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Mathieu L, Ballini E, Morel JB, Méteignier LV. The root of plant-plant interactions: Belowground special cocktails. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102547. [PMID: 38749206 DOI: 10.1016/j.pbi.2024.102547] [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: 03/13/2024] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 06/14/2024]
Abstract
Plants interact with each other via a multitude of processes among which belowground communication facilitated by specialized metabolites plays an important but overlooked role. Until now, the exact targets, modes of action, and resulting phenotypes that these metabolites induce in neighboring plants have remained largely unknown. Moreover, positive interactions driven by the release of root exudates are prevalent in both natural field conditions and controlled laboratory environments. In particular, intraspecific positive interactions suggest a genotypic recognition mechanism in addition to non-self perception in plant roots. This review concentrates on recent discoveries regarding how plants interact with one another through belowground signals in intra- and interspecific mixtures. Furthermore, we elaborate on how an enhanced understanding of these interactions can propel the field of agroecology forward.
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Affiliation(s)
- Laura Mathieu
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Elsa Ballini
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jean-Benoit Morel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Louis-Valentin Méteignier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
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2
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Fan Y, Tcherkez G, Scafaro AP, Taylor NL, Furbank RT, von Caemmerer S, Atkin OK. Variation in leaf dark respiration among C3 and C4 grasses is associated with use of different substrates. PLANT PHYSIOLOGY 2024; 195:1475-1490. [PMID: 38324704 PMCID: PMC11142371 DOI: 10.1093/plphys/kiae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Measurements of respiratory properties have often been made at a single time point either during daytime using dark-adapted leaves or during nighttime. The influence of the day-night cycle on respiratory metabolism has received less attention but is crucial to understand photosynthesis and photorespiration. Here, we examined how CO2- and O2-based rates of leaf dark respiration (Rdark) differed between midday (after 30-min dark adaptation) and midnight in 8 C3 and C4 grasses. We used these data to calculate the respiratory quotient (RQ; ratio of CO2 release to O2 uptake), and assessed relationships between Rdark and leaf metabolome. Rdark was higher at midday than midnight, especially in C4 species. The day-night difference in Rdark was more evident when expressed on a CO2 than O2 basis, with the RQ being higher at midday than midnight in all species, except in rice (Oryza sativa). Metabolomic analyses showed little correlation of Rdark or RQ with leaf carbohydrates (sucrose, glucose, fructose, or starch) but strong multivariate relationships with other metabolites. The results suggest that rates of Rdark and differences in RQ were determined by several concurrent CO2-producing and O2-consuming metabolic pathways, not only the tricarboxylic acid cycle (organic acids utilization) but also the pentose phosphate pathway, galactose metabolism, and secondary metabolism. As such, Rdark was time-, type- (C3/C4) and species-dependent, due to the use of different substrates.
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Affiliation(s)
- Yuzhen Fan
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Guillaume Tcherkez
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Institut de Recherche en Horticulture et Semences, INRAe, Université d'Angers, Beaucouzé 49100, France
| | - Andrew P Scafaro
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nicolas L Taylor
- School of Molecular Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA 6009, Australia
| | - Robert T Furbank
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Susanne von Caemmerer
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Owen K Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
- Division of Plant Sciences, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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3
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Xu X, Zhang C, Lai C, Zhang Z, Wu J, Su Q, Gan Y, Zhang Z, Chen Y, Guo R, Lin Y, Lai Z. Genome-Wide Identification and Expression Analysis of Bx Involved in Benzoxazinoids Biosynthesis Revealed the Roles of DIMBOA during Early Somatic Embryogenesis in Dimocarpus longan Lour. PLANTS (BASEL, SWITZERLAND) 2024; 13:1373. [PMID: 38794443 PMCID: PMC11125010 DOI: 10.3390/plants13101373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/04/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]
Abstract
Benzoxazinoids (BXs) are tryptophan-derived indole metabolites and play a role in various physiological processes, such as auxin metabolism. Auxin is essential in the process of somatic embryogenesis (SE) in plants. In this study, we used bioinformatics, transcriptome data, exogenous treatment experiments, and qPCR analysis to study the evolutionary pattern of Bx genes in green plants, the regulatory mechanism of DlBx genes during early SE, and the effect of 2,4-dihydroxy-7-methoxy-1,4-benzoxazine-3-one (DIMBOA) on the early SE in Dimocarpus longan Lour. The results showed that 27 putative DlBxs were identified in the longan genome; the Bx genes evolved independently in monocots and dicots, and the main way of gene duplication for the DlBx was tandem duplication (TD) and the DlBx were strongly constrained by purification selection during evolution. The transcriptome data indicated varying expression levels of DlBx during longan early SE, and most DlBxs responded to light, temperature, drought stress, and 2,4-dichlorophenoxyacetic acid (2,4-D) treatment; qRT-PCR results showed DlBx1, DlBx6g and DlBx6h were responsive to auxin, and treatment with 0.1mg/L DIMBOA for 9 days significantly upregulated the expression levels of DlBx1, DlBx3g, DlBx6c, DlBx6f, DlB6h, DlBx7d, DlBx8, and DlBx9b. The correlation analysis showed a significantly negative correlation between the expression level of DlBx1 and the endogenous IAA contents; DIMBOA significantly promoted the early SE and significantly changed the endogenous IAA content, and the IAA content increased significantly at the 9th day and decreased significantly at the 13th day. Therefore, the results suggested that DIMBOA indirectly promote the early SE by changing the endogenous IAA content via affecting the expression level of DlBx1 and hydrogen peroxide (H2O2) content in longan.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.X.); (C.Z.); (C.L.); (Z.Z.); (J.W.); (Q.S.); (Y.G.); (Z.Z.); (Y.C.); (R.G.); (Y.L.)
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4
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Cen Z, Hu B, Yang S, Ma G, Zheng Y, Dong Y. Mechanism of benzoxazinoids affecting the growth and development of Fusarium oxysporum f. sp. fabae. PLANT MOLECULAR BIOLOGY 2024; 114:42. [PMID: 38630198 DOI: 10.1007/s11103-024-01439-8] [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: 11/28/2023] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
Continuous cropping of faba bean (Vicia faba L.) has led to a high incidence of wilt disease. The implementation of an intercropping system involving wheat and faba bean can effectively control the propagation of faba bean wilt disease. To investigate the mechanisms of wheat in mitigating faba bean wilt disease in a wheat-faba bean intercropping system. A comprehensive investigation was conducted to assess the temporal variations in Fusarium oxysporum f. sp. fabae (FOF) on the chemotaxis of benzoxazinoids (BXs) and wheat root through indoor culture tests. The effects of BXs on FOF mycelial growth, spore germination, spore production, and electrical conductivity were examined. The influence of BXs on the ultrastructure of FOF was investigated through transmission electron microscopy. Eukaryotic mRNA sequencing was utilized to analyze the differentially expressed genes in FOF upon treatment with BXs. FOF exhibited a significant positive chemotactic effect on BXs in wheat roots and root secretions. BXs possessed the potential to exert significant allelopathic effects on the mycelial growth, spore germination, and sporulation of FOF. In addition, BXs demonstrated a remarkable ability to disrupt the structural integrity and stability of the membrane and cell wall of the FOF mycelia. BXs possessed the capability of posing threats to the integrity and stability of the cell membrane and cell wall. This ultimately resulted in physiological dysfunction, effectively inhibiting the regular growth and developmental processes of the FOF.
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Affiliation(s)
- Zixuan Cen
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Bijie Hu
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Siyin Yang
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Guanglei Ma
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Yiran Zheng
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China
| | - Yan Dong
- College of Resources and Environment, Yunnan Agricultural University, Kunming, China.
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Chen K, Yang H, Wu D, Peng Y, Lian L, Bai L, Wang L. Weed biology and management in the multi-omics era: Progress and perspectives. PLANT COMMUNICATIONS 2024; 5:100816. [PMID: 38219012 PMCID: PMC11009161 DOI: 10.1016/j.xplc.2024.100816] [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: 09/13/2023] [Revised: 11/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Weeds pose a significant threat to crop production, resulting in substantial yield reduction. In addition, they possess robust weedy traits that enable them to survive in extreme environments and evade human control. In recent years, the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits. In this review, we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology, including the origins of weed species, weed classification, and the underlying genetic and molecular bases of important weedy traits such as crop-weed interactions, adaptability to different environments, photoperiodic flowering responses, and herbicide resistance. In addition, we discuss limitations to the application of multi-omics techniques in weed science, particularly compared with their extensive use in model plants and crops. In this regard, we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research. These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits. The resulting advances will facilitate the development of sustainable and highly effective weed management strategies, promoting greener practices in agriculture.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Lei Lian
- Qingdao Kingagroot Compounds Co. Ltd, Qingdao 266000, China
| | - Lianyang Bai
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
| | - Lifeng Wang
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China; State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha 410125, China; Longping Branch, College of Biology, Hunan University, Changsha 410125, China; Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou 510715, China; Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
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6
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Ahmad N, Xu Y, Zang F, Li D, Liu Z. The evolutionary trajectories of specialized metabolites towards antiviral defense system in plants. MOLECULAR HORTICULTURE 2024; 4:2. [PMID: 38212862 PMCID: PMC10785382 DOI: 10.1186/s43897-023-00078-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Viral infections in plants pose major challenges to agriculture and global food security in the twenty-first century. Plants have evolved a diverse range of specialized metabolites (PSMs) for defenses against pathogens. Although, PSMs-mediated plant-microorganism interactions have been widely discovered, these are mainly confined to plant-bacteria or plant-fungal interactions. PSM-mediated plant-virus interaction, however, is more complicated often due to the additional involvement of virus spreading vectors. Here, we review the major classes of PSMs and their emerging roles involved in antiviral resistances. In addition, evolutionary scenarios for PSM-mediated interactions between plant, virus and virus-transmitting vectors are presented. These advancements in comprehending the biochemical language of PSMs during plant-virus interactions not only lay the foundation for understanding potential co-evolution across life kingdoms, but also open a gateway to the fundamental principles of biological control strategies and beyond.
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Affiliation(s)
- Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, 210095, China
| | - Faheng Zang
- National Key Laboratory of Advanced Micro and Nano Manufacture Technology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dapeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEPMS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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7
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Li P, Yan MX, Liu P, Yang DJ, He ZK, Gao Y, Jiang Y, Kong Y, Zhong X, Wu S, Yang J, Wang HX, Huang YB, Wang L, Chen XY, Hu YH, Zhao Q, Xu P. Multiomics analyses of two Leonurus species illuminate leonurine biosynthesis and its evolution. MOLECULAR PLANT 2024; 17:158-177. [PMID: 37950440 DOI: 10.1016/j.molp.2023.11.003] [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: 07/10/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 11/12/2023]
Abstract
The Lamiaceae family is renowned for its terpenoid-based medicinal components, but Leonurus, which has traditional medicinal uses, stands out for its alkaloid-rich composition. Leonurine, the principal active compound found in Leonurus, has demonstrated promising effects in reducing blood lipids and treating strokes. However, the biosynthetic pathway of leonurine remains largely unexplored. Here, we present the chromosome-level genome sequence assemblies of Leonurus japonicus, known for its high leonurine production, and Leonurus sibiricus, characterized by very limited leonurine production. By integrating genomics, RNA sequencing, metabolomics, and enzyme activity assay data, we constructed the leonurine biosynthesis pathway and identified the arginine decarboxylase (ADC), uridine diphosphate glucosyltransferase (UGT), and serine carboxypeptidase-like (SCPL) acyltransferase enzymes that catalyze key reactions in this pathway. Further analyses revealed that the UGT-SCPL gene cluster evolved by gene duplication in the ancestor of Leonurus and neofunctionalization of SCPL in L. japonicus, which contributed to the accumulation of leonurine specifically in L. japonicus. Collectively, our comprehensive study illuminates leonurine biosynthesis and its evolution in Leonurus.
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Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Meng-Xiao Yan
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Pan Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Dan-Jie Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Ze-Kun He
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Gao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yan Jiang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Yu Kong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Xin Zhong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Sheng Wu
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hong-Xia Wang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Bo Huang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Le Wang
- College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Hong Hu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Qing Zhao
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.
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8
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Gupta P, Sharma A, Nagegowda DA. Multi-omics: Powerful accelerator for uncovering plant specialized metabolic pathways: The case of leonurine. MOLECULAR PLANT 2024; 17:13-15. [PMID: 38102830 DOI: 10.1016/j.molp.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Affiliation(s)
- Priyanka Gupta
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Anuj Sharma
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Dinesh A Nagegowda
- Molecular Plant Biology and Biotechnology Lab, CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru 560065, India; Academy of Scientific and Innovative Research, Ghaziabad 201002, India.
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9
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Raimondeau P, Bianconi ME, Pereira L, Parisod C, Christin PA, Dunning LT. Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage. THE NEW PHYTOLOGIST 2023; 240:2072-2084. [PMID: 37793435 DOI: 10.1111/nph.19272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/30/2023] [Indexed: 10/06/2023]
Abstract
Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.
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Affiliation(s)
- Pauline Raimondeau
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Laboratoire Evolution et Diversité Biologique, UMR5174, CNRS/IRD/Université Toulouse 3, Toulouse, 31062, France
| | - Matheus E Bianconi
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Lara Pereira
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, 1700, Switzerland
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, 1700, Switzerland
| | - Luke T Dunning
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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10
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Marcotrigiano AR, Carluccio AV, Unachukwu N, Adeoti SR, Abdulsalam T, Gedil M, Menkir A, Gisel A, Stavolone L. Hydroxamic acids: New players in the multifactorial mechanisms of maize resistance to Striga hermonthica. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 204:108134. [PMID: 37883916 DOI: 10.1016/j.plaphy.2023.108134] [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: 06/26/2023] [Revised: 09/25/2023] [Accepted: 10/21/2023] [Indexed: 10/28/2023]
Abstract
Striga hermonthica is the most widespread and destructive plant parasite infesting maize and other major crops in sub-Saharan Africa where it causes severe yield losses and threatens food security. Several tolerant maize lines supporting reduced S. hermonthica emergence have been deployed. However, the molecular bases of such resistance are yet poorly understood. Based on a time course comparative gene expression analysis between susceptible and resistant maize lines we have confirmed resistance mechanisms known to be activated upon plant parasite infestation and identified potential novel players worth further investigation e.g. iron homeostasis and mitochondrial respiration-related genes. Most intriguingly, we show a previously unknown strategy of maize post-attachment resistance based on DIMBOA accumulation in S. hermonthica-infested maize roots. S. hermonthica infestation triggers positive regulation of gene expression in the hydroxamic acid (HA) pathway culminating with an accumulation of benzoxazinoids (BX), known for their antifeedant, insecticidal, antimicrobial, and allelopathic activities. We demonstrate that HA root content is positively correlated with S. hermonthica resistance in the resistant parent and its progenies and in unrelated maize lines. Downregulation of HA genes causes increased susceptibility to S. hermonthica infestation in loss-of-function maize mutants. While the mechanism of BX action in parasitic plant resistance is yet to be uncovered, the potential of this discovery for developing effective control and breeding strategies is enormous.
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Affiliation(s)
- Angelo Raffaele Marcotrigiano
- International Institute of Tropical Agriculture, Ibadan, Nigeria; Department of Soil, Plant and Food Sciences, University of Bari, Italy
| | - Anna Vittoria Carluccio
- International Institute of Tropical Agriculture, Ibadan, Nigeria; Institute for Sustainable Plant Protection, CNR, Bari, Italy
| | - Nnanna Unachukwu
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Toyin Abdulsalam
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Abebe Menkir
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Andreas Gisel
- International Institute of Tropical Agriculture, Ibadan, Nigeria; Institute for Biomedical Technologies, CNR, Bari, Italy
| | - Livia Stavolone
- International Institute of Tropical Agriculture, Ibadan, Nigeria; Institute for Sustainable Plant Protection, CNR, Bari, Italy.
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11
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Yan XM, Zhou SS, Liu H, Zhao SW, Tian XC, Shi TL, Bao YT, Li ZC, Jia KH, Nie S, Guo JF, Kong L, Porth IM, Mao JF. Unraveling the evolutionary dynamics of the TPS gene family in land plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1273648. [PMID: 37900760 PMCID: PMC10600500 DOI: 10.3389/fpls.2023.1273648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/15/2023] [Indexed: 10/31/2023]
Abstract
Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.
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Affiliation(s)
- Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shan-Shan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Shuangyushu No.1 Primary School, Beijing, China
| | - Hui Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Personnel Section, Qufu Nishan National Forest Park Management Service Center, Qufu, China
| | - Ilga M. Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, Québec, QC, Canada
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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12
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Huang Y, Wu D, Huang Z, Li X, Merotto A, Bai L, Fan L. Weed genomics: yielding insights into the genetics of weedy traits for crop improvement. ABIOTECH 2023; 4:20-30. [PMID: 37220539 PMCID: PMC10199979 DOI: 10.1007/s42994-022-00090-5] [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: 10/27/2022] [Accepted: 12/06/2022] [Indexed: 05/25/2023]
Abstract
Weeds cause tremendous economic and ecological damage worldwide. The number of genomes established for weed species has sharply increased during the recent decade, with some 26 weed species having been sequenced and de novo genomes assembled. These genomes range from 270 Mb (Barbarea vulgaris) to almost 4.4 Gb (Aegilops tauschii). Importantly, chromosome-level assemblies are now available for 17 of these 26 species, and genomic investigations on weed populations have been conducted in at least 12 species. The resulting genomic data have greatly facilitated studies of weed management and biology, especially origin and evolution. Available weed genomes have indeed revealed valuable weed-derived genetic materials for crop improvement. In this review, we summarize the recent progress made in weed genomics and provide a perspective for further exploitation in this emerging field.
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Affiliation(s)
- Yujie Huang
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
| | - Zhaofeng Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xiangyu Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School Federal University of Rio Grande do Sul, Porto Alegre, 91540-000 Brazil
| | - Lianyang Bai
- Hunan Weed Science Key Laboratory, Hunan Academy of Agriculture Sciences, Changshang, 410125 China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058 China
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13
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Méteignier LV, Nützmann HW, Papon N, Osbourn A, Courdavault V. Emerging mechanistic insights into the regulation of specialized metabolism in plants. NATURE PLANTS 2023; 9:22-30. [PMID: 36564633 DOI: 10.1038/s41477-022-01288-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Plants biosynthesize a broad range of natural products through specialized and species-specific metabolic pathways that are fuelled by core metabolism, together forming a metabolic network. Specialized metabolites have important roles in development and adaptation to external cues, and they also have invaluable pharmacological properties. A growing body of evidence has highlighted the impact of translational, transcriptional, epigenetic and chromatin-based regulation and evolution of specialized metabolism genes and metabolic networks. Here we review the forefront of this research field and extrapolate to medicinal plants that synthetize rare molecules. We also discuss how this new knowledge could help in improving strategies to produce useful plant-derived pharmaceuticals.
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Affiliation(s)
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Nicolas Papon
- IRF, SFR ICAT, Université Angers and Université de Bretagne-Occidentale, Angers, France
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK.
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
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14
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Conneely LJ, Berkowitz O, Lewsey MG. Emerging trends in genomic and epigenomic regulation of plant specialised metabolism. PHYTOCHEMISTRY 2022; 203:113427. [PMID: 36087823 DOI: 10.1016/j.phytochem.2022.113427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Regulation of specialised metabolism genes is multilayered and complex, influenced by an array of genomic, epigenetic and epigenomic mechanisms. Here, we review the most recent knowledge in this field, drawing from discoveries in several plant species. Our aim is to improve understanding of how plant genome structure and function influence specialised metabolism. We also highlight key areas for future exploration. Gene regulatory mechanisms influencing specialised metabolism include gene duplication and neo-functionalization, conservation of operon-like clusters of specialised metabolism genes, local chromatin modifications, and the organisation of higher order chromatin structures within the nucleus. Genomic and epigenomic research to-date in the discipline have focused on a relatively small number of plant species, primarily at whole organ or tissue level. This is largely due to the technical demands of the experimental methods needed. However, a high degree of cell-type specificity of function exists in specialised metabolism, driven by similarly specific gene regulation. In this review we focus on the genomic characteristics of genes that are found in different types of clusters within the genome. We propose that acquisition of cell-resolution epigenomic datasets in emerging models, such as the glandular trichomes of Cannabis sativa, will yield important advances. Data such as chromatin accessibility and histone modification profiles can pinpoint which regulatory sequences are active in individual cell types and at specific times in development. These could provide fundamental biological insight as well as novel targets for genetic engineering and crop improvement.
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Affiliation(s)
- Lee J Conneely
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Oliver Berkowitz
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia
| | - Mathew G Lewsey
- La Trobe Institute for Agriculture and Food, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia; Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC, 3086, Australia.
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15
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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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16
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Wu D, Hu Y, Akashi S, Nojiri H, Guo L, Ye C, Zhu Q, Okada K, Fan L. Lateral transfers lead to the birth of momilactone biosynthetic gene clusters in grass. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1354-1367. [PMID: 35781905 PMCID: PMC9544640 DOI: 10.1111/tpj.15893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 05/31/2023]
Abstract
Momilactone A, an important plant labdane-related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC-like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC-like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT-mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.
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Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Yiyu Hu
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Shota Akashi
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Hideaki Nojiri
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longbiao Guo
- State Key Laboratory for Rice Biology, China National Rice Research InstituteChinese Academy of Agricultural SciencesHangzhou310006China
| | - Chu‐Yu Ye
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
| | - Qian‐Hao Zhu
- CSIRO Agriculture and Food, Black Mountain LaboratoriesCanberraACT2601Australia
| | - Kazunori Okada
- Biotechnology Research CenterUniversity of Tokyo113‐8657TokyoJapan
| | - Longjiang Fan
- Hainan Institute of Zhejiang UniversityYonyou Industrial ParkSanya572025China
- Institute of Crop Science & Institute of BioinformaticsZhejiang UniversityHangzhou310058China
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