1
|
Rocha J, Shapiro LR, Chimileski S, Kolter R. Complementary roles of EPS, T3SS and Expansin for virulence of Erwinia tracheiphila, the causative agent of cucurbit wilt. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600446. [PMID: 38979168 PMCID: PMC11230154 DOI: 10.1101/2024.06.24.600446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Erwinia tracheiphila (Smith) is a recently emerged plant pathogen that causes severe economic losses in cucurbit crops in temperate Eastern North America. E. tracheiphila is xylem restricted, and virulence is thought to be related to Exopolysaccharides (EPS) and biofilm formation, which occlude the passage of sap in xylem vessels and causes systemic wilt. However, the role of EPS and biofilm formation, and their contribution to disease in relation to other virulence loci are unknown. Here, we use deletion mutants to explore the roles of EPS, Hrp Type III secretion system (Hrp T3SS) and Expansin in plant colonization and virulence. Then, we quantify the expression of the genes encoding these factors during infection. Our results show that Exopolysaccharides are essential for E. tracheiphila survival in host plants, while Hrp T3SS and Expansin are dispensable for survival but needed for systemic wilt symptom development. EPS and Hrp T3SS display contrasting expression patterns in the plant, reflecting their relevance in different stages of the infection. Finally, we show that expression of the eps and hrpT3SS operons is downregulated in mildly increased temperatures, suggesting a link between expression of these virulence factors and geographic restriction of E. tracheiphila to temperate regions. Our work highlights how E. tracheiphila virulence is a complex trait where several loci are coordinated during infection. These results further shed light into the relationship between virulence factors and the ecology of this pathosystem, which will be essential for developing sustainable management strategies for this emerging pathogen.
Collapse
Affiliation(s)
- Jorge Rocha
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
- Progama de Agricultura en Zonas Áridas; Centro de Investigaciones Biológicas del Noroeste. Av. Instituto Politécnico Nacional 195, La Paz, B.C.S. México 23096
| | - Lori R Shapiro
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
| | - Scott Chimileski
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory; Woods Hole, MA, US 02543
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
| |
Collapse
|
2
|
Lonjon F, Lai Y, Askari N, Aiyar N, Bundalovic-Torma C, Laflamme B, Wang PW, Desveaux D, Guttman DS. The effector-triggered immunity landscape of tomato against Pseudomonas syringae. Nat Commun 2024; 15:5102. [PMID: 38877009 PMCID: PMC11178782 DOI: 10.1038/s41467-024-49425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/31/2024] [Indexed: 06/16/2024] Open
Abstract
Tomato (Solanum lycopersicum) is one of the world's most important food crops, and as such, its production needs to be protected from infectious diseases that can significantly reduce yield and quality. Here, we survey the effector-triggered immunity (ETI) landscape of tomato against the bacterial pathogen Pseudomonas syringae. We perform comprehensive ETI screens in five cultivated tomato varieties and two wild relatives, as well as an immunodiversity screen on a collection of 149 tomato varieties that includes both wild and cultivated varieties. The screens reveal a tomato ETI landscape that is more limited than what was previously found in the model plant Arabidopsis thaliana. We also demonstrate that ETI eliciting effectors can protect tomato against P. syringae infection when the effector is delivered by a non-virulent strain either prior to or simultaneously with a virulent strain. Overall, our findings provide a snapshot of the ETI landscape of tomatoes and demonstrate that ETI can be used as a biocontrol treatment to protect crop plants.
Collapse
Affiliation(s)
- Fabien Lonjon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Yan Lai
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Nasrin Askari
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Niharikaa Aiyar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | | | - Bradley Laflamme
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Pauline W Wang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada
| | - Darrell Desveaux
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada.
| | - David S Guttman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
- Centre for the Analysis of Genome Evolution & Function, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
3
|
Ramírez Martínez J, Guillou S, Le Prieur S, Di Vittorio P, Bonal F, Taliadoros D, Gueret E, Fournier E, Stukenbrock EH, Valade R, Gladieux P. Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen. Microb Genom 2024; 10:001241. [PMID: 38713188 PMCID: PMC11170133 DOI: 10.1099/mgen.0.001241] [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: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
Collapse
Affiliation(s)
- Julie Ramírez Martínez
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | - Pauline Di Vittorio
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florelle Bonal
- UMR AGAP (Amélioration génétique et adaptation des plantes), Montpellier, France
| | - Demetris Taliadoros
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Eva H. Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | | | - Pierre Gladieux
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
4
|
Saubin M, Tellier A, Stoeckel S, Andrieux A, Halkett F. Approximate Bayesian Computation applied to time series of population genetic data disentangles rapid genetic changes and demographic variations in a pathogen population. Mol Ecol 2024; 33:e16965. [PMID: 37150947 DOI: 10.1111/mec.16965] [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: 11/07/2022] [Revised: 04/04/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023]
Abstract
Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.
Collapse
Affiliation(s)
- Méline Saubin
- Université de Lorraine, INRAE, IAM, Nancy, France
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Aurélien Tellier
- Department for Life Science Systems, Technical University of Munich, Freising, Germany
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | | | | |
Collapse
|
5
|
Mullett MS, Harris AR, Scanu B, Van Poucke K, LeBoldus J, Stamm E, Bourret TB, Christova PK, Oliva J, Redondo MA, Talgø V, Corcobado T, Milenković I, Jung MH, Webber J, Heungens K, Jung T. Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae. MOLECULAR PLANT PATHOLOGY 2024; 25:e13450. [PMID: 38590129 PMCID: PMC11002350 DOI: 10.1111/mpp.13450] [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: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.
Collapse
Affiliation(s)
- Martin S. Mullett
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | | | - Bruno Scanu
- Department of Agricultural SciencesUniversity of SassariSassariItaly
| | - Kris Van Poucke
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitMerelbekeBelgium
| | - Jared LeBoldus
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
- Department of Forest Engineering, Resources, and ManagementOregon State UniversityCorvallisOregonUSA
| | - Elizabeth Stamm
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Tyler B. Bourret
- USDA‐ARS Mycology and Nematology Genetic Diversity and Biology LaboratoryBeltsvilleMarylandUSA
- Department of Plant PathologyUC DavisDavisCaliforniaUSA
| | | | - Jonás Oliva
- Department of Agricultural and Forest Sciences and EngineeringUniversity of LleidaLleidaSpain
- Joint Research Unit CTFC–AGROTECNIO–CERCALleidaSpain
| | - Miguel A. Redondo
- National Bioinformatics Infrastructure Sweden, Science for Life LaboratorySweden
- Department of Cell and Molecular BiologyUppsala UniversityUppsalaSweden
| | - Venche Talgø
- Division of Biotechnology and Plant HealthNorwegian Institute of Bioeconomy Research (NIBIO)ÅsNorway
| | - Tamara Corcobado
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Ivan Milenković
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | - Marília Horta Jung
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| | | | - Kurt Heungens
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Plant Sciences UnitMerelbekeBelgium
| | - Thomas Jung
- Department of Forest Protection and Wildlife ManagementMendel University in BrnoBrnoCzech Republic
| |
Collapse
|
6
|
Daba G, Daelemans R, Berecha G, Geerinck MWJ, Verreth C, Crauwels S, Lievens B, Honnay O. Genetic diversity and structure of the coffee leaf rust fungus Hemileia vastatrix across different coffee management systems in Ethiopia. Int Microbiol 2024; 27:525-534. [PMID: 37507629 DOI: 10.1007/s10123-023-00409-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 07/07/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023]
Abstract
Although coffee leaf rust (CLR), caused by Hemileia vastatrix, poses an increasing threat to coffee production in Ethiopia, little is known regarding its genetic diversity and structure and how these are affected by coffee management. Here, we used genetic fingerprinting based on sequence-related amplified polymorphism (SRAP) markers to genotype H. vastatrix samples from different coffee shrubs, across 40 sites, covering four coffee production systems (forest coffee, semi plantation coffee, home garden coffee, and plantation coffee) and different altitudes in Ethiopia. In total, 96 H. vastatrix samples were successfully genotyped with three primer combinations, producing a total of 79 scorable bands. We found 35.44% of amplified bands to be polymorphic, and the polymorphic information content (PIC) was 0.45, suggesting high genetic diversity among our CLR isolates. We also found significant isolation-by-distance across the samples investigated and detected significant differences in fungal genetic composition among plantation coffee and home garden coffee and a marginally significant difference among plantation coffee and forest coffee. Furthermore, we found a significant effect of altitude on CLR genetic composition in the forest coffee and plantation systems. Our results suggest that both spore dispersal and different selection pressures in the different coffee management systems are likely responsible for the observed high genetic diversity and genetic structure of CLR isolates in Ethiopia. When selecting Ethiopian coffee genotypes for crop improvement, it is important that these genotypes carry some resistance against CLR. Because our study shows large variation in genetic composition across relatively short geographical distances, a broad selection of rust isolates must be used for coffee resistance screening.
Collapse
Affiliation(s)
- Gerba Daba
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium.
- College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia.
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium.
| | - Robin Daelemans
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
| | - Gezahegn Berecha
- College of Agriculture and Veterinary Medicine, Department of Horticulture and Plant Sciences, Jimma University, PO Box 307, Jimma, Ethiopia
| | - Margot W J Geerinck
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Christel Verreth
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Department of Microbial and Molecular Systems, KU Leuven, Willem De Croylaan 46, B-3001, Louvain, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, Biology Department, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Belgium
- KU Leuven Plant Institute (LPI), B-3001, Louvain, Belgium
| |
Collapse
|
7
|
Jiang G, Zhang Y, Chen M, Ramoneda J, Han L, Shi Y, Peyraud R, Wang Y, Shi X, Chen X, Ding W, Jousset A, Hikichi Y, Ohnishi K, Zhao FJ, Xu Y, Shen Q, Dini-Andreote F, Zhang Y, Wei Z. Effects of plant tissue permeability on invasion and population bottlenecks of a phytopathogen. Nat Commun 2024; 15:62. [PMID: 38167266 PMCID: PMC10762237 DOI: 10.1038/s41467-023-44234-7] [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: 03/28/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90 of these strains to inoculate tomato plants with different degrees of physical permeability to invasion (intact roots, wounded roots and xylem inoculation) and quantify the phytopathogen population dynamics during invasion. Our results reveal that the permeability of plant roots impacts the degree of population bottleneck, genetic diversity, and composition of Ralstonia populations. We also find that selection is the main driver structuring pathogen populations when barriers to infection are less permeable, i.e., intact roots, the removal of root physical and immune barriers results in the predominance of stochasticity in population assembly. Taken together, our study suggests that plant root permeability constitutes a bottleneck for phytopathogen invasion and genetic diversity.
Collapse
Affiliation(s)
- Gaofei Jiang
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yuling Zhang
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Min Chen
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China
| | - Josep Ramoneda
- Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Liangliang Han
- Department of Biomedical Science, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Rémi Peyraud
- iMEAN, Ramonville Saint Agne, Occitanie, FR, France
| | - Yikui Wang
- Vegetable Research Institute, Guangxi Academy of Agricultural Science, Nanning, China
| | - Xiaojun Shi
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Xinping Chen
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Wei Ding
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China
| | - Alexandre Jousset
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yasufumi Hikichi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Kouhei Ohnishi
- Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Japan
| | - Fang-Jie Zhao
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Yangchun Xu
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- The One Health Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Yong Zhang
- College of Resources and Environment, College of Plant Protection, Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing, China.
- College of Environmental Science and Engineering, Shaanxi University of Science & Technology, Xi'an, China.
| | - Zhong Wei
- Key Laboratory of Plant Immunity, Jiangsu Provincial Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, China.
| |
Collapse
|
8
|
Ascari JP, Cazón LI, Rahnama M, Lamour K, Fernandes JMC, Farman ML, Ponte EMD. Pyricularia Are Mostly Host-Specialized with Limited Reciprocal Cross-Infection Between Wheat and Endemic Grasses in Minas Gerais, Brazil. PHYTOPATHOLOGY 2024; 114:226-240. [PMID: 37399001 DOI: 10.1094/phyto-01-23-0024-r] [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] [Indexed: 07/04/2023]
Abstract
Wheat blast, caused by Pyricularia oryzae Triticum (PoT), is an emerging threat to global wheat production. The current understanding of the population biology of the pathogen and epidemiology of the disease has been based on phylogenomic studies that compared the wheat blast pathogen with isolates collected from grasses that were invasive to Brazilian wheat fields. In this study, we performed a comprehensive sampling of blast lesions in wheat crops and endemic grasses found in and away from wheat fields in Minas Gerais. A total of 1,368 diseased samples were collected (976 leaves of wheat and grasses and 392 wheat heads), which yielded a working collection of 564 Pyricularia isolates. We show that, contrary to earlier implications, PoT was rarely found on endemic grasses, and, conversely, members of grass-adapted lineages were rarely found on wheat. Instead, most lineages were host-specialized, with constituent isolates usually grouping according to their host of origin. With regard to the dominant role proposed for signalgrass in wheat blast epidemiology, we found only one PoT member in 67 isolates collected from signalgrass grown away from wheat fields and only three members of Urochloa-adapted lineages among hundreds of isolates from wheat. Cross-inoculation assays on wheat and a signalgrass used in pastures (U. brizantha) suggested that the limited cross-infection observed in the field may be due to innate compatibility differences. Whether or not the observed level of cross-infection would be sufficient to provide an inoculum reservoir, or serve as a bridge between wheat growing regions, is questionable and, therefore, deserves further investigation.
Collapse
Affiliation(s)
- João P Ascari
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Luis I Cazón
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
- Department of Biology, Tennessee Tech University, Cookeville, TN 38501, U.S.A
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
| | | | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| |
Collapse
|
9
|
Poulicard N, Pagán I, González-Jara P, Mora MÁ, Hily JM, Fraile A, Piñero D, García-Arenal F. Repeated loss of the ability of a wild pepper disease resistance gene to function at high temperatures suggests that thermoresistance is a costly trait. THE NEW PHYTOLOGIST 2024; 241:845-860. [PMID: 37920100 DOI: 10.1111/nph.19371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023]
Abstract
Specificity in plant-pathogen gene-for-gene (GFG) interactions is determined by the recognition of pathogen proteins by the products of plant resistance (R) genes. The evolutionary dynamics of R genes in plant-virus systems is poorly understood. We analyse the evolution of the L resistance locus to tobamoviruses in the wild pepper Capsicum annuum var. glabriusculum (chiltepin), a crop relative undergoing incipient domestication. The frequency, and the genetic and phenotypic diversity, of the L locus was analysed in 41 chiltepin populations under different levels of human management over its distribution range in Mexico. The frequency of resistance was lower in Cultivated than in Wild populations. L-locus genetic diversity showed a strong spatial structure with no isolation-by-distance pattern, suggesting environment-specific selection, possibly associated with infection by the highly virulent tobamoviruses found in the surveyed regions. L alleles differed in recognition specificity and in the expression of resistance at different temperatures, broad-spectrum recognition of P0 + P1 pathotypes and expression above 32°C being ancestral traits that were repeatedly lost along L-locus evolution. Overall, loss of resistance co-occurs with incipient domestication and broad-spectrum resistance expressed at high temperatures has apparent fitness costs. These findings contribute to understand the role of fitness trade-offs in plant-virus coevolution.
Collapse
Affiliation(s)
- Nils Poulicard
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Pablo González-Jara
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Miguel Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Jean-Michel Hily
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, 04510, Ciudad de México, Mexico
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223, Pozuelo de Alarcón, Madrid, Spain
| |
Collapse
|
10
|
Taliadoros D, Feurtey A, Wyatt N, Barrès B, Gladieux P, Friesen TL, Stukenbrock EH. Emergence and spread of the barley net blotch pathogen coincided with crop domestication and cultivation history. PLoS Genet 2024; 20:e1010884. [PMID: 38285729 PMCID: PMC10852282 DOI: 10.1371/journal.pgen.1010884] [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: 07/27/2023] [Revised: 02/08/2024] [Accepted: 12/11/2023] [Indexed: 01/31/2024] Open
Abstract
Fungal pathogens cause devastating disease in crops. Understanding the evolutionary origin of pathogens is essential to the prediction of future disease emergence and the potential of pathogens to disperse. The fungus Pyrenophora teres f. teres causes net form net blotch (NFNB), an economically significant disease of barley. In this study, we have used 104 P. teres f. teres genomes from four continents to explore the population structure and demographic history of the fungal pathogen. We showed that P. teres f. teres is structured into populations that tend to be geographically restricted to different regions. Using Multiple Sequentially Markovian Coalescent and machine learning approaches we demonstrated that the demographic history of the pathogen correlates with the history of barley, highlighting the importance of human migration and trade in spreading the pathogen. Exploring signatures of natural selection, we identified several population-specific selective sweeps that colocalized with genomic regions enriched in putative virulence genes, and loci previously identified as determinants of virulence specificities by quantitative trait locus analyses. This reflects rapid adaptation to local hosts and environmental conditions of P. teres f. teres as it spread with barley. Our research highlights how human activities can contribute to the spread of pathogens that significantly impact the productivity of field crops.
Collapse
Affiliation(s)
- Demetris Taliadoros
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, Zurich, Switzerland
| | - Nathan Wyatt
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
- Sugar Beet and Potato Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Benoit Barrès
- Université de Lyon, Anses, INRAE, USC CASPER, Lyon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Timothy L. Friesen
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, North Dakota, United States of America
| | - Eva H. Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| |
Collapse
|
11
|
Farman ML, Ascari JP, Rahnama M, Ponte EMD, Pedley KF, Martinez S, Fernandes JMC, Valent B. A Reevaluation of Phylogenomic Data Reveals that Current Understanding in Wheat Blast Population Biology and Epidemiology Is Obfuscated by Oversights in Population Sampling. PHYTOPATHOLOGY 2024; 114:220-225. [PMID: 37486092 DOI: 10.1094/phyto-01-23-0025-r] [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: 07/25/2023]
Abstract
Wheat blast, caused by the Pyricularia oryzae Triticum lineage (PoT), first emerged in Brazil and quickly spread to neighboring countries. Its recent appearance in Bangladesh and Zambia highlights a need to understand the disease's population biology and epidemiology so as to mitigate pandemic outbreaks. Current knowledge is mostly based on characterizations of Brazilian wheat blast isolates and comparison with isolates from non-wheat, endemic grasses. These foregoing studies concluded that the wheat blast population lacks host specificity and, as a result, undergoes extensive gene flow with populations infecting non-wheat hosts. Additionally, based on genetic similarity between wheat blast and isolates infecting Urochloa species, it was proposed that the disease originally emerged via a host jump from this grass and that Urochloa likely plays a central role in wheat blast epidemiology owing to its widespread use as a pasture grass. However, due to inconsistencies with broader phylogenetic studies, we suspected that these seminal studies had not actually sampled the populations normally found on endemic grasses and, instead, had repeatedly isolated members of PoT and the related Lolium pathogen lineage (PoL1). Re-analysis of the Brazilian data as part of a comprehensive, global, phylogenomic dataset that included a small number of South American isolates sampled away from wheat confirmed our suspicion and identified four new P. oryzae lineages on grass hosts. As a result, the conclusions underpinning current understanding in wheat blast's evolution, population biology, and epidemiology are unsubstantiated and could be equivocal.
Collapse
Affiliation(s)
- Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Joao P Ascari
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Kerry F Pedley
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease Weed Science Research Unit, Fort Detrick, MD 21702, U.S.A
| | - Sebastián Martinez
- Instituto Nacional de Investigación Agropecuaria, INIA Treinta y Tres, 33000 Treinta y Tres, Uruguay
| | | | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| |
Collapse
|
12
|
Savary S. A Global Assessment of the State of Plant Health. PLANT DISEASE 2023; 107:3649-3665. [PMID: 37172970 DOI: 10.1094/pdis-01-23-0166-fe] [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: 05/15/2023]
Abstract
The Global Plant Health Assessment (GPHA) is a collective, volunteer-based effort to assemble expert opinions on plant health and disease impacts on ecosystem services based on published scientific evidence. The GPHA considers a range of forest, agricultural, and urban systems worldwide. These are referred to as (Ecoregion × Plant System), i.e., selected case examples involving keystone plants in given parts of the world. The GPHA focuses on infectious plant diseases and plant pathogens, but encompasses the abiotic (e.g., temperature, drought, and floods) and other biotic (e.g., animal pests and humans) factors associated with plant health. Among the 33 (Ecoregion × Plant System) considered, 18 are assessed as in fair or poor health, and 20 as in declining health. Much of the observed state of plant health and its trends are driven by a combination of forces, including climate change, species invasions, and human management. Healthy plants ensure (i) provisioning (food, fiber, and material), (ii) regulation (climate, atmosphere, water, and soils), and (iii) cultural (recreation, inspiration, and spiritual) ecosystem services. All these roles that plants play are threatened by plant diseases. Nearly none of these three ecosystem services are assessed as improving. Results indicate that the poor state of plant health in sub-Saharan Africa gravely contributes to food insecurity and environmental degradation. Results further call for the need to improve crop health to ensure food security in the most populated parts of the world, such as in South Asia, where the poorest of the poor, the landless farmers, are at the greatest risk. The overview of results generated from this work identifies directions for future research to be championed by a new generation of scientists and revived public extension services. Breakthroughs from science are needed to (i) gather more data on plant health and its consequences, (ii) identify collective actions to manage plant systems, (iii) exploit the phytobiome diversity in breeding programs, (iv) breed for plant genotypes with resilience to biotic and abiotic stresses, and (v) design and implement plant systems involving the diversity required to ensure their adaptation to current and growing challenges, including climate change and pathogen invasions.
Collapse
Affiliation(s)
- Serge Savary
- National Research Institute of Science and Technology for Environment and Agriculture (INRAE), Paris, France
- Govind Ballabh Pant University of Agriculture and Technology (GBPUAT), Pantnagar, Uttarakhand, India
- University of California-Davis, Davis, CA, U.S.A
- ITC, University of Twente, the Netherlands
| |
Collapse
|
13
|
Dorigan AF, Moreira SI, da Silva Costa Guimarães S, Cruz-Magalhães V, Alves E. Target and non-target site mechanisms of fungicide resistance and their implications for the management of crop pathogens. PEST MANAGEMENT SCIENCE 2023; 79:4731-4753. [PMID: 37592727 DOI: 10.1002/ps.7726] [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: 03/31/2023] [Revised: 06/14/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
Fungicides are indispensable for high-quality crops, but the rapid emergence and evolution of fungicide resistance have become the most important issues in modern agriculture. Hence, the sustainability and profitability of agricultural production have been challenged due to the limited number of fungicide chemical classes. Resistance to site-specific fungicides has principally been linked to target and non-target site mechanisms. These mechanisms change the structure or expression level, affecting fungicide efficacy and resulting in different and varying resistance levels. This review provides background information about fungicide resistance mechanisms and their implications for developing anti-resistance strategies in plant pathogens. Here, our purpose was to review changes at the target and non-target sites of quinone outside inhibitor (QoI) fungicides, methyl-benzimidazole carbamate (MBC) fungicides, demethylation inhibitor (DMI) fungicides, and succinate dehydrogenase inhibitor (SDHI) fungicides and to evaluate if they may also be associated with a fitness cost on crop pathogen populations. The current knowledge suggests that understanding fungicide resistance mechanisms can facilitate resistance monitoring and assist in developing anti-resistance strategies and new fungicide molecules to help solve this issue. © 2023 Society of Chemical Industry.
Collapse
Affiliation(s)
| | | | | | | | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, Lavras, Brazil
| |
Collapse
|
14
|
Mansfeld BN, Yocca A, Ou S, Harkess A, Burchard E, Gutierrez B, van Nocker S, Gottschalk C. A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:989-1002. [PMID: 37639371 DOI: 10.1111/tpj.16433] [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: 03/22/2023] [Revised: 07/08/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
SUMMARYThe Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus × domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for the development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca have been hampered by the lack of genomic resources. Here, we present a high‐quality, haplotype‐resolved, chromosome‐scale genome assembly and annotation for M. fusca. The genome was assembled using high‐fidelity long‐reads and scaffolded using genetic maps and high‐throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co‐linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference‐quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA‐informed introgression breeding.
Collapse
Affiliation(s)
- Ben N Mansfeld
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Shujun Ou
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Erik Burchard
- USDA ARS, Appalachian Fruit Research Station, Kearneysville, West Virginia, USA
| | | | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, Michigan, USA
| | | |
Collapse
|
15
|
Röhrs I, Linde M, Przetakiewicz J, Zelya A, Zelya G, Pucher A, Tlapák H, Debener T. Potato Wart Isolates from Europe and North America Form Distinct Clusters of Genetic Variation. Life (Basel) 2023; 13:1883. [PMID: 37763287 PMCID: PMC10532758 DOI: 10.3390/life13091883] [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: 08/01/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
We have extended previously published sets of simple sequence repeat markers for Synchytrium endobioticum, selected to be polymorphic for the German-standard isolates of pathotypes P1, P2, P6, P8, and P18. These markers also complement the extensive published information on DNA polymorphisms for the mitogenomes of Synchytrium endobioticum. This extended set of 35 markers representing 73 alleles differentiated 51 isolates from Europe and North America into three large, well-separated clusters and subclusters using dendrogram analysis, principal coordinates analysis (PCoA), and population substructure analysis using STRUCTURE 2.3.4 software. This suggests a limited number of introgressions of the wart disease pathogen into current potato growing areas, followed by recombination and admixture of populations through human activities. The new markers extend the published marker sets and are useful tools for future analyses of population structure and dynamics in Synchytrium endobioticum, which are necessary to understand the biology of the interaction between the pathogen and its potato host and to develop future control strategies.
Collapse
Affiliation(s)
- Ina Röhrs
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
| | - Marcus Linde
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
| | - Jaroslaw Przetakiewicz
- Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland;
| | - Avrelia Zelya
- National Academy of Agrarian Sciences, Institute of Plant Protection, Ukrainian Scientific-Research Plant Quarantine Station, 60321 Boyany, Chernivtskiy Region, Ukraine
| | - George Zelya
- National Academy of Agrarian Sciences, Institute of Plant Protection, Ukrainian Scientific-Research Plant Quarantine Station, 60321 Boyany, Chernivtskiy Region, Ukraine
| | - Anna Pucher
- Institute for Plant Protection in Crops and Grassland, Julius Kühn-Institute, 14532 Kleinmachnow, Germany;
| | - Hana Tlapák
- Robert Koch-Institute, 13353 Berlin, Germany;
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz University Hannover, 30419 Hanover, Germany; (I.R.); (M.L.)
| |
Collapse
|
16
|
Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
Collapse
Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
| |
Collapse
|
17
|
Ouaja M, Bahri BA, Ferjaoui S, Medini M, Sripada UM, Hamza S. Unlocking the story of resistance to Zymoseptoria tritici in Tunisian old durum wheat germplasm based on population structure analysis. BMC Genomics 2023; 24:328. [PMID: 37322410 DOI: 10.1186/s12864-023-09395-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/20/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Septoria tritici blotch (STB) remains a significant obstacle to durum wheat cultivation on a global scale. This disease remains a challenge for farmers, researchers, and breeders, who are collectively dedicated to reduce its damage and improve wheat resistance. Tunisian durum wheat landraces have been recognized as valuable genetic ressources that exhibit resistance to biotic and abiotic stresses and therefore play a crucial role in breeding program aimed at creating new wheat varieties resistant to fungal diseases as STB, as well as adapted to climate change constraints. RESULTS A total of 366 local durum wheat accessions were assessed for resistance to two virulent Tunisian isolates of Zymoseptoria tritici Tun06 and TM220 under field conditions. Population structure analysis of the durum wheat accessions, performed with 286 polymorphic SNPs (PIC > 0.3) covering the entire genome, identified three genetic subpopulations (GS1, GS2 and GS3) with 22% of admixed genotypes. Interestingly, all of the resistant genotypes were among GS2 or admixed with GS2. CONCLUSIONS This study revealed the population structure and the genetic distribution of the resistance to Z. tritici in the Tunisian durum wheat landraces. Accessions grouping pattern reflected the geographical origins of the landraces. We suggested that GS2 accessions were mostly derived from eastern Mediterranean populations, unlike GS1 and GS3 that originated from the west. Resistant GS2 accessions belonged to landraces Taganrog, Sbei glabre, Richi, Mekki, Badri, Jneh Khotifa and Azizi. Furthermore, we suggested that admixture contributed to transmit STB resistance from GS2 resistant landraces to initially susceptible landraces such as Mahmoudi (GS1), but also resulted in the loss of resistance in the case of GS2 susceptible Azizi and Jneh Khotifa accessions.
Collapse
Affiliation(s)
- Maroua Ouaja
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
| | - Bochra A Bahri
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin, GA, 30223, USA
| | - Sahbi Ferjaoui
- Field Crops Laboratory, Regional Field Crops Research Center of Beja (CRRGC), P.O. Box 350, Beja, 9000, Tunisia
| | - Maher Medini
- Banque Nationale des Gènes (BNG), Boulevard du Leader Yasser Arafat Z. I Charguia 1, Tunis, 1080, Tunisie
| | - Udupa M Sripada
- International Center for Agricultural Research in the Dry Areas (ICARDA), Avenue Hafiane Cherkaoui, Rabat, Marocco
| | - Sonia Hamza
- Department of agronomy and plant biotechnology, Laboratory of genetics and cereal breeding (LR14AGR01), The National Agronomic Institute of Tunisia (INAT), University of Carthage, 43 Avenue Charles-Nicolle, Tunis, 1082, Tunisia.
| |
Collapse
|
18
|
Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
Collapse
Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
| |
Collapse
|
19
|
Gilabert A, Rieux A, Robert S, Vitalis R, Zapater M, Abadie C, Carlier J, Ravigné V. Revisiting the historical scenario of a disease dissemination using genetic data and Approximate Bayesian Computation methodology: The case of Pseudocercospora fijiensis invasion in Africa. Ecol Evol 2023; 13:e10013. [PMID: 37091563 PMCID: PMC10116021 DOI: 10.1002/ece3.10013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/17/2023] [Accepted: 03/29/2023] [Indexed: 04/25/2023] Open
Abstract
The reconstruction of geographic and demographic scenarios of dissemination for invasive pathogens of crops is a key step toward improving the management of emerging infectious diseases. Nowadays, the reconstruction of biological invasions typically uses the information of both genetic and historical information to test for different hypotheses of colonization. The Approximate Bayesian Computation framework and its recent Random Forest development (ABC-RF) have been successfully used in evolutionary biology to decipher multiple histories of biological invasions. Yet, for some organisms, typically plant pathogens, historical data may not be reliable notably because of the difficulty to identify the organism and the delay between the introduction and the first mention. We investigated the history of the invasion of Africa by the fungal pathogen of banana Pseudocercospora fijiensis, by testing the historical hypothesis against other plausible hypotheses. We analyzed the genetic structure of eight populations from six eastern and western African countries, using 20 microsatellite markers and tested competing scenarios of population foundation using the ABC-RF methodology. We do find evidence for an invasion front consistent with the historical hypothesis, but also for the existence of another front never mentioned in historical records. We question the historical introduction point of the disease on the continent. Crucially, our results illustrate that even if ABC-RF inferences may sometimes fail to infer a single, well-supported scenario of invasion, they can be helpful in rejecting unlikely scenarios, which can prove much useful to shed light on disease dissemination routes.
Collapse
Affiliation(s)
- A. Gilabert
- Université de la Réunion, UMR PVBMTSaint‐PierreFrance
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
- Present address:
CIRAD, UMR AGAP InstitutMontpellierFrance
- Present address:
UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - A. Rieux
- CIRAD, UMR PVBMTSaint‐PierreFrance
| | - S. Robert
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - R. Vitalis
- CBGPUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - M.‐F. Zapater
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - C. Abadie
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - J. Carlier
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| | - V. Ravigné
- CIRAD, UMR PHIMMontpellierFrance
- PHIM Plant Health InstituteUniv Montpellier, CIRAD, INRAE, Institut Agro, IRDMontpellierFrance
| |
Collapse
|
20
|
The use of evolutionary analyses to predict functionally relevant traits in filamentous plant pathogens. Curr Opin Microbiol 2023; 73:102244. [PMID: 36889024 DOI: 10.1016/j.mib.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 03/08/2023]
Abstract
Identifying traits involved in plant-pathogen interactions is one of the major objectives in molecular plant pathology. Evolutionary analyses may assist in the identification of genes encoding traits that are involved in virulence and local adaptation, including adaptation to agricultural intervention strategies. In the past decades, the number of available genome sequences of fungal plant pathogens has rapidly increased, providing a rich source for the discovery of functionally important genes as well as inference of species histories. Positive selection in the form of diversifying or directional selection leaves particular signatures in genome alignments and can be identified with statistical genetics methods. This review summarises the concepts and approaches used in evolutionary genomics and lists major discoveries related to plant-pathogen adaptative evolution. We underline the significant contribution of evolutionary genomics in discovering virulence-related traits and the study of plant-pathogen ecology and adaptive evolution.
Collapse
|
21
|
Ababa G, Kesho A, Tadesse Y, Amare D. Reviews of taxonomy, epidemiology, and management practices of the barley scald ( Rhynchosporium graminicola) disease. Heliyon 2023; 9:e14315. [PMID: 36938428 PMCID: PMC10018571 DOI: 10.1016/j.heliyon.2023.e14315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023] Open
Abstract
Barley scald is very important in temperate and wet regions worldwide and has become one of the most important foliar diseases. Before the development of recent technologies, several scientists had argued that Rhynchosporium secalis is the causal agent of scald disease. However, the causal agent of this disease was revised and recognized as Rhynchosporium commune. Again recently, Rhynchosporium graminicola was suggested to be replaced as the causal agent of R. commune. The disease outbreak is depending on cool and frequent rainfall. Because of scald disease significance, numerous management practices have been advocated. Then, resistance materials, and mixing of resistant and susceptible cultivars have been used as the best management methods. Several studies have demonstrated that some cultivars and landraces of barley are resistant to scald disease during the seedling and adult growth stages. The first cultivar is "Atlas 46″ which was created from the cultivar "Turk". From biological method: Bacillus polymyxa, Paenibacillus polymyxa KaI245, and Bacillus subtilis are very effective in treating this disease. Finally, as a last option, different fungicides have been suggested. Pathogenicity testing, seed treatments, tillage, cultivar mixtures, and biological control are all commonly overlooked in developing countries. Cultural practices such as times of fungicide application, appropriate time of sowing to scape disease, and tillage practices which are adopted for other diseases are greatly missed for scald disease. Then, we are intended to assess the various findings available on barley scald biology, taxonomy, and management.
Collapse
|
22
|
Santiago MFM, King KC, Drew GC. Interactions between insect vectors and plant pathogens span the parasitism-mutualism continuum. Biol Lett 2023; 19:20220453. [PMID: 36883313 PMCID: PMC9993222 DOI: 10.1098/rsbl.2022.0453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Agricultural crops infected with vector-borne pathogens can suffer severe negative consequences, but the extent to which phytopathogens affect the fitness of their vector hosts remains unclear. Evolutionary theory predicts that selection on vector-borne pathogens will favour low virulence or mutualistic phenotypes in the vector, traits facilitating effective transmission between plant hosts. Here, we use a multivariate meta-analytic approach on 115 effect sizes across 34 unique plant-vector-pathogen systems to quantify the overall effect of phytopathogens on vector host fitness. In support of theoretical models, we report that phytopathogens overall have a neutral fitness effect on vector hosts. However, the range of fitness outcomes is diverse and span the parasitism-mutualism continuum. We found no evidence that various transmission strategies, or direct effects and indirect (plant-mediated) effects, of phytopathogens have divergent fitness outcomes for the vector. Our finding emphasizes diversity in tripartite interactions and the necessity for pathosystem-specific approaches to vector control.
Collapse
Affiliation(s)
| | - Kayla C King
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| | - Georgia C Drew
- Department of Biology, University of Oxford, Oxford OX1 2JD, UK
| |
Collapse
|
23
|
Rogério F, Baroncelli R, Cuevas-Fernández FB, Becerra S, Crouch J, Bettiol W, Azcárate-Peril MA, Malapi-Wight M, Ortega V, Betran J, Tenuta A, Dambolena JS, Esker PD, Revilla P, Jackson-Ziems TA, Hiltbrunner J, Munkvold G, Buhiniček I, Vicente-Villardón JL, Sukno SA, Thon MR. Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose. mBio 2023; 14:e0287822. [PMID: 36533926 PMCID: PMC9973043 DOI: 10.1128/mbio.02878-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022] Open
Abstract
Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.
Collapse
Affiliation(s)
- Flávia Rogério
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Riccardo Baroncelli
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Francisco Borja Cuevas-Fernández
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Sioly Becerra
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - JoAnne Crouch
- Foreign Disease and Weed Science Unit, United States Department of Agriculture, Fort Detrick, Maryland, USA
| | | | - M. Andrea Azcárate-Peril
- Center for Gastrointestinal Biology and Disease, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
- UNC Microbiome Core, Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Martha Malapi-Wight
- USDA Animal and Plant Health Inspection Services, Biotechnology Regulatory Services, Riverdale, Maryland, USA
| | | | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food, and Rural Affairs, University of Guelph-Ridgetown, Ridgetown, Ontario, Canada
| | - José S. Dambolena
- Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, IMBIV-CONICET-ICTA, Córdoba, Argentina
| | - Paul D. Esker
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, Pennsylvania, USA
| | - Pedro Revilla
- Misión Biológica de Galicia, Spanish National Research Council (CSIC), Pontevedra, Spain
| | | | | | - Gary Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ivica Buhiniček
- BC Institute for Breeding and Production of Field Crops, Dugo Selo, Croatia
| | | | - Serenella A. Sukno
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Michael R. Thon
- Instituto de Investigación en Agrobiotecnología (CIALE), Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| |
Collapse
|
24
|
Feurtey A, Lorrain C, McDonald MC, Milgate A, Solomon PS, Warren R, Puccetti G, Scalliet G, Torriani SFF, Gout L, Marcel TC, Suffert F, Alassimone J, Lipzen A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Goodwin SB, Genissel A, Seidl MF, Stukenbrock EH, Lebrun MH, Kema GHJ, McDonald BA, Croll D. A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nat Commun 2023; 14:1059. [PMID: 36828814 PMCID: PMC9958100 DOI: 10.1038/s41467-023-36674-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.
Collapse
Affiliation(s)
- Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cécile Lorrain
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Megan C McDonald
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rachael Warren
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332, Stein, Switzerland
| | | | | | - Lilian Gout
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Thierry C Marcel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Frédéric Suffert
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 9472, USA
| | | | - Anne Genissel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Michael F Seidl
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
- Utrecht University, Theoretical Biology and Bioinformatics, Utrecht, The Netherlands
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Gert H J Kema
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Bruce A McDonald
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
| |
Collapse
|
25
|
Ballu A, Despréaux P, Duplaix C, Dérédec A, Carpentier F, Walker AS. Antifungal alternation can be beneficial for durability but at the cost of generalist resistance. Commun Biol 2023; 6:180. [PMID: 36797413 PMCID: PMC9935548 DOI: 10.1038/s42003-023-04550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/03/2023] [Indexed: 02/18/2023] Open
Abstract
The evolution of resistance to pesticides is a major burden in agriculture. Resistance management involves maximizing selection pressure heterogeneity, particularly by combining active ingredients with different modes of action. We tested the hypothesis that alternation may delay the build-up of resistance not only by spreading selection pressure over longer periods, but also by decreasing the rate of evolution of resistance to alternated fungicides, by applying an experimental evolution approach to the economically important crop pathogen Zymoseptoria tritici. Our results show that alternation is either neutral or slows the overall resistance evolution rate, relative to continuous fungicide use, but results in higher levels of generalism in evolved lines. We demonstrate that the nature of the fungicides, and therefore their relative intrinsic risk of resistance may underly this trade-off, more so than the number of fungicides and the rhythm of alternation. This trade-off is also dynamic over the course of resistance evolution. These findings open up new possibilities for tailoring resistance management effectively while optimizing interplay between alternation components.
Collapse
Affiliation(s)
- Agathe Ballu
- grid.507621.7Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Philomène Despréaux
- grid.507621.7Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Clémentine Duplaix
- grid.507621.7Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Anne Dérédec
- grid.507621.7Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Florence Carpentier
- grid.507621.7Université Paris-Saclay, INRAE, UR MaIAGE, 78350 Jouy-en-Josas, France ,grid.417885.70000 0001 2185 8223AgroParisTech, 91120 Palaiseau, France
| | | |
Collapse
|
26
|
Hulbert JM, Hallett RA, Roy HE, Cleary M. Citizen science can enhance strategies to detect and manage invasive forest pests and pathogens. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1113978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
Incorporating a citizen science approach into biological invasion management strategies can enhance biosecurity. Many citizen science projects exist to strengthen the management of forest pest and pathogen invasions within both pre- and post-border scenarios. Besides the value of citizen science initiatives for early detection and monitoring, they also contribute widely to raising awareness, informing decisions about eradication and containment efforts to minimize pest and pathogen spread, and even finding resistant plant material for restoration of landscapes degraded by disease. Overall, many projects actively engage citizens in the different stages of forest pest and pathogen invasions, but it is unclear how they work together across all stages of the entire biological invasion process to enhance biosecurity. Here we provide examples of citizen science projects for each stage of the biological invasion process, discuss options for developing a citizen science program to enhance biosecurity, and suggest approaches for integrating citizen science into biosecurity measures to help safeguard forest resources in the future.
Collapse
|
27
|
Resistance of Black Aspergilli Species from Grape Vineyards to SDHI, QoI, DMI, and Phenylpyrrole Fungicides. J Fungi (Basel) 2023; 9:jof9020221. [PMID: 36836335 PMCID: PMC9961879 DOI: 10.3390/jof9020221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Fungicide applications constitute a management practice that reduces the size of fungal populations and by acting as a genetic drift factor, may affect pathogen evolution. In a previous study, we showed that the farming system influenced the population structure of the Aspergillus section Nigri species in Greek vineyards. The current study aimed to test the hypothesis that the differences in the population structure may be associated with the selection of fungicide-resistant strains within the black aspergilli populations. To achieve this, we determined the sensitivity of 102, 151, 19, and 22 for the A. uvarum, A. tubingensis, A. niger, and A. carbonarious isolates, respectively, originating either from conventionally-treated or organic vineyards to the fungicides fluxapyroxad-SDHIs, pyraclostrobin-QoIs, tebuconazole-DMIs, and fludioxonil-phenylpyrroles. The results showed widespread resistance to all four fungicides tested in the A. uvarum isolates originating mostly from conventional vineyards. In contrast, all the A. tubingensis isolates tested were sensitive to pyraclostrobin, while moderate frequencies of only lowly resistant isolates were identified for tebuconazole, fludioxonil, and fluxapyroxad. Sequencing analysis of the corresponding fungicide target encoding genes revealed the presence of H270Y, H65Q/S66P, and G143A mutations in the sdhB, sdhD, and cytb genes of A. uvarum resistant isolates, respectively. No mutations in the Cyp51A and Cyp51B genes were detected in either the A. uvarum or A. tubingensis isolates exhibiting high or low resistance levels to DMIs, suggesting that other resistance mechanisms are responsible for the observed phenotype. Our results support the initial hypothesis for the contribution of fungicide resistance in the black aspergilli population structure in conventional and organic vineyards, while this is the first report of A. uvarum resistance to SDHIs and the first documentation of H270Y or H65Q/S66P mutations in sdhB, sdhD, and of the G143A mutation in the cytb gene of this fungal species.
Collapse
|
28
|
Drug repurposing strategy II: from approved drugs to agri-fungicide leads. J Antibiot (Tokyo) 2023; 76:131-182. [PMID: 36707717 PMCID: PMC9880955 DOI: 10.1038/s41429-023-00594-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023]
Abstract
Epidemic diseases of crops caused by fungi deeply affected the course of human history and processed a major restriction on social and economic development. However, with the enormous misuse of existing antimicrobial drugs, an increasing number of fungi have developed serious resistance to them, making the diseases caused by pathogenic fungi even more challenging to control. Drug repurposing is an attractive alternative, it requires less time and investment in the drug development process than traditional R&D strategies. In this work, we screened 600 existing commercially available drugs, some of which had previously unknown activity against pathogenic fungi. From the primary screen at a fixed concentration of 100 μg/mL, 120, 162, 167, 85, 102, and 82 drugs were found to be effective against Rhizoctonia solani, Sclerotinia sclerotiorum, Botrytis cinerea, Phytophthora capsici, Fusarium graminearum and Fusarium oxysporum, respectively. They were divided into nine groups lead compounds, including quinoline alkaloids, benzimidazoles/carbamate esters, azoles, isothiazoles, pyrimidines, pyridines, piperidines/piperazines, ionic liquids and miscellaneous group, and simple structure-activity relationship analysis was carried out. Comparison with fungicides to identify the most promising drugs or lead structures for the development of new antifungal agents in agriculture.
Collapse
|
29
|
Lassagne A, Brun S, Malagnac F, Adreit H, Milazzo J, Fournier E, Tharreau D. Male fertility in Pyricularia oryzae: Microconidia are spermatia. Environ Microbiol 2022; 24:6365-6375. [PMID: 36165613 PMCID: PMC10092719 DOI: 10.1111/1462-2920.16226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/25/2022] [Indexed: 01/12/2023]
Abstract
Sexual reproduction in Ascomycetes is well described in several model organisms such as Neurospora crassa or Podospora anserina. Deciphering the biological process of sexual reproduction (from the recognition between compatible partners to the formation of zygote) can be a major advantage to better control sexually reproducing pathogenic fungi. In Pyricularia oryzae, the fungal pathogen causing blast diseases on several Poaceae species, the biology of sexual reproduction remains poorly documented. Besides the well-documented production of asexual macroconidia, the production of microconidia was seldom reported in P. oryzae, and their role as male gamete (i.e., spermatia) and in male fertility has never been explored. Here, we characterised the morphological features of microconidia and demonstrated that they are bona fide spermatia. Contrary to macroconidia, microconidia are not able to germinate and seem to be the only male gametes in P. oryzae. We show that fruiting body (perithecium) formation requires microconidia to get in contact with mycelium of strains of opposite mating type, to presumably fertilise the female gametes.
Collapse
Affiliation(s)
- Alexandre Lassagne
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France.,Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sylvain Brun
- Institut Jacques Monod, Université Paris Cité, CNRS, Paris, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Henri Adreit
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Joëlle Milazzo
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Elisabeth Fournier
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| |
Collapse
|
30
|
Viral cross-class transmission results in disease of a phytopathogenic fungus. THE ISME JOURNAL 2022; 16:2763-2774. [PMID: 36045287 PMCID: PMC9428384 DOI: 10.1038/s41396-022-01310-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 12/15/2022]
Abstract
Interspecies transmission of viruses is a well-known phenomenon in animals and plants whether via contacts or vectors. In fungi, interspecies transmission between distantly related fungi is often suspected but rarely experimentally documented and may have practical implications. A newly described double-strand RNA (dsRNA) virus found asymptomatic in the phytopathogenic fungus Leptosphaeria biglobosa of cruciferous crops was successfully transmitted to an evolutionarily distant, broad-host range pathogen Botrytis cinerea. Leptosphaeria biglobosa botybirnavirus 1 (LbBV1) was characterized in L. biglobosa strain GZJS-19. Its infection in L. biglobosa was asymptomatic, as no significant differences in radial mycelial growth and pathogenicity were observed between LbBV1-infected and LbBV1-free strains. However, cross-species transmission of LbBV1 from L. biglobosa to infection in B. cinerea resulted in the hypovirulence of the recipient B. cinerea strain t-459-V. The cross-species transmission was succeeded only by inoculation of mixed spores of L. biglobosa and B. cinerea on PDA or on stems of oilseed rape with the efficiency of 4.6% and 18.8%, respectively. To investigate viral cross-species transmission between L. biglobosa and B. cinerea in nature, RNA sequencing was carried out on L. biglobosa and B. cinerea isolates obtained from Brassica samples co-infected by these two pathogens and showed that at least two mycoviruses were detected in both fungal groups. These results indicate that cross-species transmission of mycoviruses may occur frequently in nature and result in the phenotypical changes of newly invaded phytopathogenic fungi. This study also provides new insights for using asymptomatic mycoviruses as biocontrol agent.
Collapse
|
31
|
Leuchtmann A, Schardl CL. Genetic Diversity of Epichloë Endophytes Associated with Brachypodium and Calamagrostis Host Grass Genera including Two New Species. J Fungi (Basel) 2022; 8:jof8101086. [PMID: 36294651 PMCID: PMC9605649 DOI: 10.3390/jof8101086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
Fungi of genus Epichloë (Ascomycota, Clavicipitaceae) are common endophytic symbionts of Poaceae, including wild and agronomically important cool-season grass species (subfam. Poöideae). Here, we examined the genetic diversity of Epichloë from three European species of Brachypodium (B. sylvaticum, B. pinnatum and B. phoenicoides) and three species of Calamagrostis (C. arundinacea, C. purpurea and C. villosa), using DNA sequences of tubB and tefA genes. In addition, microsatellite markers were obtained from a larger set of isolates from B. sylvaticum sampled across Europe. Based on phylogenetic analyses the isolates from Brachypodium hosts were placed in three different subclades within the Epichloë typhina complex (ETC) but did not strictly group according to host grass species, suggesting that the host does not always select for particular endophyte genotypes. Analysis of microsatellite markers confirmed the presence of genetically distinct lineages of Epichloësylvatica on B. sylvaticum, which appeared to be tied to different modes of reproduction (sexual or asexual). Among isolates from Calamagrostis hosts, two subclades were detected which were placed outside ETC. These endophyte lineages are recognized as distinct species for which we propose the names E. calamagrostidis Leuchtm. & Schardl, sp. nov. and E. ftanensis Leuchtm. & A.D. Treindl, sp. nov. This study extends knowledge of the phylogeny and evolutionary diversification of Epichloë endophytes that are symbionts of wild Brachypodium and Calamagrostis host grasses.
Collapse
Affiliation(s)
- Adrian Leuchtmann
- Institute of Integrative Biology, ETH Zürich, CH-8092 Zürich, Switzerland
- Correspondence:
| | | |
Collapse
|
32
|
McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
Collapse
Affiliation(s)
| | | | | | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | | |
Collapse
|
33
|
Jenner BN, Henry PM. Pathotypes of Fusarium oxysporum f. sp. fragariae express discrete repertoires of accessory genes and induce distinct host transcriptional responses during root infection. Environ Microbiol 2022; 24:4570-4586. [PMID: 35706142 PMCID: PMC9796522 DOI: 10.1111/1462-2920.16101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/16/2022] [Accepted: 06/11/2022] [Indexed: 01/01/2023]
Abstract
Convergent evolution of phytopathogenicity is poorly described, especially among multiple strains of a single microbial species. We investigated this phenomenon with genetically diverse isolates of Fusarium oxysporum f. sp. fragariae (Fof) that cause one of two syndromes: chlorosis and wilting (the 'yellows-fragariae' pathotype), or only wilting (the 'wilt-fragariae' pathotype). We challenged strawberry (Fragaria × ananassa) plants to root infection by five fungal isolates: three yellows-fragariae, one wilt-fragariae and one that is not pathogenic to strawberry. All Fof isolates had chromosome-level assemblies; three were newly generated. The two pathotypes triggered distinct host responses, especially among phytohormone-associated genes; yellows-fragariae isolates strongly induced jasmonic acid-associated genes, whereas the wilt-fragariae isolate primarily induced ethylene biosynthesis and signalling. The differentially expressed genes on fungal accessory chromosomes were almost entirely distinct between pathotypes. We identified an ~150 kbp 'pathogenicity island' that was horizontally transferred between wilt-fragariae strains. This predicted pathogenicity island was enriched with differentially expressed genes whose predicted functions were related to plant infection, and only one of these genes was also upregulated in planta by yellows-fragariae isolates. These results support the conclusion that wilt- and yellows-fragariae cause physiologically distinct syndromes by the expression of discrete repertoires of genes on accessory chromosomes.
Collapse
Affiliation(s)
- Bradley N. Jenner
- Department of Plant PathologyUniversity of California at DavisDavisCaliforniaUSA
| | - Peter M. Henry
- United States Department of Agriculture, Agricultural Research ServiceSalinasCaliforniaUSA
| |
Collapse
|
34
|
Makris G, Nikoloudakis N, Samaras A, Karaoglanidis GS, Kanetis LI. Under Pressure: A Comparative Study of Botrytis cinerea Populations from Conventional and Organic Farms in Cyprus and Greece. PHYTOPATHOLOGY 2022; 112:2236-2247. [PMID: 35671479 DOI: 10.1094/phyto-12-21-0510-r] [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: 06/15/2023]
Abstract
The highly heterogeneous nature of Botrytis cinerea provides adaptive benefits to variable environmental regimes. Disentangling pathogen population structure in anthropogenic agroecosystems is crucial to designing more effective management schemes. Herein, we studied how evolutionary forces exerted in different farming systems, in terms of agrochemicals-input, shape B. cinerea populations. In total, 360 B. cinerea isolates were collected from conventional and organic, strawberry and tomato farms in Cyprus and Greece. The occurrence and frequency of sensitivities to seven botryticides were estimated. Results highlighted widespread fungicide resistance in conventional farms since only 15.5% of the isolates were sensitive. A considerable frequency of fungicide-resistant isolates was also detected in the organic farms (14.9%). High resistance frequencies were observed for boscalid (67.7%), pyraclostrobin (67.3%), cyprodinil (65.9%), and thiophanate-methyl (61.4%) in conventional farms, while high levels of multiple fungicide resistance were also evident. Furthermore, B. cinerea isolates were genotyped using a set of seven microsatellite markers (simple sequence repeat [SSR] markers). Index of association analyses (Ia and rBarD) suggest asexual reproduction of the populations, even though the mating-type idiomorphs were equally distributed, indicating frequency-dependent selection. Fungicide resistance was correlated with farming systems across countries and crops, while SSRs were able to detect population structure associated with resistance to thiophanate-methyl, pyraclostrobin, boscalid, and cyprodinil. The expected heterozygosity in organic farms was significantly higher than in conventional, suggesting the absence of selective pressure that may change the allelic abundance in organic farms. However, genetic variance among strawberry and tomato populations was high, ranking host specificity higher than other selection forces studied.
Collapse
Affiliation(s)
- Georgios Makris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Nikolaos Nikoloudakis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Anastasios Samaras
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Georgios S Karaoglanidis
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Loukas I Kanetis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| |
Collapse
|
35
|
Rodrigues ASB, Silva DN, Várzea V, Paulo OS, Batista D. Worldwide Population Structure of the Coffee Rust Fungus Hemileia vastatrix Is Strongly Shaped by Local Adaptation and Breeding History. PHYTOPATHOLOGY 2022; 112:1998-2011. [PMID: 35322716 DOI: 10.1094/phyto-09-21-0376-r] [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: 06/14/2023]
Abstract
The devastating disease coffee leaf rust, caused by Hemileia vastatrix, has been a major constraint to worldwide coffee production. Recently, H. vastatrix populations were shown to be structured into three divergent genetic lineages with marked host specialization (C1, C2, and C3). However, there is yet no overall understanding of the population dynamics and adaptation of the most widespread and epidemiological relevant H. vastatrix group (C3). We used restriction site-associated DNA sequencing to generate 13,804 single nucleotide polymorphisms (SNPs) across a worldwide collection of 99 H. vastatrix isolates. Phylogenetic analyses uncovered a well-supported structuring within C3, with three main subgroups (SGs; SGI, SGII, and SGIII), which seem to reflect the historical distribution, breeding, and exchange of coffee cultivars. SGI shows a ladder-like diversification pattern and occurs across all four continents sampled, SGII is mainly restricted to Africa, and SGIII is observed only in Timor, revealing a higher genetic differentiation. Outlier and association tests globally identified 112 SNPs under putative positive selection, which impacted population structure. In particular, 29 overlapping SNPs per se seemed to have an extremely strong effect on H. vastatrix population divergence. We also found exclusive and fixed alleles associated with the SGs supporting local adaptation. Functional annotation revealed that transposable elements may play a role in host adaptation. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix on cultivated coffee, showing its strong ability to adapt and the strength of the selective force imposed by coffee hosts, which should be taken into account when designing strategies for pathogen dissemination control and selective breeding.
Collapse
Affiliation(s)
- Ana Sofia B Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Diogo Nuno Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Vitor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Octávio S Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Dora Batista
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG2), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC)/Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| |
Collapse
|
36
|
Malmstrom CM, Martin MD, Gagnevin L. Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:187-209. [PMID: 35483672 DOI: 10.1146/annurev-phyto-021021-041830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.
Collapse
Affiliation(s)
- Carolyn M Malmstrom
- Department of Plant Biology and Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, Michigan, USA
| | - Michael D Martin
- Department of Natural History, University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Lionel Gagnevin
- Plant Health Institute of Montpellier, CIRAD, Montpellier, France;
| |
Collapse
|
37
|
Saubin M, Louet C, Bousset L, Fabre F, Frey P, Fudal I, Grognard F, Hamelin F, Mailleret L, Stoeckel S, Touzeau S, Petre B, Halkett F. Improving sustainable crop protection using population genetics concepts. Mol Ecol 2022; 32:2461-2471. [PMID: 35906846 DOI: 10.1111/mec.16634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 10/16/2022]
Abstract
Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of pesticides. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) 'plant breeding' (generating new genetic material), (ii) 'molecular interactions' (exploring the molecular dialogue governing plant-pathogen interactions) and (iii) 'epidemiology and evolution' (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, in particular via evolutionary-epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practices for developing and managing genetically resistant cultivars.
Collapse
Affiliation(s)
| | - Clémentine Louet
- Université de Lorraine, INRAE, IAM, Nancy, France.,Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Lydia Bousset
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, F-33882 Villenave d'Ornon, France
| | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Isabelle Fudal
- Université Paris Saclay, INRAE, BIOGER, Thiverval-Grignon, France
| | - Frédéric Grognard
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
| | - Frédéric Hamelin
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Ludovic Mailleret
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France.,Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Solenn Stoeckel
- INRAE, Agrocampus Ouest, Université de Rennes, IGEPP, Le Rheu, France
| | - Suzanne Touzeau
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore team, Sophia Antipolis, France
| | | | | |
Collapse
|
38
|
Sotiropoulos AG, Arango-Isaza E, Ban T, Barbieri C, Bourras S, Cowger C, Czembor PC, Ben-David R, Dinoor A, Ellwood SR, Graf J, Hatta K, Helguera M, Sánchez-Martín J, McDonald BA, Morgounov AI, Müller MC, Shamanin V, Shimizu KK, Yoshihira T, Zbinden H, Keller B, Wicker T. Global genomic analyses of wheat powdery mildew reveal association of pathogen spread with historical human migration and trade. Nat Commun 2022; 13:4315. [PMID: 35882860 PMCID: PMC9315327 DOI: 10.1038/s41467-022-31975-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 07/13/2022] [Indexed: 12/25/2022] Open
Abstract
The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, we study its spread and evolution by analyzing a global sample of 172 mildew genomes. Our analyses show that B.g. tritici emerged in the Fertile Crescent during wheat domestication. After it spread throughout Eurasia, colonization brought it to America, where it hybridized with unknown grass mildew species. Recent trade brought USA strains to Japan, and European strains to China. In both places, they hybridized with local ancestral strains. Thus, although mildew spreads by wind regionally, our results indicate that humans drove its global spread throughout history and that mildew rapidly evolved through hybridization. The fungus Blumeria graminis f. sp. tritici causes wheat powdery mildew disease. Here, Sotiropoulos et al. analyze a global sample of 172 mildew genomes, providing evidence that humans drove global spread of the pathogen throughout history and that mildew rapidly evolved through hybridization with local fungal strains.
Collapse
Affiliation(s)
| | - Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Tomohiro Ban
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christina Cowger
- USDA-ARS Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Paweł C Czembor
- Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Roi Ben-David
- Department of Vegetables and Field crops, Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZion, 7528809, Israel
| | - Amos Dinoor
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Simon R Ellwood
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Johannes Graf
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Koichi Hatta
- Hokkaido Agricultural Research Center Field Crop Research and Development, National Agricultural Research Organization, Sapporo, Hokkaido, Japan
| | - Marcelo Helguera
- Centro de Investigaciones Agropecuarias (CIAP), INTA, Córdoba, Argentina
| | - Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Alexey I Morgounov
- Food and Agriculture Organization of the United Nations, Riyadh, Saudi Arabia
| | - Marion C Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
| | - Taiki Yoshihira
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Helen Zbinden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
39
|
Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
Collapse
Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
| |
Collapse
|
40
|
Chaisiri C, Liu X, Lin Y, Luo C. Diaporthe citri: A Fungal Pathogen Causing Melanose Disease. PLANTS 2022; 11:plants11121600. [PMID: 35736750 PMCID: PMC9227384 DOI: 10.3390/plants11121600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 06/12/2022] [Indexed: 11/16/2022]
Abstract
Citrus melanose is a fungal disease caused by Diaporthe citri F.A. Wolf. It is found in various citrus-growing locations across the world. The host range of D. citri is limited to plants of the Citrus genus. The most economically important hosts are Citrus reticulata (mandarin), C. sinensis (sweet orange), C. grandis or C. maxima (pumelo), and C. paradisi (grapefruit). In the life cycle of D. citri throughout the citrus growing season, pycnidia can be seen in abundance on dead branches, especially after rain, with conidia appearing as slimy masses discharged from the dead twigs. Raindrops can transmit conidia to leaves, twigs, and fruits, resulting in disease dispersion throughout small distances. Persistent rains and warm climatic conditions generally favor disease onset and development. The melanose disease causes a decline in fruit quality, which lowers the value of fruits during marketing and exportation. High rainfall areas should avoid planting susceptible varieties. In this article, information about the disease symptoms, history, geographic distribution, epidemiology, impact, and integrated management practices, as well as the pathogen morphology and identification, was reviewed and discussed.
Collapse
Affiliation(s)
- Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Liu
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoxi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
| |
Collapse
|
41
|
The population genetics of the causative agent of snake fungal disease indicate recent introductions to the USA. PLoS Biol 2022; 20:e3001676. [PMID: 35737674 PMCID: PMC9223401 DOI: 10.1371/journal.pbio.3001676] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/13/2022] [Indexed: 11/19/2022] Open
Abstract
Snake fungal disease (SFD; ophidiomycosis), caused by the pathogen Ophidiomyces ophiodiicola (Oo), has been documented in wild snakes in North America and Eurasia, and is considered an emerging disease in the eastern United States of America. However, a lack of historical disease data has made it challenging to determine whether Oo is a recent arrival to the USA or whether SFD emergence is due to other factors. Here, we examined the genomes of 82 Oo strains to determine the pathogen’s history in the eastern USA. Oo strains from the USA formed a clade (Clade II) distinct from European strains (Clade I), and molecular dating indicated that these clades diverged too recently (approximately 2,000 years ago) for transcontinental dispersal of Oo to have occurred via natural snake movements across Beringia. A lack of nonrecombinant intermediates between clonal lineages in Clade II indicates that Oo has actually been introduced multiple times to North America from an unsampled source population, and molecular dating indicates that several of these introductions occurred within the last few hundred years. Molecular dating also indicated that the most common Clade II clonal lineages have expanded recently in the USA, with time of most recent common ancestor mean estimates ranging from 1985 to 2007 CE. The presence of Clade II in captive snakes worldwide demonstrates a potential mechanism of introduction and highlights that additional incursions are likely unless action is taken to reduce the risk of pathogen translocation and spillover into wild snake populations. Snake fungal disease is an emerging disease in eastern North America, but the origins of the disease have been unclear. This study uses population genetic data to show that the fungus that causes the disease was introduced multiple times to North America over the last few hundred years.
Collapse
|
42
|
Clin P, Grognard F, Andrivon D, Mailleret L, Hamelin FM. Host mixtures for plant disease control: benefits from pathogen selection and immune priming. Evol Appl 2022; 15:967-975. [PMID: 35782013 PMCID: PMC9234633 DOI: 10.1111/eva.13386] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 03/28/2022] [Accepted: 04/05/2022] [Indexed: 11/29/2022] Open
Abstract
Multiline and cultivar mixtures are highly effective methods for agroecological plant disease control. Priming‐induced cross protection, occurring when plants are challenged by avirulent pathogen genotypes and resulting in increased resistance to subsequent infection by virulent ones, is one critical key to their lasting performance against polymorphic pathogen populations. Strikingly, this mechanism was until recently absent from mathematical models aiming at designing optimal host mixtures. We developed an epidemiological model to explore the effect of host mixtures composed of variable numbers of single‐resistance cultivars on the equilibrium prevalence of the disease caused by pathogen populations polymorphic for virulence complexity. This model shows that a relatively large amount of resistance genes must be deployed to achieve low disease prevalence, as pathogen competition in mixtures tends to select for intermediate virulence complexity. By contrast, priming significantly reduces the number of plant genotypes needed to drop disease prevalence below an acceptable threshold. Given the limited availability of resistance genes in cultivars, this mechanism of plant immunity should be assessed when designing host mixtures.
Collapse
Affiliation(s)
- Pauline Clin
- Institut Agro Univ Rennes INRAE IGEPP 35000 Rennes France
- Université Côte d’Azur INRAE CNRS, ISA France
| | - Frédéric Grognard
- Université Côte d’Azur Inria, INRAE CNRS Sorbonne Université Biocore France
| | | | - Ludovic Mailleret
- Université Côte d’Azur INRAE CNRS, ISA France
- Université Côte d’Azur Inria, INRAE CNRS Sorbonne Université Biocore France
| | | |
Collapse
|
43
|
Modelling the emergence dynamics of the western corn rootworm beetle (Diabrotica virgifera virgifera). Sci Rep 2022; 12:2340. [PMID: 35149696 PMCID: PMC8837793 DOI: 10.1038/s41598-022-05032-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 11/18/2021] [Indexed: 11/08/2022] Open
Abstract
The western corn rootworm is an invasive species to Europe and is a major agricultural pest that causes widespread economic and yield losses to maize producers. The Gompertz curve was originally used to model human population mortality. It is a sigmoidal curve where the beginning and end of a period shows the slowest time for growth, and adequately describes observed dynamics of many phenomena. We propose the use of the Gompertz function in a Bayesian Hierarchical framework to model the emergence dynamics of the western corn rootworm beetle. The proposed model includes the use of climatic variables to assess how weather can influence the observed dynamics. We apply the model to Austrian monitoring data collected in 2004–2015.
Collapse
|
44
|
Anand G, Rajeshkumar KC. Challenges and Threats Posed by Plant Pathogenic Fungi on Agricultural Productivity and Economy. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
45
|
Mercier A, Simon A, Lapalu N, Giraud T, Bardin M, Walker AS, Viaud M, Gladieux P. Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal Pathogen Botrytis cinerea in France. PHYTOPATHOLOGY 2021; 111:2355-2366. [PMID: 33829853 DOI: 10.1094/phyto-07-20-0302-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help to prevent the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the gray mold pathogen Botrytis cinerea parasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host of origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization of B. cinerea populations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision of B. cinerea pathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and nonsynonymous sites, and analyses of presence and absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
Collapse
Affiliation(s)
- Alex Mercier
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
- Université Paris-Saclay, Orsay, France
| | - Adeline Simon
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Nicolas Lapalu
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Marc Bardin
- UR0407 Pathologie Végétale, INRAE, 84143 Montfavet, France
| | - Anne-Sophie Walker
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, Institut National de la Recherche Agronomique (INRAE), AgroParisTech, UMR BIOGER, 78850 Thiverval-Grignon, France
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| |
Collapse
|
46
|
Louet C, Saubin M, Andrieux A, Persoons A, Gorse M, Pétrowski J, Fabre B, De Mita S, Duplessis S, Frey P, Halkett F. A point mutation and large deletion at the candidate avirulence locus AvrMlp7 in the poplar rust fungus correlate with poplar RMlp7 resistance breakdown. Mol Ecol 2021; 32:2472-2483. [PMID: 34843142 DOI: 10.1111/mec.16294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 01/29/2023]
Abstract
The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R-mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici-populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici-populina that probably corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28-year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a nonsynonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre-existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7-mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Pascal Frey
- Université de Lorraine, INRAE, IAM, Nancy, France
| | | |
Collapse
|
47
|
Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
Collapse
Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | |
Collapse
|
48
|
Singh NK, Karisto P, Croll D. Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici. Microb Genom 2021; 7. [PMID: 34617882 PMCID: PMC8627204 DOI: 10.1099/mgen.0.000678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pathogens cause significant challenges to global food security. On annual crops, pathogens must re-infect from environmental sources in every growing season. Fungal pathogens have evolved mixed reproductive strategies to cope with the distinct challenges of colonizing growing plants. However, how pathogen diversity evolves during growing seasons remains largely unknown. Here, we performed a deep hierarchical sampling in a single experimental wheat field infected by the major fungal pathogen Zymoseptoria tritici. We analysed whole genome sequences of 177 isolates collected from 12 distinct cultivars replicated in space at three time points of the growing season to maximize capture of genetic diversity. The field population was highly diverse with 37 SNPs per kilobase, a linkage disequilibrium decay within 200-700 bp and a high effective population size. Using experimental infections, we tested a subset of the collected isolates on the dominant cultivar planted in the field. However, we found no significant difference in virulence of isolates collected from the same cultivar compared to isolates collected on other cultivars. About 20 % of the isolate genotypes were grouped into 15 clonal groups. Pairs of clones were disproportionally found at short distances (<5 m), consistent with experimental estimates for per-generation dispersal distances performed in the same field. This confirms predominant leaf-to-leaf transmission during the growing season. Surprisingly, levels of clonality did not increase over time in the field although reproduction is thought to be exclusively asexual during the growing season. Our study shows that the pathogen establishes vast and stable gene pools in single fields. Monitoring short-term evolutionary changes in crop pathogens will inform more durable strategies to contain diseases.
Collapse
Affiliation(s)
- Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Petteri Karisto
- Plant Health, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
- *Correspondence: Daniel Croll,
| |
Collapse
|
49
|
Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen Diaporthe citri in Southern China. J Fungi (Basel) 2021; 7:jof7090749. [PMID: 34575787 PMCID: PMC8468327 DOI: 10.3390/jof7090749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
The fungal pathogen Diaporthe citri is a major cause of diseases in citrus. One common disease is melanose, responsible for large economic losses to the citrus fruit industry. However, very little is known about the epidemiology and genetic structure of D. citri. In this study, we analyzed 339 isolates from leaves and fruits with melanose symptoms from five provinces in southern China at 14 polymorphic simple sequence repeat (SSR) loci and the mating type idiomorphs. The genetic variations were analyzed at three levels with separate samples: among provinces, among orchards within one county, and among trees within one orchard. The five provincial populations from Fujian, Zhejiang, Jiangxi, Hunan, and Guizhou were significantly differentiated, while limited differences were found among orchards from the same county or among trees from the same orchard. STRUCTURE analysis detected two genetic clusters in the total sample, with different provincial subpopulations showing different frequencies of isolates in these two clusters. Mantel analysis showed significant positive correlation between genetic and geographic distances, consistent with geographic separation as a significant barrier to gene flow in D. citri in China. High levels of genetic diversity were found within individual subpopulations at all three spatial scales of analyses. Interestingly, most subpopulations at all three spatial scales had the two mating types in similar frequencies and with alleles at the 14 SSR loci not significantly different from linkage equilibrium. Indeed, strains with different mating types and different multilocus genotypes were frequently isolated from the same leaves and fruits. The results indicate that sexual reproduction plays an important role in natural populations of D. citri in southern China and that its ascospores likely represent an important contributor to citrus disease.
Collapse
|
50
|
Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road. Proc Natl Acad Sci U S A 2021; 118:2021221118. [PMID: 33741737 PMCID: PMC8000540 DOI: 10.1073/pnas.2021221118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Our article presents the most comprehensive reconstruction of the evolutionary and phylogeographic history of a major plant pathogen of brassica vegetables in Eurasia. Sampling across such a large landmass poses considerable challenges, and our study attempts to describe the spatial and temporal patterns of migration for a plant pathogen on a large scale. Our phylogeographic and molecular clock analyses show that the migration pathways of turnip mosaic potyvirus retrace some of the historical trade arteries of the Silk Road. This study demonstrates how a comprehensive genetic analysis can provide a large-scale view of the epidemiology and human-mediated spread of a plant pathogen across centuries of evolutionary history. Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.
Collapse
|