, North Macedonia
| | - Vladimir Ranđelović
- Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia
| | - Eleni Eleftheriadou
- School of Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, 10000 Zagreb, Croatia
- Faculty of Agriculture, University of Zagreb, Svetošimunska 25, 10000 Zagreb, Croatia
| | - Zlatko Liber
- Faculty of Science, University of Zagreb, Marulićev trg 9A, 10000 Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, 10000 Zagreb, Croatia
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16
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Hao DC, He CN, Spjut RW, Xiao PG. Editorial: Plant-derived natural compounds in drug discovery: The prism perspective between plant phylogeny, chemical composition, and medicinal efficacy. FRONTIERS IN PLANT SCIENCE 2022; 13:1042695. [PMID: 36275571 PMCID: PMC9585347 DOI: 10.3389/fpls.2022.1042695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Da-Cheng Hao
- School of Environment and Chemical Engineering, Biotechnology Institute, Dalian Jiaotong University, Dalian, China
- Institute of Molecular Plant Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Chun-Nian He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Pei-Gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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17
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Chen T, Dai X, Eiseman C. A checklist of gymnosperm-feeding leafminers (Arthopoda, Insecta) in North America and Europe. Biodivers Data J 2022; 10:e91313. [PMID: 36761634 PMCID: PMC9848575 DOI: 10.3897/bdj.10.e91313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/19/2022] [Indexed: 02/11/2023] Open
Abstract
The leafminers on gymnosperms receive much less attention than those on either angiosperms or ferns. Given the distinctly different leaf shape and leaf venation found in gymnosperms, they would be expected to host significantly different leafminer groups. Very few comprehensive reports on gymnosperm-feeding leafminers have been presented. Based on the well-studied fauna in North America and Europe, we compiled a list of 133 species, 30 genera and 13 families of gymnosperm-feeding leafminers. The gymnosperm-mining families (in descending order of leafminer number) included Tortricidae, Gelechiidae, Argyresthiidae, Yponomeutidae, Batrachedridae, Pyralidae, Adelidae, Agromyzidae, Blastobasidae, Bucculatricidae, Coleophoridae, Curculionidae and Noctuidae. There were 109 species, 22 genera and ten families in North America and 34 species, 19 genera and nine families in Europe. We compiled a list of 102 species and 16 genera of host plants, belonging to four families: Pinaceae, Cupressaceae, Taxaceae and Zamiaceae. There were 84 host species, 15 genera and three host families in North America and 46 host species, ten genera and three host families in Europe. Dominant gymnosperm-mining families and dominant host families were generally the same in the two continents.
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Affiliation(s)
- Taibin Chen
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou, ChinaLeafminer Group, School of Life Sciences, Gannan Normal UniversityGanzhouChina,National Navel-Orange Engineering Research Center, Ganzhou, ChinaNational Navel-Orange Engineering Research CenterGanzhouChina,Ganzhou Key Laboratory of Nanling Insect Biology, Ganzhou, ChinaGanzhou Key Laboratory of Nanling Insect BiologyGanzhouChina
| | - Charles Eiseman
- none, Northfield, MA, United States of AmericanoneNorthfield, MAUnited States of America
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Milliken W, Walker BE, Howes MJR, Forest F, Nic Lughadha E. Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines. JOURNAL OF ETHNOPHARMACOLOGY 2021; 279:114221. [PMID: 34029639 DOI: 10.1016/j.jep.2021.114221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Malaria remains a serious and challenging disease. Traditional antimalarial medicines are largely based on plants, and ethnopharmacological research has inspired the development of antimalarial pharmaceuticals such as artemisinin. Antimalarial drug resistance is an increasing problem in Plasmodium species, and new therapeutic strategies to combat malaria are needed. Although the number of malaria cases has been decreasing in Latin America, malaria remains a significant threat in many regions. Local people in Latin America have been using numerous plant species to treat malaria, some of which have been scientifically studied, but many others have not. AIM OF THE STUDY Our principal objective is to harness ethnobotanical data on species used traditionally to treat malaria, combined with phylogenetic approaches, to understand how ethnobotany could help identify plant genera as potential sources of new medicines. MATERIALS AND METHODS Plants used to treat malaria in Latin America were compiled from published and grey literature, unpublished data, and herbarium specimens. Initial assessment of potentially important species/genera/families included compiling the number of species used within the genus, the number of use reports per genus and species, and the geographic distribution of their use. The analysis of taxonomic distribution of species reported as antimalarial in Latin America (excluding the Southern Cone) was conducted, to determine which genera and families with reputed antimalarial properties are over-represented, and phylogenetic analyses were performed to identify if there was evidence for antimalarial species being dispersed/clustered throughout the tree or at its tips. This approach enabled 'hot-nodes' in certain families to be identified, to predict new genera with potential antimalarial properties. RESULTS Over 1000 plant species have been used to treat malaria in Latin America, of which over 600 species were cited only once. The genera with the highest number of antimalarial species were Aspidosperma, Solanum, Piper, Croton and Aristolochia. In terms of geographic distribution, the most widely used genera were Aspidosperma, Momordica, Cinchona, Senna and Stachytarpheta. Significant phylogenetic signal was detected in the distribution of native species used for malaria, analysed in a genus-level phylogenetic framework. The eudicot and magnoliidae lineages were over-represented, while monocots were not. CONCLUSION Analysis of ethnobotanical use reports in a phylogenetic framework reveals the existence of hot nodes for malaria across the Latin American flora. We demonstrate how species and genera currently lacking such reports could be pinpointed as of potential interest based on their evolutionary history. Extending this approach to other regions of the world and other diseases could accelerate the discovery of novel medicines and enhance healthcare in areas where new therapeutic strategies are needed.
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Affiliation(s)
| | | | - Melanie-Jayne R Howes
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, SE1 9NH, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
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19
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Tracing molecular properties throughout evolution: A chemoinformatic approach. J Theor Biol 2021; 515:110601. [PMID: 33508327 DOI: 10.1016/j.jtbi.2021.110601] [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: 09/02/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/24/2022]
Abstract
Evolution of metabolism is a longstanding yet unresolved question, and several hypotheses were proposed to address this complex process from a Darwinian point of view. Modern statistical bioinformatic approaches targeted to the comparative analysis of genomes are being used to detect signatures of natural selection at the gene and population level, as an attempt to understand the origin of primordial metabolism and its expansion. These studies, however, are still mainly centered on genes and the proteins they encode, somehow neglecting the small organic chemicals that support life processes. In this work, we selected steroids as an ancient family of metabolites widely distributed in all eukaryotes and applied unsupervised machine learning techniques to reveal the traits that natural selection has imprinted on molecular properties throughout the evolutionary process. Our results clearly show that sterols, the primal steroids that first appeared, have more conserved properties and that, from then on, more complex compounds with increasingly diverse properties have emerged, suggesting that chemical diversification parallels the expansion of biological complexity. In a wider context, these findings highlight the worth of chemoinformatic approaches to a better understanding the evolution of metabolism.
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