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Popović M, Nuskern L, Peranić K, Vuković R, Katanić Z, Krstin L, Ćurković-Perica M, Leigh DM, Poljak I, Idžojtić M, Rigling D, Ježić M. Physiological variations in hypovirus-infected wild and model long-term laboratory strains of Cryphonectria parasitica. Front Microbiol 2023; 14:1192996. [PMID: 37426020 PMCID: PMC10324583 DOI: 10.3389/fmicb.2023.1192996] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/25/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Forest ecosystems are highly threatened by the simultaneous effects of climate change and invasive pathogens. Chestnut blight, caused by the invasive phytopathogenic fungus Cryphonectria parasitica, has caused severe damage to European chestnut groves and catastrophic dieback of American chestnut in North America. Within Europe, the impacts of the fungus are widely mitigated through biological control that utilizes the RNA mycovirus: Cryphonectria hypovirus 1 (CHV1). Viral infections, similarly to abiotic factors, can cause oxidative stress in their hosts leading to physiological attrition through stimulating ROS (reactive oxygen species) and NOx production. Methods To fully understand the interactions leading to the biocontrol of chestnut blight, it is vital to determine oxidative stress damage arising during CHV1 infection, especially considering that other abiotic factors, like long-term cultivation of model fungal strains, can also impact oxidative stress. Our study compared CHV1-infected C. parasitica isolates from two Croatian wild populations with CHV1-infected model strains (EP713, Euro7 and CR23) that have experienced long-term laboratory cultivation. Results and Discussion We determined the level of oxidative stress in the samples by measuring stress enzymes' activity and oxidative stress biomarkers. Furthermore, for the wild populations, we studied the activity of fungal laccases, expression of the laccase gene lac1, and a possible effect of CHV1 intra-host diversity on the observed biochemical responses. Relative to the wild isolates, the long-term model strains had lower enzymatic activities of superoxide dismutase (SOD) and glutathione S-transferase (GST), and higher content of malondialdehyde (MDA) and total non-protein thiols. This indicated generally higher oxidative stress, likely arising from their decades-long history of subculturing and freeze-thaw cycles. When comparing the two wild populations, differences between them in stress resilience and levels of oxidative stress were also observed, as evident from the different MDA content. The intra-host genetic diversity of the CHV1 had no discernible effect on the stress levels of the virus-infected fungal cultures. Our research indicated that an important determinant modulating both lac1 expression and laccase enzyme activity is intrinsic to the fungus itself, possibly related to the vc type of the fungus, i.e., vegetative incompatibility genotype.
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Affiliation(s)
- Maja Popović
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Lucija Nuskern
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Karla Peranić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Rosemary Vuković
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Zorana Katanić
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Ljiljana Krstin
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | | | | | - Igor Poljak
- Faculty of Forestry and Wood Technology, University of Zagreb, Zagreb, Croatia
| | - Marilena Idžojtić
- Faculty of Forestry and Wood Technology, University of Zagreb, Zagreb, Croatia
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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2
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Müller M, Kües U, Budde KB, Gailing O. Applying molecular and genetic methods to trees and their fungal communities. Appl Microbiol Biotechnol 2023; 107:2783-2830. [PMID: 36988668 PMCID: PMC10106355 DOI: 10.1007/s00253-023-12480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.
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Affiliation(s)
- Markus Müller
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany.
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany.
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Katharina B Budde
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Goettingen, Büsgenweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, 37073, Göttingen, Germany
- Center of Sustainable Land Use (CBL), Georg-August-University Göttingen, 37077, Göttingen, Germany
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3
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Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy). FORESTS 2022. [DOI: 10.3390/f13020344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cryphonectria parasitica, which causes chestnut blight, is one of the most important pathogens of forest trees. In Europe, mycovirus-mediated biocontrol is the most efficient method to control the disease but can be impeded by the lack of information about the population structure of the fungus within a region. In particular, sexual reproduction and the new introduction of the pathogen can complicate biocontrol strategies. For this reason, this study aimed to determine the population structure of C. parasitica, which causes chestnut blight, in the northern Italian region of South Tyrol, using eleven multilocus microsatellite markers. Fifty-one haplotypes were found across South Tyrol, belonging to three divergent clusters. Recombinant genotypes demonstrated that sexual reproduction occurs across the different clusters. The most dominant genotypes in the region were also the most dominant in neighboring areas, such as Switzerland, northern Italy and France. All of the clusters from South Tyrol were related to the Italian genotype pool and are thought to have been introduced from northern Italian and other European populations due to naturally occurring gene flow or human-mediated introduction. At least three separate introduction events of C. parasitica might have happened in South Tyrol that could be separated by time. This study demonstrated a high genetic diversity of C. parasitica in South Tyrol and helped to shed light on the sexual reproduction and introduction events in the local populations.
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4
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Chandelier A. The Use of qPCR to Detect Cryphonectria parasitica in Plants. Methods Mol Biol 2022; 2536:167-177. [PMID: 35819605 DOI: 10.1007/978-1-0716-2517-0_11] [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] [Indexed: 06/15/2023]
Abstract
Cryphonectria parasitica is a fungal pathogen that causes lethal bark necrosis in chestnut. A duplex qPCR allowing detection of the pathogen and its host, Castanea sativa, is described. The method can be used for early detection of the pathogen in chestnut bark tissues with an internal control of false-negative results caused by PCR inhibitors and/or DNA extraction failure. A positive amplification control of qPCR that allows detection of any deviation from a normal qPCR run based on a control chart is also described. As C. parasitica is a regulated pathogen in Europe, the protocol also provides information on the way to collect and handle bark samples to fulfil biosecurity rules.
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Affiliation(s)
- Anne Chandelier
- Walloon Agricultural Research Centre, Department Life Sciences, Crops and Forests Health Unit, Gembloux, Belgium.
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5
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Treindl AD, Stapley J, Winter DJ, Cox MP, Leuchtmann A. Chromosome-level genomes provide insights into genome evolution, organization and size in Epichloe fungi. Genomics 2021; 113:4267-4275. [PMID: 34774981 DOI: 10.1016/j.ygeno.2021.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Epichloe fungi are endophytes of cool season grasses, both wild species and commercial cultivars, where they may exhibit mutualistic or pathogenic lifestyles. The Epichloe-grass symbiosis is of great interest to agricultural research for the fungal bioprotective properties conferred to host grasses but also serves as an ideal system to study the evolution of fungal plant-pathogens in natural environments. Here, we assembled and annotated gapless chromosome-level genomes of two pathogenic Epichloe sibling species. Both genomes have a bipartite genome organization, with blocks of highly syntenic gene-rich regions separated by blocks of AT-rich DNA. The AT-rich regions show an extensive signature of RIP (repeat-induced point mutation) and the expansion of this compartment accounts for the large difference in genome size between the two species. This study reveals how the rapid evolution of repeat structure can drive divergence between closely related taxa and highlights the evolutionary role of dynamic compartments in fungal genomes.
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Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland.
| | - Jessica Stapley
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - David J Winter
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Adrian Leuchtmann
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
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6
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Ježić M, Schwarz JM, Prospero S, Sotirovski K, Risteski M, Ćurković-Perica M, Nuskern L, Krstin L, Katanić Z, Maleničić E, Poljak I, Idžojtić M, Rigling D. Temporal and Spatial Genetic Population Structure of Cryphonectria parasitica and Its Associated Hypovirus Across an Invasive Range of Chestnut Blight in Europe. PHYTOPATHOLOGY 2021; 111:1327-1337. [PMID: 33417482 DOI: 10.1094/phyto-09-20-0405-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chestnut blight has spread throughout Europe since the introduction of its causal agent, Cryphonectria parasitica, >70 years ago. In our study, we analyzed the diversity of vegetative compatibility (vc) and microsatellite genotypes of C. parasitica, as well as sequence diversity of Cryphonectria hypovirus 1 (CHV1) in six populations from Switzerland, Croatia, and North Macedonia. Resampling of local populations that were already investigated more than a decade ago allowed us to analyze the spatial and temporal population structure across an invasive range of the pathogen in Europe. Regardless of which genetic marker was used, the >60-year-old Swiss and Croatian populations had high population diversity, whereas more recent North Macedonian populations were mostly clonal. These diversity differences between the investigated populations remained stable over time. A high diversity of CHV1 was observed in all three countries, with North Macedonian strains forming a separate cluster from strains obtained in other countries. No correlation between vc diversity and CHV1 prevalence was observed, suggesting a well-established and maintained natural hypovirulence in all countries, further corroborated by an observed increase in genetic diversity of Croatian C. parasitica populations over time, without collapse of CHV1 prevalence.
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Affiliation(s)
- Marin Ježić
- University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Zagreb, Croatia
| | | | - Simone Prospero
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
| | - Kiril Sotirovski
- Ss Cyril and Methodius University in Skopje, Hans Em Faculty of Forest Sciences, Landscape Architecture and Environmental Engineering, 1000 Skopje, North Macedonia
| | - Mihajlo Risteski
- Ss Cyril and Methodius University in Skopje, Hans Em Faculty of Forest Sciences, Landscape Architecture and Environmental Engineering, 1000 Skopje, North Macedonia
| | - Mirna Ćurković-Perica
- University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Zagreb, Croatia
| | - Lucija Nuskern
- University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Zagreb, Croatia
| | - Ljiljana Krstin
- University J. J. Strossmayer of Osijek, Department of Biology, 31000 Osijek, Croatia
| | - Zorana Katanić
- University J. J. Strossmayer of Osijek, Department of Biology, 31000 Osijek, Croatia
| | - Ema Maleničić
- University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Zagreb, Croatia
| | - Igor Poljak
- University of Zagreb, Faculty of Forestry and Wood Technology, Department of Forest Genetics, Dendrology and Botany, 10000 Zagreb, Croatia
| | - Marilena Idžojtić
- University of Zagreb, Faculty of Forestry and Wood Technology, Department of Forest Genetics, Dendrology and Botany, 10000 Zagreb, Croatia
| | - Daniel Rigling
- Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
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Stauber L, Badet T, Feurtey A, Prospero S, Croll D. Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe. eLife 2021; 10:e56279. [PMID: 33666552 PMCID: PMC7935491 DOI: 10.7554/elife.56279] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 02/17/2021] [Indexed: 12/18/2022] Open
Abstract
Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or a small number of genotypes, yet the underlying factors driving invasions are poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated the North American chestnut, and a more recent outbreak threatens European chestnut stands. To unravel the chestnut blight invasion of southeastern Europe, we sequenced 230 genomes of predominantly European strains. Genotypes outside of the invasion zone showed high levels of diversity with evidence for frequent and ongoing recombination. The invasive lineage emerged from the highly diverse European genotype pool rather than a secondary introduction from Asia or North America. The expansion across southeastern Europe was mostly clonal and is dominated by a single mating type, suggesting a fitness advantage of asexual reproduction. Our findings show how an intermediary, highly diverse bridgehead population gave rise to an invasive, largely clonally expanding pathogen.
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Affiliation(s)
- Lea Stauber
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)BirmensdorfSwitzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürichSwitzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)BirmensdorfSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
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Schmidt R, Auge H, Deising HB, Hensen I, Mangan SA, Schädler M, Stein C, Knight TM. Abundance, origin, and phylogeny of plants do not predict community-level patterns of pathogen diversity and infection. Ecol Evol 2020; 10:5506-5516. [PMID: 32607170 PMCID: PMC7319236 DOI: 10.1002/ece3.6292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 11/17/2022] Open
Abstract
Pathogens have the potential to shape plant community structure, and thus, it is important to understand the factors that determine pathogen diversity and infection in communities. The abundance, origin, and evolutionary relationships of plant hosts are all known to influence pathogen patterns and are typically studied separately. We present an observational study that examined the influence of all three factors and their interactions on the diversity of and infection of several broad taxonomic groups of foliar, floral, and stem pathogens across three sites in a temperate grassland in the central United States. Despite that pathogens are known to respond positively to increases in their host abundances in other systems, we found no relationship between host abundance and either pathogen diversity or infection. Native and exotic plants did not differ in their infection levels, but exotic plants hosted a more generalist pathogen community compared to native plants. There was no phylogenetic signal across plants in pathogen diversity or infection. The lack of evidence for a role of abundance, origin, and evolutionary relationships in shaping patterns of pathogens in our study might be explained by the high generalization and global distributions of our focal pathogen community, as well as the high diversity of our plant host community. In general, the community-level patterns of aboveground pathogen infections have received less attention than belowground pathogens, and our results suggest that their patterns might not be explained by the same drivers.
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Affiliation(s)
- Robin Schmidt
- Department of Community EcologyHelmholtz‐Centre for Environmental Research–UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Harald Auge
- Department of Community EcologyHelmholtz‐Centre for Environmental Research–UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Holger B. Deising
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Agricultural and Nutritional Sciences, Phytopathology and Plant ProtectionMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Isabell Hensen
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
| | - Scott A. Mangan
- Tyson Research Center & Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
| | - Martin Schädler
- Department of Community EcologyHelmholtz‐Centre for Environmental Research–UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Claudia Stein
- Tyson Research Center & Department of BiologyWashington University in St. LouisSt. LouisMissouriUSA
- Department of Biology and Environmental SciencesAuburn University at MontgomeryMontgomeryALUSA
| | - Tiffany M. Knight
- Department of Community EcologyHelmholtz‐Centre for Environmental Research–UFZHalle (Saale)Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle‐WittenbergHalle (Saale)Germany
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9
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Gent DH, Claassen BJ, Gadoury DM, Grünwald NJ, Knaus BJ, Radišek S, Weldon W, Wiseman MS, Wolfenbarger SN. Population Diversity and Structure of Podosphaera macularis in the Pacific Northwestern United States and Other Populations. PHYTOPATHOLOGY 2020; 110:1105-1116. [PMID: 32091314 DOI: 10.1094/phyto-12-19-0448-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Powdery mildew, caused by Podosphaera macularis, is one of the most important diseases of hop. The disease was first reported in the Pacific Northwestern United States, the primary hop-growing region in this country, in the mid-1990s. More recently, the disease has reemerged in newly planted hopyards of the eastern United States, as hop production has expanded to meet demands of local craft brewers. The spread of strains virulent on previously resistant cultivars, the paucity of available fungicides, and the potential introduction of the MAT1-2 mating type to the western United States, all threaten sustainability of hop production. We sequenced the transcriptome of 104 isolates of P. macularis collected throughout the western United States, eastern United States, and Europe to quantify genetic diversity of pathogen populations and elucidate the possible origins of pathogen populations in the western United States. Discriminant analysis of principal components grouped isolates within three to five geographic populations, dependent on stringency of grouping criteria. Isolates from the western United States were phenotyped and categorized into one of three pathogenic races based on disease symptoms generated on differential cultivars. Western U.S. populations were clonal, irrespective of pathogenic race, and grouped with isolates originating from Europe. Isolates originating from wild hop plants in the eastern United States were genetically differentiated from all other populations, whereas isolates from cultivated hop plants in the eastern United States mostly grouped with isolates originating from the west, consistent with origins from nursery sources. Mating types of isolates originating from cultivated western and eastern U.S. hop plants were entirely MAT1-1. In contrast, a 1:1 ratio of MAT1-1 and MAT1-2 was observed with isolates sampled from wild plants or Europe. Within the western United States a set of highly differentiated loci were identified in P. macularis isolates associated with virulence to the powdery mildew R-gene R6. The weight of genetic and phenotypic evidence suggests a European origin of the P. macularis populations in the western United States, followed by spread of the pathogen from the western United States to re-emergent production regions in the eastern United States. Furthermore, R6 compatibility appears to have been selected from an extant isolate within the western United States. Greater emphasis on sanitation measures during propagation and quarantine policies should be considered to limit further spread of novel genotypes of the pathogen, both between and within production areas.
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Affiliation(s)
- David H Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Briana J Claassen
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - David M Gadoury
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330, U.S.A
| | - Brian J Knaus
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | | | - William Weldon
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456, U.S.A
| | - Michele S Wiseman
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
| | - Sierra N Wolfenbarger
- Oregon State University, Department of Botany and Plant Pathology, Corvallis, OR 97331, U.S.A
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10
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Dennert F, Meyer JB, Rigling D, Prospero S. Assessing the Phytosanitary Risk Posed by an Intraspecific Invasion of Cryphonectria parasitica in Europe. PHYTOPATHOLOGY 2019; 109:2055-2063. [PMID: 31411547 DOI: 10.1094/phyto-06-19-0197-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Intraspecific cryptic invasions may occur when new strains of an invasive species are introduced into an area where this species had already been introduced previously. In plant pathogens, such invasions are not well studied, even if, potentially, they can have severe consequences. Here, we investigated the effects of a potential intraspecific invasion in Europe of Cryphonectria parasitica, the causal agent of chestnut blight. Specifically, we tested the hypotheses that (i) non-European strains are more virulent on Castanea sativa than those already present in Europe because they have never encountered this new host, and (ii) the variation in virulence among strains is higher within native than within introduced populations. In a greenhouse, 2-year-old C. sativa seedlings were inoculated with Cryphonectria parasitica strains from South Korea, the United States, and Switzerland, and lesion development and seedling mortality were recorded weekly. Additionally, growth and sporulation of the strains were measured in vitro on agar medium at 15 and 24°C. Although lesion growth was similar for all strains, seedlings inoculated with strains from South Korea and Switzerland died faster than seedlings inoculated with strains from the United States. Moreover, in vitro strains from South Korea grew faster and produced more spores at both temperatures than the strains from the other two countries. In conclusion, our results did not support the two hypotheses. All strains, regardless of their origin, were found to be highly virulent on the inoculated chestnut seedlings. Nevertheless, current phytosanitary measures to avoid the introduction of new genotypes of C. parasitica into Europe should be further implemented.
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Affiliation(s)
- Francesca Dennert
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
| | - Joana Beatrice Meyer
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
- Forest Protection and Forest Health Section, Federal Office for the Environment FOEN, CH-3003 Bern, Switzerland
| | - Daniel Rigling
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
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11
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Drenth A, McTaggart AR, Wingfield BD. Fungal clones win the battle, but recombination wins the war. IMA Fungus 2019; 10:18. [PMID: 32647622 PMCID: PMC7325676 DOI: 10.1186/s43008-019-0020-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
Clonal reproduction is common in fungi and fungal-like organisms during epidemics and invasion events. The success of clonal fungi shaped systems for their classification and some pathogens are tacitly treated as asexual. We argue that genetic recombination driven by sexual reproduction must be a starting hypothesis when dealing with fungi for two reasons: (1) Clones eventually crash because they lack adaptability; and (2) fungi find a way to exchange genetic material through recombination, whether sexual, parasexual, or hybridisation. Successful clones may prevail over space and time, but they are the product of recombination and the next successful clone will inevitably appear. Fungal pathogen populations are dynamic rather than static, and they need genetic recombination to adapt to a changing environment.
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Affiliation(s)
- André Drenth
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4102 Australia
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4102 Australia.,Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, Gauteng South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, Gauteng South Africa
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12
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Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe. Fungal Genet Biol 2019; 130:122-133. [DOI: 10.1016/j.fgb.2019.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 02/07/2023]
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13
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Vieira A, Silva DN, Várzea V, Paulo OS, Batista D. Novel insights on colonization routes and evolutionary potential of Colletotrichum kahawae, a severe pathogen of Coffea arabica. MOLECULAR PLANT PATHOLOGY 2018; 19:2488-2501. [PMID: 30073748 PMCID: PMC6638157 DOI: 10.1111/mpp.12726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 05/25/2018] [Accepted: 06/28/2018] [Indexed: 05/19/2023]
Abstract
Pathogenic fungi are emerging at an increasing rate on a wide range of host plants, leading to tremendous threats to the global economy and food safety. Several plant pathogens have been considered to be invasive species, rendering large-scale population genomic analyses crucial to better understand their demographic history and evolutionary potential. Colletotrichum kahawae (Ck) is a highly aggressive and specialized pathogen, causing coffee berry disease in Arabica coffee in Africa. This pathogen leads to severe production losses and its dissemination out of Africa is greatly feared. To address this issue, a population genomic approach using thousands of single nucleotide polymorphisms (SNPs) spaced throughout the genome was used to unveil its demographic history and evolutionary potential. The current study confirms that Ck is a true clonal pathogen, perfectly adapted to green coffee berries, with three completely differentiated populations (Angolan, Cameroonian and East African). Two independent clonal lineages were found within the Angolan population as opposed to the remaining single clonal populations. The most probable colonization scenario suggests that this pathogen emerged in Angola and immediately dispersed to East Africa, where these two populations began to differentiate, followed by the introduction in Cameroon from an Angolan population. However, the differentiation between the two Angolan clonal lineages masks the mechanism for the emergence of the Cameroonian population. Our results suggest that Ck is completely differentiated from the ancestral lineage, has a low evolutionary potential and a low dispersion ability, with human transport the most likely scenario for its potential dispersion, which makes the fulfilment of the quarantine measures and management practices implemented crucial.
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Affiliation(s)
- Ana Vieira
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Diogo Nuno Silva
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Victor Várzea
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
| | - Octávio Salgueiro Paulo
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
| | - Dora Batista
- CIFC—Centro de Investigação das Ferrugens do CafeeiroInstituto Superior de Agronomia, Universidade de LisboaOeiras2784‐505Portugal
- CoBiG—Computational Biology and Population Genomics Group, cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de CiênciasUniversidade de LisboaLisboa1749‐016Portugal
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, Universidade de LisboaLisboa1349‐017Portugal
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14
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Islam MS, Callicott KA, Mutegi C, Bandyopadhyay R, Cotty PJ. Aspergillus flavus resident in Kenya: High genetic diversity in an ancient population primarily shaped by clonal reproduction and mutation-driven evolution. FUNGAL ECOL 2018; 35:20-33. [PMID: 30283498 PMCID: PMC6131765 DOI: 10.1016/j.funeco.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 12/30/2022]
Abstract
Aspergillus flavus has long been considered to be an asexual species. Although a sexual stage was recently reported for this species from in vitro studies, the amount of recombination ongoing in natural populations and the genetic distance across which meiosis occurs is largely unknown. In the current study, genetic diversity, reproduction and evolution of natural A. flavus populations endemic to Kenya were examined. A total of 2744 isolates recovered from 629 maize-field soils across southern Kenya in two consecutive seasons were characterized at 17 SSR loci, revealing high genetic diversity (9-72 alleles/locus and 2140 haplotypes). Clonal reproduction and persistence of clonal lineages predominated, with many identical haplotypes occurring in multiple soil samples and both seasons. Genetic analyses predicted three distinct lineages with linkage disequilibrium and evolutionary relationships among haplotypes within each lineage suggesting mutation-driven evolution followed by clonal reproduction. Low genetic differentiation among adjacent communities reflected frequent short distance dispersal.
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Affiliation(s)
- Md-Sajedul Islam
- Agricultural Research Service, United States Department of Agriculture, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Kenneth A. Callicott
- Agricultural Research Service, United States Department of Agriculture, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Charity Mutegi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | | | - Peter J. Cotty
- Agricultural Research Service, United States Department of Agriculture, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
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15
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Ježić M, Mlinarec J, Vuković R, Katanić Z, Krstin L, Nuskern L, Poljak I, Idžojtić M, Tkalec M, Ćurković-Perica M. Changes in Cryphonectria parasitica Populations Affect Natural Biological Control of Chestnut Blight. PHYTOPATHOLOGY 2018; 108:870-877. [PMID: 29442579 DOI: 10.1094/phyto-07-17-0252-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Invasive species, especially plant pathogens, have a potential to completely eradicate native plant species and remodel landscapes. Tripartite interactions among sweet chestnut (Castanea sativa), chestnut blight-causing invasive fungus Cryphonectria parasitica, and hyperparasitic virus Cryphonectria hypovirus 1 (CHV1) were studied in two populations. The number of different vegetative compatibility (vc) types of C. parasitica more than doubled over the 10 years, while the hypovirulence incidence dropped in one population and slightly increased in the other one. Over the course of our 3-year monitoring experiment, the prevalence of hypovirulent isolates obtained from monitored cankers increased slowly (i.e., more hypovirulent isolates were being obtained from the same cankers over time). Within studied cankers, considerable changes in vc type and CHV1 presence were observed, indicating a highly dynamic system in which virulent and hypovirulent mycelia, sometimes of discordant vc types, often appeared together. The increase in hypovirulence prevalence did not have any observable curative effect on the cankers and, occasionally, reactivation of healed cankers by new, virulent C. parasitica isolates was observed. Both short- and long-term observations and revalidation of the infected plant populations are necessary to accurately estimate disease progress and formulate an adequate disease management strategy.
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Affiliation(s)
- Marin Ježić
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Jelena Mlinarec
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Rosemary Vuković
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Zorana Katanić
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Ljiljana Krstin
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Lucija Nuskern
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Igor Poljak
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Marilena Idžojtić
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Mirta Tkalec
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
| | - Mirna Ćurković-Perica
- First, second, sixth, and tenth authors: University of Zagreb, Faculty of Science, Department of Biology, Division of Microbiology, Marulicev trg 9a, Zagreb, Croatia; third, fourth, and fifth authors: J. J. Strossmayer University of Osijek, Department of Biology, Cara Hadrijana 8A, Osijek, Croatia; seventh and eighth authors: University of Zagreb, Faculty of Forestry, Department of forest genetics and dendrology, Svetosimunska 25, Zagreb, Croatia; and ninth author: University of Zagreb, Faculty of Science, Department of Biology, Division of Botany, Rooseveltov trg 6, Zagreb, Croatia
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16
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L’Heureux É, Angers B. A discreet invasion: distribution, origins, and expansion of the European slug complex Arion subfuscus s.l. in Quebec. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accurate identification of species and their geographic origins is crucial to assess the impacts of exotic species. This is particularly relevant when multiple introductions are suspected. Species complexes are therefore problematic, as different species can be treated as a single taxon. The highly diversified European complex Arion subfuscus (Draparnaud, 1805) s.l. is abundant throughout northeastern North America. However, surveys performed in the United States have reported a low mitochondrial diversity associated with a single species. To assess whether regions characterized by different human activities harbor different diversities, the taxonomic identities, distributions, and origins of the species of this complex in Quebec (Canada) were determined. The mitochondrial 16S rDNA gene was analyzed in 526 specimens from 69 locations. Both Arion fuscus (O.F. Müller, 1774) and Arion subfuscus (Draparnaud, 1805) s. str. (lineages S1 and S2) were detected. Arion fuscus was the most abundant species, contrasting with previous studies conducted in North America. An explosive range expansion occurred during the last 50 years. Moreover, the presence of different haplotypes confirmed multiple introductions of these species. These results emphasize the importance of not considering an exotic species complex as a single taxon, especially in regions with different human activities.
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Affiliation(s)
- Érik L’Heureux
- Département de sciences biologiques, Université de Montréal, Pavillon Marie-Victorin, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Département de sciences biologiques, Université de Montréal, Pavillon Marie-Victorin, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
| | - Bernard Angers
- Département de sciences biologiques, Université de Montréal, Pavillon Marie-Victorin, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
- Département de sciences biologiques, Université de Montréal, Pavillon Marie-Victorin, C.P. 6128, succursale Centre-ville, Montréal, QC H3C 3J7, Canada
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17
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Brar GS, Ali S, Qutob D, Ambrose S, Lou K, Maclachlan R, Pozniak CJ, Fu YB, Sharpe AG, Kutcher HR. Genome re-sequencing and simple sequence repeat markers reveal the existence of divergent lineages in the Canadian Puccinia striiformis
f. sp. tritici
population with extensive DNA methylation. Environ Microbiol 2018; 20:1498-1515. [DOI: 10.1111/1462-2920.14067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Gurcharn S. Brar
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Sajid Ali
- Institute of Biotechnology and Genetic Engineering; University of Agriculture; Peshawar Pakistan
| | - Dinah Qutob
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Stephen Ambrose
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Kun Lou
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Ron Maclachlan
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Curtis J. Pozniak
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Agriculture & Agri-Food Canada- Saskatoon Research and Development Centre, 107 Science Place; Saskatoon SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Hadley R. Kutcher
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
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18
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Murolo S, De Miccolis Angelini RM, Faretra F, Romanazzi G. Phenotypic and Molecular Investigations on Hypovirulent Cryphonectria parasitica in Italy. PLANT DISEASE 2018; 102:540-545. [PMID: 30673478 DOI: 10.1094/pdis-04-17-0517-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chestnut blight is caused by the fungus Cryphonectria parasitica. As one of the most ecologically important diseases of Castanea spp., C. parasitica can rapidly kill trees. In Europe, mitigation of disease severity took place spontaneously through colonization of C. parasitica by mycoviruses, which reduced the virulence of the fungus. In the framework of a survey, 138 C. parasitica isolates were identified, and virulent/hypovirulent phenotypes were determined through morphological properties and pathogenicity tests. For a pool of four hypovirulent isolates, dsRNA was extracted, cDNA synthesized, and a library subjected to next-generation sequencing. The bioinformatics analysis allowed detecting and reconstructing the complete genome of Cryphonectria hypovirus 1 (CHV-1), denoted as CHV-1 Marche. When compared with the available genomes of other hypoviruses that affected the virulence of C. parasitica, available in databases, CHV-1 Marche showed some nucleotide diversity. The approach used in this study was effective to explore the virome inside a pool of hypovirulent C. parasitica isolates. Next-generation sequencing allowed us to exclude the presence of any other ssRNA and dsRNA viruses infecting the fungus and determine CHV-1 as the only responsible of hypovirulence of C. parasitica in the analyzed samples.
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Affiliation(s)
- Sergio Murolo
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | | | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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19
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Piotrowska MJ, Riddell C, Hoebe PN, Ennos RA. Planting exotic relatives has increased the threat posed by Dothistroma septosporum to the Caledonian pine populations of Scotland. Evol Appl 2018; 11:350-363. [PMID: 29632553 PMCID: PMC5881121 DOI: 10.1111/eva.12562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/08/2017] [Indexed: 12/27/2022] Open
Abstract
To manage emerging forest diseases and prevent their occurrence in the future, it is essential to determine the origin(s) of the pathogens involved and identify the management practices that have ultimately caused disease problems. One such practice is the widespread planting of exotic tree species within the range of related native taxa. This can lead to emerging forest disease both by facilitating introduction of exotic pathogens and by providing susceptible hosts on which epidemics of native pathogens can develop. We used microsatellite markers to determine the origins of the pathogen Dothistroma septosporum responsible for the current outbreak of Dothistroma needle blight (DNB) on native Caledonian Scots pine (Pinus sylvestris) populations in Scotland and evaluated the role played by widespread planting of two exotic pine species in the development of the disease outbreak. We distinguished three races of D. septosporum in Scotland, one of low genetic diversity associated with introduced lodgepole pine (Pinus contorta), one of high diversity probably derived from the DNB epidemic on introduced Corsican pine (Pinus nigra subsp. laricio) in England and a third of intermediate diversity apparently endemic on Caledonian Scots pine. These races differed for both growth rate and exudate production in culture. Planting of exotic pine stands in the UK appears to have facilitated the introduction of two exotic races of D. septosporum into Scotland which now pose a threat to native Caledonian pines both directly and through potential hybridization and introgression with the endemic race. Our results indicate that both removal of exotic species from the vicinity of Caledonian pine populations and restriction of movement of planting material are required to minimize the impact of the current DNB outbreak. They also demonstrate that planting exotic species that are related to native species reduces rather than enhances the resilience of forests to pathogens.
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Affiliation(s)
- Marta J. Piotrowska
- Crop and Soil Systems Research GroupScotland's Rural CollegeEdinburghUK
- The Institute of Biological Chemistry, Biophysics and BioengineeringHeriot‐Watt UniversityEdinburghUK
| | - Carolyn Riddell
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghUK
- Forest ResearchNorthern Research StationRoslinUK
| | - Peter N. Hoebe
- Crop and Soil Systems Research GroupScotland's Rural CollegeEdinburghUK
| | - Richard A. Ennos
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghUK
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20
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Milgroom MG, Smith ML, Drott MT, Nuss DL. Balancing selection at nonself recognition loci in the chestnut blight fungus, Cryphonectria parasitica, demonstrated by trans-species polymorphisms, positive selection, and even allele frequencies. Heredity (Edinb) 2018; 121:511-523. [PMID: 29426879 DOI: 10.1038/s41437-018-0060-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 11/09/2022] Open
Abstract
Balancing selection has been inferred in diverse organisms for nonself recognition genes, including those involved in immunity, mating compatibility, and vegetative incompatibility. Although selective forces maintaining polymorphisms are known for genes involved in immunity and mating, mechanisms of balancing selection for vegetative incompatibility genes in fungi are being debated. We hypothesized that allorecognition and its consequent inhibition of virus transmission contribute to the maintenance of polymorphisms in vegetative incompatibility loci (vic) in the chestnut blight fungus, Cryphonectria parasitica. Balancing selection was demonstrated at two loci, vic2 and vic6, by trans-species polymorphisms in C. parasitica, C. radicalis, and C. japonica and signatures of positive selection in gene sequences. In addition, more than half (31 of 54) of allele frequency estimates at six vic loci in nine field populations of C. parasitica from Asia and the eastern US were not significantly different from 0.5, as expected at equilibrium for two alleles per locus under balancing selection. At three vic loci, deviations from 0.5 were predicted based on the effects of heteroallelism on virus transmission. Twenty-five of 27 allele frequency estimates were greater than or equal to 0.5 for the allele that confers significantly stronger inhibition of virus transmission at three loci with asymmetric transmission. These results are consistent with the allorecognition hypothesis that vegetative incompatibility genes are under selection because of their role in reducing infection by viruses.
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Affiliation(s)
- Michael G Milgroom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, 14853, USA.
| | - Myron L Smith
- Department of Biology, Carleton University, Ottawa, ON, K1S 5B6, Canada
| | - Milton T Drott
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Donald L Nuss
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.,Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26506, USA
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21
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Lewis CM, Persoons A, Bebber DP, Kigathi RN, Maintz J, Findlay K, Bueno-Sancho V, Corredor-Moreno P, Harrington SA, Kangara N, Berlin A, García R, Germán SE, Hanzalová A, Hodson DP, Hovmøller MS, Huerta-Espino J, Imtiaz M, Mirza JI, Justesen AF, Niks RE, Omrani A, Patpour M, Pretorius ZA, Roohparvar R, Sela H, Singh RP, Steffenson B, Visser B, Fenwick PM, Thomas J, Wulff BBH, Saunders DGO. Potential for re-emergence of wheat stem rust in the United Kingdom. Commun Biol 2018; 1:13. [PMID: 30271900 PMCID: PMC6053080 DOI: 10.1038/s42003-018-0013-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/11/2018] [Indexed: 12/05/2022] Open
Abstract
Wheat stem rust, a devastating disease of wheat and barley caused by the fungal pathogen Puccinia graminis f. sp. tritici, was largely eradicated in Western Europe during the mid-to-late twentieth century. However, isolated outbreaks have occurred in recent years. Here we investigate whether a lack of resistance in modern European varieties, increased presence of its alternate host barberry and changes in climatic conditions could be facilitating its resurgence. We report the first wheat stem rust occurrence in the United Kingdom in nearly 60 years, with only 20% of UK wheat varieties resistant to this strain. Climate changes over the past 25 years also suggest increasingly conducive conditions for infection. Furthermore, we document the first occurrence in decades of P. graminis on barberry in the UK . Our data illustrate that wheat stem rust does occur in the UK and, when climatic conditions are conducive, could severely harm wheat and barley production.
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Affiliation(s)
- Clare M Lewis
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Rose N Kigathi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Pwani University, 195-80108, Kilifi, Kenya
| | - Jens Maintz
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kim Findlay
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | | | | | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Richard García
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Silvia E Germán
- Instituto Nacional de Investigación Agropecuaria (INIA) La Estanzuela, Mailbox 39173, Colonia, Uruguay
| | - Alena Hanzalová
- Crop Research Institute, Ruzyně, 161 06 Praha 6, Czech Republic
| | - David P Hodson
- International Maize and Wheat Improvement Center (CIMMYT), 5689, Addis Ababa, Ethiopia
| | | | | | | | - Javed Iqbal Mirza
- Crop Disease Research Program, National Agriculture Research Center, Islamabad, 44000, Pakistan
| | | | - Rients E Niks
- Wageningen University, Wageningen, 6700, The Netherlands
| | - Ali Omrani
- Faculty of Agriculture, Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 5166616471, Iran
| | | | | | - Ramin Roohparvar
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), 4119, Karaj, Iran
| | - Hanan Sela
- Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ravi P Singh
- CIMMYT, Apdo. Postal 6-641, D. F. México, 06600, Mexico
| | | | - Botma Visser
- University of the Free State, Bloemfontein, 9301, South Africa
| | | | - Jane Thomas
- National Institute of Agricultural Botany, Cambridge, CB3 0LE, UK
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Mlinarec J, Nuskern L, Ježić M, Rigling D, Ćurković-Perica M. Molecular evolution and invasion pattern of Cryphonectria hypovirus 1 in Europe: Mutation rate, and selection pressure differ between genome domains. Virology 2018; 514:156-164. [PMID: 29179038 DOI: 10.1016/j.virol.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 01/08/2023]
Abstract
Understanding virus evolution is a fundamental goal of virology, evolutionary biology, and disease epidemiology. We provide a detailed analysis of evolution and origin of Cryphonectria hypovirus 1 (CHV1) populations in Europe, based on the complete genome sequence of all European subtypes. Phylogenetic analyses divided European strains into two closely related clades. Strains of the subtype I belong to the first, while strains of the subtypes F1, D and E belong to the second clade suggesting that the subtypes F1, D and E are more closely related than previously thought. Strains of the subtype F2 appeared to be recombinant; subtypes F1/D/E contributed a larger fraction of sequence while subtype I contributed a smaller fraction. The p29 was the most variable domain, while the replication-associated large ORF B protein was the most conserved domain within the CHV1. Low sequence similarity, predominant negative selection and frequent recombination characterise the evolution of CHV1.
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Affiliation(s)
- Jelena Mlinarec
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Lucija Nuskern
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia
| | - Daniel Rigling
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
| | - Mirna Ćurković-Perica
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10 000 Zagreb, Croatia.
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Rigling D, Prospero S. Cryphonectria parasitica, the causal agent of chestnut blight: invasion history, population biology and disease control. MOLECULAR PLANT PATHOLOGY 2018; 19:7-20. [PMID: 28142223 PMCID: PMC6638123 DOI: 10.1111/mpp.12542] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 05/25/2023]
Abstract
Chestnut blight, caused by Cryphonectria parasitica, is a devastating disease infecting American and European chestnut trees. The pathogen is native to East Asia and was spread to other continents via infected chestnut plants. This review summarizes the current state of research on this pathogen with a special emphasis on its interaction with a hyperparasitic mycovirus that acts as a biological control agent of chestnut blight. TAXONOMY Cryphonectria parasitica (Murr.) Barr. is a Sordariomycete (ascomycete) fungus in the family Cryphonectriaceae (Order Diaporthales). Closely related species that can also be found on chestnut include Cryphonectria radicalis, Cryphonectria naterciae and Cryphonectria japonica. HOST RANGE Major hosts are species in the genus Castanea (Family Fagaceae), particularly the American chestnut (C. dentata), the European chestnut (C. sativa), the Chinese chestnut (C. mollissima) and the Japanese chestnut (C. crenata). Minor incidental hosts include oaks (Quercus spp.), maples (Acer spp.), European hornbeam (Carpinus betulus) and American chinkapin (Castanea pumila). DISEASE SYMPTOMS Cryphonectria parasitica causes perennial necrotic lesions (so-called cankers) on the bark of stems and branches of susceptible host trees, eventually leading to wilting of the plant part distal to the infection. Chestnut blight cankers are characterized by the presence of mycelial fans and fruiting bodies of the pathogen. Below the canker the tree may react by producing epicormic shoots. Non-lethal, superficial or callusing cankers on susceptible host trees are usually associated with mycovirus-induced hypovirulence. DISEASE CONTROL After the introduction of C. parasitica into a new area, eradication efforts by cutting and burning the infected plants/trees have mostly failed. In Europe, the mycovirus Cryphonectria hypovirus 1 (CHV-1) acts as a successful biological control agent of chestnut blight by causing so-called hypovirulence. CHV-1 infects C. parasitica and reduces its parasitic growth and sporulation capacity. Individual cankers can be therapeutically treated with hypovirus-infected C. parasitica strains. The hypovirus may subsequently spread to untreated cankers and become established in the C. parasitica population. Hypovirulence is present in many chestnut-growing regions of Europe, either resulting naturally or after biological control treatments. In North America, disease management of chestnut blight is mainly focused on breeding with the goal to backcross the Chinese chestnut's blight resistance into the American chestnut genome.
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Affiliation(s)
- Daniel Rigling
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
| | - Simone Prospero
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
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Grünwald NJ, Everhart SE, Knaus BJ, Kamvar ZN. Best Practices for Population Genetic Analyses. PHYTOPATHOLOGY 2017; 107:1000-1010. [PMID: 28513284 DOI: 10.1094/phyto-12-16-0425-rvw] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.
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Affiliation(s)
- N J Grünwald
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - S E Everhart
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - B J Knaus
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - Z N Kamvar
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
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Depotter JRL, Seidl MF, van den Berg GCM, Thomma BPHJ, Wood TA. A distinct and genetically diverse lineage of the hybrid fungal pathogen Verticillium longisporum population causes stem striping in British oilseed rape. Environ Microbiol 2017; 19:3997-4009. [PMID: 28523726 DOI: 10.1111/1462-2920.13801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/30/2022]
Abstract
Population genetic structures illustrate evolutionary trajectories of organisms adapting to differential environmental conditions. Verticillium stem striping disease on oilseed rape was mainly observed in continental Europe, but has recently emerged in the United Kingdom. The disease is caused by the hybrid fungal species Verticillium longisporum that originates from at least three separate hybridization events, yet hybrids between Verticillium progenitor species A1 and D1 are mainly responsible for Verticillium stem striping. We reveal a hitherto un-described dichotomy within V. longisporum lineage A1/D1 that correlates with the geographic distribution of the isolates with an 'A1/D1 West' and an 'A1/D1 East' cluster. Genome comparison between representatives of the A1/D1 West and East clusters excluded population distinctiveness through separate hybridization events. Remarkably, the A1/D1 West population that is genetically more diverse than the entire A1/D1 East cluster caused the sudden emergence of Verticillium stem striping in the UK, whereas in continental Europe Verticillium stem striping is predominantly caused by the more genetically uniform A1/D1 East population. The observed genetic diversity of the A1/D1 West population argues against a recent introduction of the pathogen into the UK, but rather suggests that the pathogen previously established in the UK and remained latent or unnoticed as oilseed rape pathogen until recently.
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Affiliation(s)
- Jasper R L Depotter
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.,Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Grardy C M van den Berg
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Thomas A Wood
- Department of Crops and Agronomy, National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 0LE, UK
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Dutech C, Labbé F, Capdevielle X, Lung-Escarmant B. Genetic analysis reveals efficient sexual spore dispersal at a fine spatial scale in Armillaria ostoyae, the causal agent of root-rot disease in conifers. Fungal Biol 2017; 121:550-560. [PMID: 28606350 DOI: 10.1016/j.funbio.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 11/24/2022]
Abstract
Armillaria ostoyae (sometimes named Armillaria solidipes) is a fungal species causing root diseases in numerous coniferous forests of the northern hemisphere. The importance of sexual spores for the establishment of new disease centres remains unclear, particularly in the large maritime pine plantations of southwestern France. An analysis of the genetic diversity of a local fungal population distributed over 500 ha in this French forest showed genetic recombination between genotypes to be frequent, consistent with regular sexual reproduction within the population. The estimated spatial genetic structure displayed a significant pattern of isolation by distance, consistent with the dispersal of sexual spores mostly at the spatial scale studied. Using these genetic data, we inferred an effective density of reproductive individuals of 0.1-0.3 individuals/ha, and a second moment of parent-progeny dispersal distance of 130-800 m, compatible with the main models of fungal spore dispersal. These results contrast with those obtained for studies of A. ostoyae over larger spatial scales, suggesting that inferences about mean spore dispersal may be best performed at fine spatial scales (i.e. a few kilometres) for most fungal species.
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Affiliation(s)
- Cyril Dutech
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France.
| | - Frédéric Labbé
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France
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Robin C, Andanson A, Saint-Jean G, Fabreguettes O, Dutech C. What was old is new again: thermal adaptation within clonal lineages during range expansion in a fungal pathogen. Mol Ecol 2017; 26:1952-1963. [PMID: 28141894 DOI: 10.1111/mec.14039] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/27/2016] [Accepted: 01/17/2017] [Indexed: 12/25/2022]
Abstract
Range-expanding species are expected to gain an increasing importance in the context of global change. They provide a great opportunity to study contemporary evolutionary changes and to unravel the mechanisms of evolution. Cryphonectria parasitica, the causal agent of chestnut blight, originating from Asia, has been spread since the beginning of the 20th century into different continents. We took advantage of the C. parasitica recent emergence in northern France to study the changes in population genetic structure and in phenotypic traits along this colonization and climatic gradient. Four hundred twenty-seven C. parasitica isolates were sampled in 47 chestnut sites in northern France. The C. parasitica outbreak in the north was found to be due to the expansion of five dominant clonal groups from southern France and to the emergence of a few rare recombined genotypes. The evolutionary changes during C. parasitica range expansion were studied by analysing phenotypic changes in isolates from the same clonal lineage, with or without a geographic shift. Growth rates were assessed in vitro, at four temperatures. The northern isolates grew faster at 12 and 15 °C and more slowly at 28 and 32 °C than the southern isolates. These results strongly suggest local adaptation to low temperatures in C. parasitica, with a trade-off of slower growth at high temperatures. They also reflect the high evolutionary potential of C. parasitica along a colonization gradient and show that clonal evolution is not a limitation for the rapid thermal adaptation of this invasive fungal species.
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Affiliation(s)
- Cécile Robin
- BIOGECO, INRA, University of Bordeaux, 69 route d'Arcachon, 33610, Cestas, France
| | - Audrey Andanson
- BIOGECO, INRA, University of Bordeaux, 69 route d'Arcachon, 33610, Cestas, France
| | - Gilles Saint-Jean
- BIOGECO, INRA, University of Bordeaux, 69 route d'Arcachon, 33610, Cestas, France
| | - Olivier Fabreguettes
- BIOGECO, INRA, University of Bordeaux, 69 route d'Arcachon, 33610, Cestas, France
| | - Cyril Dutech
- BIOGECO, INRA, University of Bordeaux, 69 route d'Arcachon, 33610, Cestas, France
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McTaggart LR, Brown EM, Richardson SE. Phylogeographic Analysis of Blastomyces dermatitidis and Blastomyces gilchristii Reveals an Association with North American Freshwater Drainage Basins. PLoS One 2016; 11:e0159396. [PMID: 27428521 PMCID: PMC4948877 DOI: 10.1371/journal.pone.0159396] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/03/2016] [Indexed: 11/25/2022] Open
Abstract
Blastomyces dermatitidis and Blastomyces gilchristii are dimorphic fungal pathogens that cause serious pulmonary and systemic infections in humans. Although their natural habitat is in the environment, little is known about their specific ecologic niche(s). Here, we analyzed 25 microsatellite loci from 169 strains collected from various regions throughout their known endemic range in North America, representing the largest and most geographically diverse collection of isolates studied to date. Genetic analysis of multilocus microsatellite data divided the strains into four populations of B. dermatitidis and four populations of B. gilchristii. B. dermatitidis isolates were recovered from areas throughout North America, while the B. gilchristii strains were restricted to Canada and some northern US states. Furthermore, the populations of both species were associated with major freshwater drainage basins. The four B. dermatitidis populations were partitioned among (1) the Nelson River drainage basin, (2) the St. Lawrence River and northeast Atlantic Ocean Seaboard drainage basins, (3) the Mississippi River System drainage basin, and (4) the Gulf of Mexico Seaboard and southeast Atlantic Ocean Seaboard drainage basins. A similar partitioning of the B. gilchristii populations was observed among the more northerly drainage basins only. These associations suggest that the ecologic niche where the sexual reproduction, growth, and dispersal of B. dermatitidis and B. gilchristii occur is intimately linked to freshwater systems. For most populations, sexual reproduction was rare enough to produce significant linkage disequilibrium among loci but frequent enough that mating-type idiomorphic ratios were not skewed from 1:1. Furthermore, the evolutionary divergence of B. dermatitidis and B. gilchristii was estimated at 1.9 MYA during the Pleistocene epoch. We suggest that repeated glaciations during the Pleistocene period and resulting biotic refugia may have provided the impetus for speciation as theorized for other species associated with temperate freshwater systems.
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Affiliation(s)
- Lisa R. McTaggart
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- * E-mail:
| | - Elizabeth M. Brown
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Susan E. Richardson
- Public Health Laboratories Toronto, Public Health Ontario, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Microbiology, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Delmas CEL, Fabre F, Jolivet J, Mazet ID, Richart Cervera S, Delière L, Delmotte F. Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew. Evol Appl 2016; 9:709-25. [PMID: 27247621 PMCID: PMC4869412 DOI: 10.1111/eva.12368] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/27/2016] [Indexed: 01/29/2023] Open
Abstract
An understanding of the evolution of pathogen quantitative traits in response to host selective pressures is essential for the development of durable management strategies for resistant crops. However, we still lack experimental data on the effects of partial host resistance on multiple phenotypic traits (aggressiveness) and evolutionary strategies in pathogens. We performed a cross‐inoculation experiment with four grapevine hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola) sampled from susceptible and partially resistant grapevine varieties. We analysed the neutral and adaptive genetic differentiation of five quantitative traits relating to pathogen transmission. Isolates from resistant hosts were more aggressive than isolates from susceptible hosts, as they had a shorter latency period and higher levels of spore production. This pattern of adaptation contrasted with the lack of neutral genetic differentiation, providing evidence for directional selection. No specificity for a particular host variety was detected. Adapted isolates had traits that were advantageous on all resistant varieties. There was no fitness cost associated with this genetic adaptation, but several trade‐offs between pathogen traits were observed. These results should improve the accuracy of prediction of fitness trajectories for this biotrophic pathogen, an essential element for the modelling of durable deployment strategies for resistant varieties.
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Affiliation(s)
- Chloé E L Delmas
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Frédéric Fabre
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Jérôme Jolivet
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Isabelle D Mazet
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Sylvie Richart Cervera
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Laurent Delière
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - François Delmotte
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
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Thach T, Ali S, de Vallavieille-Pope C, Justesen A, Hovmøller M. Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past. Fungal Genet Biol 2016; 87:1-8. [DOI: 10.1016/j.fgb.2015.12.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 12/23/2022]
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Ashu EE, Xu J. The roles of sexual and asexual reproduction in the origin and dissemination of strains causing fungal infectious disease outbreaks. INFECTION GENETICS AND EVOLUTION 2015; 36:199-209. [PMID: 26394109 DOI: 10.1016/j.meegid.2015.09.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/16/2015] [Accepted: 09/18/2015] [Indexed: 12/15/2022]
Abstract
Sexual reproduction commonly refers to the reproductive process in which genomes from two sources are combined into a single cell through mating and then the zygote genomes are partitioned to progeny cells through meiosis. Reproduction in the absence of mating and meiosis is referred to as asexual or clonal reproduction. One major advantage of sexual reproduction is that it generates genetic variation among progeny which may allow for faster adaptation of the population to novel and/or stressful environments. However, adaptation to stressful or new environments can still occur through mutation, in the absence of sex. In this review, we analyzed the relative contributions of sexual and asexual reproduction in the origin and spread of strains causing fungal infectious diseases outbreaks. The necessity of sex and the ability of asexual fungi to initiate outbreaks are discussed. We propose a framework that relates the modes of reproduction to the origin and propagation of fungal disease outbreaks. Our analyses suggest that both sexual and asexual reproduction can play critical roles in the origin of outbreak strains and that the rapid spread of outbreak strains is often accomplished through asexual expansion.
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Affiliation(s)
- Eta Ebasi Ashu
- Department of Biology, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4K1, Canada
| | - Jianping Xu
- Department of Biology, McMaster University, 1280 Main St. W, Hamilton, ON L8S 4K1, Canada.
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Multilocus PCR Assays Elucidate Vegetative Incompatibility Gene Profiles of Cryphonectria parasitica in the United States. Appl Environ Microbiol 2015; 81:5736-42. [PMID: 26070681 DOI: 10.1128/aem.00926-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/08/2015] [Indexed: 11/20/2022] Open
Abstract
Chestnut blight is a devastating disease of Castanea spp. Mycoviruses that reduce virulence (hypovirulence) of the causative agent, Cryphonectria parasitica, can be used to manage chestnut blight. However, vegetative incompatibility (vic) barriers that restrict anastomosis-mediated virus transmission hamper hypovirulence efficacy. In order to effectively determine the vegetative incompatibility genetic structure of C. parasitica field populations, we have designed PCR primer sets that selectively amplify and distinguish alleles for each of the six known diallelic C. parasitica vic genetic loci. PCR assay results were validated using a panel of 64 European tester strains with genetically determined vic genotypes. Analysis of 116 C. parasitica isolates collected from five locations in the eastern United States revealed 39 unique vic genotypes and generally good agreement between PCR and tester strain coculturing assays in terms of vic diversity and genotyping. However, incongruences were observed for isolates from multiple locations and suggested that the coculturing assay can overestimate diversity at the six known vic loci. The availability of molecular tools for rapid and precise vic genotyping significantly improves the ability to predict and evaluate the efficacy of hypovirulence and related management strategies.
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Burokiene D, Prospero S, Jung E, Marciulyniene D, Moosbrugger K, Norkute G, Rigling D, Lygis V, Schoebel CN. Genetic population structure of the invasive ash dieback pathogen Hymenoscyphus fraxineus in its expanding range. Biol Invasions 2015. [DOI: 10.1007/s10530-015-0911-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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Walker AS, Gladieux P, Decognet V, Fermaud M, Confais J, Roudet J, Bardin M, Bout A, C. Nicot P, Poncet C, Fournier E. Population structure and temporal maintenance of the multihost fungal pathogenBotrytis cinerea: causes and implications for disease management. Environ Microbiol 2014; 17:1261-74. [DOI: 10.1111/1462-2920.12563] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/04/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Anne-Sophie Walker
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Pierre Gladieux
- CNRS, UMR 8079 Ecologie Systématique Evolution; Bâtiment 360 Orsay F-91405 France
- University of Paris-Sud; Orsay F-91405 France
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
| | - Véronique Decognet
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Marc Fermaud
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Johann Confais
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Jean Roudet
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Marc Bardin
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Alexandre Bout
- INRA, UMR 1355 ISA, TEAPEA; Sophia-Antipolis F-06903 France
| | - Philippe C. Nicot
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | | | - Elisabeth Fournier
- INRA, UMR BGPI; TA A 54/K; Campus International de Baillarguet Montpellier F-34398 France
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Ciampi-Guillardi M, Baldauf C, Souza AP, Silva-Junior GJ, Amorim L. Recent introduction and recombination in Colletotrichum acutatum populations associated with citrus postbloom fruit drop epidemics in São Paulo, Brazil. PHYTOPATHOLOGY 2014; 104:769-778. [PMID: 24423403 DOI: 10.1094/phyto-06-13-0165-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Citrus crops in São Paulo State, Brazil, have been severely affected by postbloom fruit drop disease (PFD), which is caused by Colletotrichum acutatum. This disease leads to the drop of up to 100% of young fruits. Previous studies have assumed that this pathogen exhibits a clonal reproductive mode, although no population genetic studies have been conducted so far. Thus, the genetic structure of six C. acutatum populations from sweet orange orchards showing PFD symptoms was determined using nine microsatellite markers, enabling inference on predominant mode of reproduction. C. acutatum populations exhibit a nearly panmictic genetic structure and a high degree of admixture, indicating either ongoing contemporary gene flow at a regional scale or a recent introduction from a common source, since this pathogen was introduced in Brazil only very recently. Sharing haplotypes among orchards separated by 400 km suggests the natural dispersal of fungal propagules, with the possible involvement of pollinators. A significant population expansion was detected, which was consistent with an increase in host density associated with crop expansion toward new areas across the state. Findings of moderate to high levels of haplotypic diversity and gametic equilibrium suggest that recombination might play an important role in these pathogen populations, possibly via parasexual reproduction or a cryptic sexual cycle. This study provides additional tools for epidemiological studies of C. acutatum to improve prevention and management strategies for this disease.
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Feau N, Dutech C, Brusini J, Rigling D, Robin C. Multiple introductions and recombination in Cryphonectria hypovirus 1: perspective for a sustainable biological control of chestnut blight. Evol Appl 2014; 7:580-96. [PMID: 24944571 PMCID: PMC4055179 DOI: 10.1111/eva.12157] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/26/2022] Open
Abstract
Cryphonectria hypovirus 1 (CHV1) is a mycovirus which decreases the virulence of its fungal host Cryphonectria parasitica, the causal agent of chestnut blight recently introduced in Europe. The understanding of the evolutionary processes which have shaped CHV1 populations in Europe is required to develop a sustainable biocontrol strategy targeting chestnut blight and effective in European chestnut forests. To retrace the evolutionary history of CHV1, we analyzed sequences from two genomic regions on a collection of 55 CHV1 strains from France and northern Spain, two countries where multiple introductions of C. parasitica occurred. Several recombination events and variable selection pressures contributed to CHV1 evolution, agreeing with a non-clock-like diversification rate. These two mechanisms may be at the origin of CHV1 population diversity observed in western Europe. Considering the actual prevalence of CHV1 and its association with host genotypes, multiple introductions of CHV1 may have occurred in Europe, some of them directly from Asia and some of them through North America. Although some viral strains remained with low frequency in their introduction area, multiple infections might have allowed homologous recombination within parental sequences. Some of these recombinant lineages are associated with the spread of CHV1 in European regions.
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Affiliation(s)
- Nicolas Feau
- INRA, UMR1202 BIOGECO F-33610, Cestas, France ; University Bordeaux, BIOGECO, UMR 1202 F-33400, Talence, France ; TAIGA-Lab, Forest Sciences Centre, University of British Columbia #3618-2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Cyril Dutech
- INRA, UMR1202 BIOGECO F-33610, Cestas, France ; University Bordeaux, BIOGECO, UMR 1202 F-33400, Talence, France
| | - Jérémie Brusini
- INRA, UMR1202 BIOGECO F-33610, Cestas, France ; University Bordeaux, BIOGECO, UMR 1202 F-33400, Talence, France ; Department of Ecology and Evolutionary Biology, Earth and Marine Sciences Building, University of California Santa Cruz, CA, 95064, USA
| | - Daniel Rigling
- WSL Swiss Federal Research Institute CH-8903, Birmensdorf, Switzerland
| | - Cécile Robin
- INRA, UMR1202 BIOGECO F-33610, Cestas, France ; University Bordeaux, BIOGECO, UMR 1202 F-33400, Talence, France
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Saleh D, Milazzo J, Adreit H, Fournier E, Tharreau D. South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae. THE NEW PHYTOLOGIST 2014; 201:1440-1456. [PMID: 24320224 PMCID: PMC4265293 DOI: 10.1111/nph.12627] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/23/2013] [Indexed: 05/11/2023]
Abstract
• Inferring invasion routes and identifying reservoirs of diversity of plant pathogens are essential in proposing new strategies for their control. Magnaporthe oryzae, the fungus responsible for rice blast disease, has invaded all rice growing areas. Virulent genotypes regularly (re)emerge, causing rapid resistance breakdowns. However, the world-wide genetic subdivision of M. oryzae populations on rice and its past history of invasion have never been elucidated. • In order to investigate the centers of diversity, origin and migration of M. oryzae on rice, we analyzed the genetic diversity of 55 populations from 15 countries. • Three genetic clusters were identified world-wide. Asia was the center of diversity and the origin of most migrations to other continents. In Asia, two centers of diversity were revealed in the Himalayan foothills: South China-Laos-North Thailand, and western Nepal. Sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all M. oryzae populations on rice. • Our results suggest a scenario of early evolution of M. oryzae on rice that matches the past history of rice domestication. This study confirms that crop domestication may have considerable influence on the pestification process of natural enemies.
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Affiliation(s)
- Dounia Saleh
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
- INRA, UMR BGPITA A54/K, F 34398, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
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41
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Ali S, Gladieux P, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. Origin, migration routes and worldwide population genetic structure of the wheat yellow rust pathogen Puccinia striiformis f.sp. tritici. PLoS Pathog 2014; 10:e1003903. [PMID: 24465211 PMCID: PMC3900651 DOI: 10.1371/journal.ppat.1003903] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/12/2013] [Indexed: 11/24/2022] Open
Abstract
Analyses of large-scale population structure of pathogens enable the identification of migration patterns, diversity reservoirs or longevity of populations, the understanding of current evolutionary trajectories and the anticipation of future ones. This is particularly important for long-distance migrating fungal pathogens such as Puccinia striiformis f.sp. tritici (PST), capable of rapid spread to new regions and crop varieties. Although a range of recent PST invasions at continental scales are well documented, the worldwide population structure and the center of origin of the pathogen were still unknown. In this study, we used multilocus microsatellite genotyping to infer worldwide population structure of PST and the origin of new invasions based on 409 isolates representative of distribution of the fungus on six continents. Bayesian and multivariate clustering methods partitioned the set of multilocus genotypes into six distinct genetic groups associated with their geographical origin. Analyses of linkage disequilibrium and genotypic diversity indicated a strong regional heterogeneity in levels of recombination, with clear signatures of recombination in the Himalayan (Nepal and Pakistan) and near-Himalayan regions (China) and a predominant clonal population structure in other regions. The higher genotypic diversity, recombinant population structure and high sexual reproduction ability in the Himalayan and neighboring regions suggests this area as the putative center of origin of PST. We used clustering methods and approximate Bayesian computation (ABC) to compare different competing scenarios describing ancestral relationship among ancestral populations and more recently founded populations. Our analyses confirmed the Middle East-East Africa as the most likely source of newly spreading, high-temperature-adapted strains; Europe as the source of South American, North American and Australian populations; and Mediterranean-Central Asian populations as the origin of South African populations. Although most geographic populations are not markedly affected by recent dispersal events, this study emphasizes the influence of human activities on recent long-distance spread of the pathogen.
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Affiliation(s)
- Sajid Ali
- INRA UR 1290 BIOGER-CPP, Thiverval-Grignon, France
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture, Peshawar, Pakistan
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | - Pierre Gladieux
- UMR 8079 Ecologie Systematique Evolution, Univ. Paris-Sud., CNRS-F, Orsay, France
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Marc Leconte
- INRA UR 1290 BIOGER-CPP, Thiverval-Grignon, France
| | | | | | | | - Jérôme Enjalbert
- INRA UMR 320 Génétique Végétale, Ferme du Moulon, Gif sur Yvette, France
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42
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Peters FS, Busskamp J, Prospero S, Rigling D, Metzler B. Genetic diversification of the chestnut blight fungus Cryphonectria parasitica and its associated hypovirus in Germany. Fungal Biol 2013; 118:193-210. [PMID: 24528641 DOI: 10.1016/j.funbio.2013.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 11/06/2013] [Accepted: 11/20/2013] [Indexed: 10/25/2022]
Abstract
Chestnut blight in south-western Germany was first reported in 1992 and is since expanding in distribution. Here we investigated the invasion history of Cryphonectria parasitica and its associated hypovirus. For this, we characterized 284 isolates collected between 1992 and 2012 for hypovirulence, vegetative compatibility (vc), mating type, and microsatellite haplotype. A total of 27 haplotypes and 15 vc types were observed, although the C. parasitica population analyzed is currently dominated to 50 % by one haplotype and to 64 % by the vc type EU-2. Structure analysis indicated two divergent genetic pools. Over 66 % of the haplotypes belonged to a pool probably originating from northern Italy. Further diversification is expected due to ongoing sexual recombination, but also to new migration and additional introductions. Cryphonectria hypovirus 1 (CHV-1) was found in four of five C. parasitica populations from Baden-Württemberg. Genetic analysis of the 35 CHV-1 isolates obtained revealed that they all belong to the German subtype, although they have clearly diverged from the first German hypovirus isolated in 1992. Our study suggests that C. parasitica has been introduced into Germany several times from two different gene pools, whereas the hypovirus most probably has a single origin.
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Affiliation(s)
- Franziska S Peters
- FVA Forest Research Institute of Baden-Württemberg (FVA-BW), Dept. Forest Protection, Wonnhaldestr. 4, D-79100 Freiburg, Germany.
| | - Johanna Busskamp
- FVA Forest Research Institute of Baden-Württemberg (FVA-BW), Dept. Forest Protection, Wonnhaldestr. 4, D-79100 Freiburg, Germany.
| | - Simone Prospero
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
| | - Daniel Rigling
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
| | - Berthold Metzler
- FVA Forest Research Institute of Baden-Württemberg (FVA-BW), Dept. Forest Protection, Wonnhaldestr. 4, D-79100 Freiburg, Germany.
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Darras H, Leniaud L, Aron S. Large-scale distribution of hybridogenetic lineages in a Spanish desert ant. Proc Biol Sci 2013; 281:20132396. [PMID: 24225458 DOI: 10.1098/rspb.2013.2396] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recently, a unique case of hybridogenesis at a social level was reported in local populations of the desert ants Cataglyphis. Queens mate with males originating from a different genetic lineage than their own to produce hybrid workers, but they use parthenogenesis for the production of reproductive offspring (males and females). As a result, non-reproductive workers are all inter-lineage hybrids, whereas the sexual line is purely maternal. Here, we show that this unorthodox reproductive system occurs in all populations of the ant Cataglyphis hispanica. Remarkably, workers are hybrids of the same two genetic lineages along a 400 km transect crossing the whole distribution range of the species. These results indicate that social hybridogenesis in C. hispanica allows their maintenance over time and across a large geographical scale of two highly divergent genetic lineages, despite their constant hybridization. The widespread distribution of social hybridogenesis in C. hispanica supports that this reproductive strategy has been evolutionarily conserved over a long period.
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Affiliation(s)
- Hugo Darras
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, , Avenue Franklin D. Roosevelt, 50, CP 160/12, Brussels 1050, Belgium, I.R.B.I. UMR CNRS 7261, Faculté des Sciences, Université François Rabelais Tours, 37200 Tours, France
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44
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Garbelotto M, Guglielmo F, Mascheretti S, Croucher PJP, Gonthier P. Population genetic analyses provide insights on the introduction pathway and spread patterns of the North American forest pathogen Heterobasidion irregulare in Italy. Mol Ecol 2013; 22:4855-69. [PMID: 24033583 DOI: 10.1111/mec.12452] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 07/12/2013] [Accepted: 07/15/2013] [Indexed: 11/26/2022]
Abstract
A population genetics approach is used to identify the most likely introduction site and introduction pathway for the North American forest pathogen Heterobasidion irregulare using 101 isolates from six sites in Italy and 34 isolates from five sites in North America. Diversity indices based on sequences from ten loci indicate the highest diversity in Italy is found in Castelfusano/Castelporziano and that diversity progressively decreases with increasing distance from that site. AMOVA, Bayesian clustering and principal coordinates analyses based on 12 SSR loci indicate high levels of gene flow among sites, high frequency of admixing, and fail to identify groups of genotypes exclusive to single locations. Cumulatively, these analyses suggest the current infestation is the result of multiple genotypes expanding their range from a single site. Based on two sequenced loci, a single source site in North America could provide enough variability to explain the variability observed in Italy. These results support the notion that H. irregulare was introduced originally in Castelporziano: because Castelporziano has been sealed off from the rest of the world for centuries except for a camp set up by the US military in 1944, we conclude the fungus may have been transported in infected wood used by the military. Finally, spatial autocorrelation analyses using SSR data indicate a significant under-dispersion of alleles up to 0.5-10 km, while a significant overdispersion of alleles was detected at distances over 80 km: these ranges can be used to make predictions on the likely dispersal potential of the invasive pathogen.
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Affiliation(s)
- M Garbelotto
- Department of Environmental Science, Policy and Management, University of California at Berkeley, 37 Mulford Hall, Berkeley, CA, 94720, USA
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45
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Prospero S, Lutz A, Tavadze B, Supatashvili A, Rigling D. Discovery of a new gene pool and a high genetic diversity of the chestnut blight fungus Cryphonectria parasitica in Caucasian Georgia. INFECTION GENETICS AND EVOLUTION 2013; 20:131-9. [PMID: 23994123 DOI: 10.1016/j.meegid.2013.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/08/2013] [Accepted: 08/12/2013] [Indexed: 11/24/2022]
Abstract
In this study, we investigated the population genetic structure and possible origins of the plant pathogen Cryphonectria parasitica in Caucasian Georgia, a region within the centre of origin of the host species Castanea sativa. A total of 427 C. parasitica isolates from nine populations were genotyped at 10 microsatellite loci. A high genetic diversity was detected, but the overall Georgian population was dominated by three haplotypes which were present in most individual populations. Two of them have not been previously found in Europe. Bayesian clustering analysis and principal component analysis could not identify their source population, neither in Asia nor in North America. On the other hand, one haplotype is frequent in Central Europe and probably naturally invaded Caucasian Georgia from neighbouring Turkey. Seventy-three haplotypes were unique to specific populations, and 66 of them were represented by a single isolate. Allele patterns suggest that most of these haplotypes emerged locally through sexual recombination between haplotypes of the Georgian and the central European gene pool. Due to the high incidence of haplotypes not otherwise present in Europe, Caucasian Georgia represents an additional source of diversity for the European C. parasitica population.
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Affiliation(s)
- S Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland.
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46
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Fontaine MC, Gladieux P, Hood ME, Giraud T. History of the invasion of the anther smut pathogen on Silene latifolia in North America. THE NEW PHYTOLOGIST 2013; 198:946-956. [PMID: 23406496 DOI: 10.1111/nph.12177] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 01/09/2013] [Indexed: 06/01/2023]
Abstract
Understanding the routes of pathogen introduction contributes greatly to efforts to protect against future disease emergence. Here, we investigated the history of the invasion in North America by the fungal pathogen Microbotryum lychnidis-dioicae, which causes the anther smut disease on the white campion Silene latifolia. This system is a well-studied model in evolutionary biology and ecology of infectious disease in natural systems. Analyses based on microsatellite markers show that the introduced American M. lychnidis-dioicae probably came from Scotland, from a single population, and thus suffered from a drastic bottleneck compared with genetic diversity in the native European range. The pattern in M. lychnidis-dioicae contrasts with that found by previous studies in its host plant species S. latifolia, also introduced in North America. In the plant, several European lineages have been introduced from across Europe. The smaller number of introductions for M. lychnidis-dioicae probably relates to its life history traits, as it is an obligate, specialized pathogen that is neither transmitted by the seeds nor persistent in the environment. The results show that even a nonagricultural, biotrophic, and insect-vectored pathogen suffering from a very strong bottleneck can successfully establish populations on its introduced host.
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Affiliation(s)
- Michael C Fontaine
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Pierre Gladieux
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
- Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Michael E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - Tatiana Giraud
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR8079, Orsay Cedex, F-91405, France
- CNRS, UMR 8079, Orsay Cedex, F-91405, France
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47
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Fontaine MC, Austerlitz F, Giraud T, Labbé F, Papura D, Richard-Cervera S, Delmotte F. Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogenPlasmopara viticola. Mol Ecol 2013; 22:2771-86. [DOI: 10.1111/mec.12293] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Michael C. Fontaine
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Univ Paris Diderot; Sorbonne Paris Cité F-75231 Paris Cedex 5 France
| | - Fréderic Austerlitz
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Univ Paris Diderot; Sorbonne Paris Cité F-75231 Paris Cedex 5 France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
| | - Frédéric Labbé
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
| | - Daciana Papura
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
| | - Sylvie Richard-Cervera
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
| | - François Delmotte
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
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48
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Morin L, Gomez DR, Evans KJ, Neill TM, Mahaffee WF, Linde CC. Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0413-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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49
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Abstract
Exotic, invasive pathogens have emerged repeatedly and continue to emerge to threaten the world's forests. Ecosystem structure and function can be permanently changed when keystone tree species such as the American chestnut (Castanea dentata) are eliminated from a whole range by disease. The fungal ascomycete pathogen Cryphonectria parasitica is responsible for causing chestnut blight. Once the pathogen was introduced into the Eastern US, where chestnuts were predominant, chestnuts were all but eliminated. This pathogen is currently causing extensive damage in Europe. A study in this issue of Molecular Ecology sheds new light on the pattern and process of emergence of this devastating plant pathogen (Dutech et al. 2012). The authors used microsatellite markers to investigate the evolutionary history of C. parasitica populations introduced into North America and Europe. To infer sources of migrants and the migration events, the authors included putative source populations endemic to China and Japan, inferred potentially unsampled populations and conducted a multivariate population genetic and complex ABC analysis. Cryphonectria parasitica emerges as an example of an introduced pathogen with limited genotypic diversity and some admixture in the invaded ranges, yet repeated invasions into different areas of Europe and the United States. This work sheds new light on the emergence of C. parasitica providing compelling evidence that this pathogen emerged by repeated migration and occasional admixture.
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Affiliation(s)
- Niklaus J Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service (ARS), Corvallis, OR 97330, USA.
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50
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Bryner SF, Rigling D, Brunner PC. Invasion history and demographic pattern of Cryphonectria hypovirus 1 across European populations of the chestnut blight fungus. Ecol Evol 2012; 2:3227-41. [PMID: 23301186 PMCID: PMC3539014 DOI: 10.1002/ece3.429] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/09/2012] [Accepted: 10/13/2012] [Indexed: 01/16/2023] Open
Abstract
We reconstructed the invasion history of the fungal virus Cryphonectria hypovirus 1 (CHV-1) in Europe, which infects the chestnut blight fungus Cryphonectria parasitica. The pattern of virus evolution was inferred based on nucleotide sequence variation from isolates sampled across a wide area in Europe at different points in time. Phylogeny and time estimates suggested that CHV-1 was introduced together with its fungal host to Europe and that it rapidly colonized the central range along the south facing slopes of the Alps and the north-east facing slopes of the Dinaric Alps. These central populations were the source for two waves of simultaneous invasions toward the southern Balkans and Turkey, as indicated by migration rates. Our results showed that the evolutionary scenarios for CHV-1 and C. parasitica were spatially congruent. As infection with CHV-1 reduces the pathogenicity of C. parasitica toward the chestnut tree, CHV-1 invasions of the newly established C. parasitica populations probably prevented the development of devastating chestnut blight epidemics in Europe. We propose that in this, and supposedly in other pathosystems, geographic, vegetation-related, demographic, economic, and political factors may help explain the correlated invasion pattern of a parasite and its host.
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Affiliation(s)
- Sarah F Bryner
- WSL Swiss Federal Research Institute CH-8903, Birmensdorf, Switzerland
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