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Liang D, Jiang Y, Zhang Y, Mao C, Ma T, Zhang C. The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families of Botryosphaeria dothidea Related to Pathogenicity on Chinese Hickory Tree. J Fungi (Basel) 2024; 10:299. [PMID: 38667970 PMCID: PMC11051394 DOI: 10.3390/jof10040299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea's pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea's pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea's genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea's pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.
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Affiliation(s)
| | | | | | | | - Tianlin Ma
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
| | - Chuanqing Zhang
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
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Leal C, Trotel-Aziz P, Gramaje D, Armengol J, Fontaine F. Exploring Factors Conditioning the Expression of Botryosphaeria Dieback in Grapevine for Integrated Management of the Disease. PHYTOPATHOLOGY 2024; 114:21-34. [PMID: 37505093 DOI: 10.1094/phyto-04-23-0136-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Species from the Botryosphaeriaceae family are the causal agents of Botryosphaeria dieback (BD), a worldwide grapevine trunk disease. Because of their lifestyle and their adaptation to a wide range of temperatures, these fungi constitute a serious threat to vineyards and viticulture, especially in the actual context of climate change. Grapevine plants from both nurseries and vineyards are very susceptible to infections by botryosphaeriaceous fungi due to several cuts and wounds made during their propagation process and their entire life cycle, respectively. When decline becomes chronic or apoplectic, it reduces the longevity of the vineyard and affects the quality of the wine, leading to huge economic losses. Given the environmental impact of fungicides, and their short period of effectiveness in protecting pruning wounds, alternative strategies are being developed to fight BD fungal pathogens and limit their propagation. Among them, biological control has been recognized as a promising and sustainable alternative. However, there is still no effective strategy for combating this complex disease, conditioned by both fungal life traits and host tolerance traits, in relationships with the whole microbiome/microbiota. To provide sound guidance for an effective and sustainable integrated management of BD, by combining the limitation of infection risk, tolerant grapevine cultivars, and biological control, this review explores some of the factors conditioning the expression of BD in grapevine. Among them, the lifestyle of BD-associated pathogens, their pathogenicity factors, the cultivar traits of tolerance or susceptibility, and the biocontrol potential of Bacillus spp. and Trichoderma spp. are discussed.
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Affiliation(s)
- Catarina Leal
- University of Reims Champagne-Ardenne, Research Unit Résistance Induite et Bioprotection des Plantes RIBP EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera S/N, 46022 Valencia, Spain
| | - Patricia Trotel-Aziz
- University of Reims Champagne-Ardenne, Research Unit Résistance Induite et Bioprotection des Plantes RIBP EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas-Universidad de la Rioja-Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Josep Armengol
- Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, Camino de Vera S/N, 46022 Valencia, Spain
| | - Florence Fontaine
- University of Reims Champagne-Ardenne, Research Unit Résistance Induite et Bioprotection des Plantes RIBP EA 4707, INRAE USC 1488, SFR Condorcet FR CNRS 3417, Reims, France
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Derviş S, Özer G. Plant-Associated Neoscytalidium dimidiatum-Taxonomy, Host Range, Epidemiology, Virulence, and Management Strategies: A Comprehensive Review. J Fungi (Basel) 2023; 9:1048. [PMID: 37998855 PMCID: PMC10672476 DOI: 10.3390/jof9111048] [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: 09/06/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Neoscytalidium dimidiatum, a plant- and human-associated fungus, has emerged as a substantial global ecological and agricultural threat aggravated by global warming. It inflicts various diseases, including canker, blight, dieback, leaf spot, root rot, and fruit rot, across a wide spectrum of fruit trees, field crops, shrubs, and arboreal species, with a host range spanning 46 plant families, 84 genera, and 126 species, primarily affecting eudicot angiosperms. Six genera are asymptomatic hosts. Neoscytalidium dimidiatum exhibits worldwide distribution, with the highest prevalence observed in Asia and North America, notably in Iran, Turkey, and California. Rising disease prevalence and severity, aggravated by climate change, particularly impact tropical arid places across 37 countries spanning all 7 continents. This comprehensive review encapsulates recent advancements in the understanding of N. dimidiatum, encompassing alterations in its taxonomic classification, host range, symptoms, geographic distribution, epidemiology, virulence, and strategies for effective management. This study also concentrates on comprehending the taxonomic relationships and intraspecific variations within N. dimidiatum, with a particular emphasis on N. oculus and N. hylocereum, proposing to consider these two species as synonymous with N. dimidiatum. Furthermore, this review identifies prospective research directions aimed at augmenting our fundamental understanding of host-N. dimidiatum interaction.
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Affiliation(s)
- Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin 47000, Turkey
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu 14030, Turkey
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Xie Y, Shi L, Cheng K, Li Y, Yu S. Host Recognition and Specific Infection of Endomelanconiopsis endophytica during Early Infection. J Fungi (Basel) 2023; 9:1040. [PMID: 37888296 PMCID: PMC10607883 DOI: 10.3390/jof9101040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
Coevolution between the pathogen and host plant drives pathogenic effector diversity. However, the molecular mechanism behind host-specific pathogenesis remains to be explored. Here, we present a 43 Mb whole-genome sequence of Endomelanconiopsis endophytica strain LS29, a host-specific pathogen of the common subtropical tree Castanopsis fissa. We described its genome annotations and identified its effector candidates. By performing temporal transcriptome sequencing of E. endophytica on C. fissa during early infection, we found that E. endophytica repressed other microbes in order to attack the tissue of the host by producing antibiotics earlier than 24 h post-inoculation (hpi). Simultaneously, a variety of effectors were secreted to recognize the host plant, but most of them showed a significantly opposing expression regulation trend after 24 hpi, indicating that 24 hpi represents a key time point between host recognition and specific infection. Furthermore, a comparison of isoenzymes showed that only a few effectors were identified as specific effectors, which were involved in hydrolyzing the compounds of the plant cell wall and releasing fatty acids during the early infection of C. fissa. Our results determined host recognition timing and identified a specific catalog of effectors, which are crucial for revealing the molecular mechanism of host-specific pathogenesis.
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Affiliation(s)
- Yan Xie
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liuqing Shi
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Keke Cheng
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yang Li
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Shixiao Yu
- Department of Ecology, School of Life Sciences/State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
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Restrepo-Leal JD, Belair M, Fischer J, Richet N, Fontaine F, Rémond C, Fernandez O, Besaury L. Differential carbohydrate-active enzymes and secondary metabolite production by the grapevine trunk pathogen Neofusicoccum parvum Bt-67 grown on host and non-host biomass. Mycologia 2023; 115:579-601. [PMID: 37358885 DOI: 10.1080/00275514.2023.2216122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/17/2023] [Indexed: 06/27/2023]
Abstract
Neofusicoccum parvum is one of the most aggressive Botryosphaeriaceae species associated with grapevine trunk diseases. This species may secrete enzymes capable of overcoming the plant barriers, leading to wood colonization. In addition to their roles in pathogenicity, there is an interest in taking advantage of N. parvum carbohydrate-active enzymes (CAZymes), related to plant cell wall degradation, for lignocellulose biorefining. Furthermore, N. parvum produces toxic secondary metabolites that may contribute to its virulence. In order to increase knowledge on the mechanisms underlying pathogenicity and virulence, as well as the exploration of its metabolism and CAZymes for lignocellulose biorefining, we evaluated the N. parvum strain Bt-67 capacity in producing lignocellulolytic enzymes and secondary metabolites when grown in vitro with two lignocellulosic biomasses: grapevine canes (GP) and wheat straw (WS). For this purpose, a multiphasic study combining enzymology, transcriptomic, and metabolomic analyses was performed. Enzyme assays showed higher xylanase, xylosidase, arabinofuranosidase, and glucosidase activities when the fungus was grown with WS. Fourier transform infrared (FTIR) spectroscopy confirmed the lignocellulosic biomass degradation caused by the secreted enzymes. Transcriptomics indicated that the N. parvum Bt-67 gene expression profiles in the presence of both biomasses were similar. In total, 134 genes coding CAZymes were up-regulated, where 94 of them were expressed in both biomass growth conditions. Lytic polysaccharide monooxygenases (LPMOs), glucosidases, and endoglucanases were the most represented CAZymes and correlated with the enzymatic activities obtained. The secondary metabolite production, analyzed by high-performance liquid chromatography-ultraviolet/visible spectophotometry-mass spectrometry (HPLC-UV/Vis-MS), was variable depending on the carbon source. The diversity of differentially produced metabolites was higher when N. parvum Bt-67 was grown with GP. Overall, these results provide insight into the influence of lignocellulosic biomass on virulence factor expressions. Moreover, this study opens the possibility of optimizing the enzyme production from N. parvum with potential use for lignocellulose biorefining.
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Affiliation(s)
- Julián D Restrepo-Leal
- AFERE Chair, Fractionnement des Agroressources et Environnement (FARE) UMR A 614, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
- MALDIVE Chair, Résistance Induite et Bioprotection des Plantes (RIBP) USC 1488, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Marie Belair
- AFERE Chair, Fractionnement des Agroressources et Environnement (FARE) UMR A 614, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Jochen Fischer
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
| | - Nicolas Richet
- Plateau Technique Mobile de Cytométrie Environnementale (MOBICYTE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne Ardenne/Institut National de l'Environnement Industriel et des Risques (INERIS), 51100 Reims, France
| | - Florence Fontaine
- MALDIVE Chair, Résistance Induite et Bioprotection des Plantes (RIBP) USC 1488, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Caroline Rémond
- AFERE Chair, Fractionnement des Agroressources et Environnement (FARE) UMR A 614, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Olivier Fernandez
- MALDIVE Chair, Résistance Induite et Bioprotection des Plantes (RIBP) USC 1488, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | - Ludovic Besaury
- AFERE Chair, Fractionnement des Agroressources et Environnement (FARE) UMR A 614, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE), UFR Sciences Exactes et Naturelles, Université de Reims Champagne-Ardenne, 51100 Reims, France
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Aparicio Chacón MV, Van Dingenen J, Goormachtig S. Characterization of Arbuscular Mycorrhizal Effector Proteins. Int J Mol Sci 2023; 24:9125. [PMID: 37298075 PMCID: PMC10252856 DOI: 10.3390/ijms24119125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Plants are colonized by various fungi with both pathogenic and beneficial lifestyles. One type of colonization strategy is through the secretion of effector proteins that alter the plant's physiology to accommodate the fungus. The oldest plant symbionts, the arbuscular mycorrhizal fungi (AMF), may exploit effectors to their benefit. Genome analysis coupled with transcriptomic studies in different AMFs has intensified research on the effector function, evolution, and diversification of AMF. However, of the current 338 predicted effector proteins from the AM fungus Rhizophagus irregularis, only five have been characterized, of which merely two have been studied in detail to understand which plant proteins they associate with to affect the host physiology. Here, we review the most recent findings in AMF effector research and discuss the techniques used for the functional characterization of effector proteins, from their in silico prediction to their mode of action, with an emphasis on high-throughput approaches for the identification of plant targets of the effectors through which they manipulate their hosts.
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Affiliation(s)
- María V. Aparicio Chacón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Judith Van Dingenen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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