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Romon-Ochoa P, Samal P, Gorton C, Lewis A, Chitty R, Eacock A, Krzywinska E, Crampton M, Pérez-Sierra A, Biddle M, Jones B, Ward L. Cryphonectria parasitica Detections in England, Jersey, and Guernsey during 2020-2023 Reveal Newly Affected Areas and Infections by the CHV1 Mycovirus. J Fungi (Basel) 2023; 9:1036. [PMID: 37888292 PMCID: PMC10607933 DOI: 10.3390/jof9101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
In England, Cryphonectria parasitica was detected for the first time in 2011 in a nursery and in 2016 in the wider environment. Surveys between 2017 and 2020 identified the disease at different sites in Berkshire, Buckinghamshire, Cornwall, Derbyshire, Devon, Dorset, London, West Sussex, and the island of Jersey, while the present study comprises the results of the 2020-2023 survey with findings in Derbyshire, Devon, Kent, Nottinghamshire, Herefordshire, Leicestershire, London, West Sussex, and the islands of Jersey and Guernsey. A total of 226 suspected samples were collected from 72 surveyed sites, as far north as Edinburgh and as far west as Plymouth (both of which were negative), and 112 samples tested positive by real-time PCR and isolation from 35 sites. The 112 isolates were tested for the vegetative compatibility group (VCG), mating type, and Cryphonectria hypovirus 1 (CHV1). Twelve VCGs were identified, with two of them (EU-5 and EU-22) being the first records in the UK. Both mating types were present (37% MAT-1 and 63% MAT-2), but only one mating type was present per site and VCG, and perithecia were never observed. Cryphonectria hypovirus 1 (CHV1), consistently subtype-I haplotype E-5, was detected in three isolates at a low concentration (5.9, 21.1, and 33.0 ng/µL) from locations in London, Nottinghamshire, and Devon.
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Affiliation(s)
- Pedro Romon-Ochoa
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Pankajini Samal
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Caroline Gorton
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Alex Lewis
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Ruth Chitty
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Amy Eacock
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Elzbieta Krzywinska
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Michael Crampton
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Ana Pérez-Sierra
- Forest Research, THDAS-Tree Health Diagnostics and Advisory Service, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (C.G.); (A.L.); (R.C.); (A.E.); (E.K.); (M.C.); (A.P.-S.)
| | - Mick Biddle
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
| | - Ben Jones
- Forestry Commission, 620 Bristol Business Park, Bristol BS16 1EJ, UK;
| | - Lisa Ward
- Forest Research, Plant Pathology Department, Alice Holt Research Station, Farnham, Surrey GU10 4LH, UK; (P.S.); (M.B.); (L.W.)
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Nuskern L, Stojanović M, Milanović-Litre M, Šibenik T, Ježić M, Poljak I, Ćurković-Perica M. Filling the Gap in Southern Europe—Diversity of Cryphonectria parasitica and Associated Mycovirus (Cryphonectria hypovirus 1) in Montenegro. J Fungi (Basel) 2022; 8:jof8060552. [PMID: 35736034 PMCID: PMC9224863 DOI: 10.3390/jof8060552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
Cryphonectria parasitica is an invasive fungal pathogen that causes blight disease on chestnut trees. Its destructive effect can be controlled with naturally occurring mycovirus Cryphonectria hypovirus 1 (CHV1). To date, the spread of C. parasitica and CHV1 in Europe is fairly well documented, but there are still several unexplored regions. Thus, we sampled blight cankers from four sweet chestnut populations in Bay of Kotor and Lake Skadar regions in Montenegro. We determined vegetative compatibility (vc) type and mating-type diversity using molecular vic and MAT1 genotyping, as well as confirming the presence of CHV1 by RT-PCR. We identified 11 vc types, with EU-12 being the dominant one represented by 58.2% of all fungal isolates. The Shannon diversity index ranged from 0.93 to 1.47. Both mating types of C. parasitica were found in all four populations. The prevalence of CHV1 ranged from 15% to 40%. All CHV1 isolates belonged to Italian subtype I of CHV1 and were closely related, with relatively recent common ancestors. Our results indicate a longer presence of C. parasitica and CHV1 in Montenegro than previously thought. Natural biocontrol with CHV1 seems to be well established. However, it has the potential for deterioration; thus, close monitoring is required.
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Affiliation(s)
- Lucija Nuskern
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia; (L.N.); (M.M.-L.); (T.Š.); (M.J.)
| | - Milena Stojanović
- Biotechnical Faculty, University of Montenegro, Mihaila Lalića Br. 15, 81000 Podgorica, Montenegro;
| | - Marija Milanović-Litre
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia; (L.N.); (M.M.-L.); (T.Š.); (M.J.)
| | - Tena Šibenik
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia; (L.N.); (M.M.-L.); (T.Š.); (M.J.)
| | - Marin Ježić
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia; (L.N.); (M.M.-L.); (T.Š.); (M.J.)
| | - Igor Poljak
- Department of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska Cesta 23, 10000 Zagreb, Croatia;
| | - Mirna Ćurković-Perica
- Division of Microbiology, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia; (L.N.); (M.M.-L.); (T.Š.); (M.J.)
- Correspondence: ; Tel.: +385-(0)1-4898-076
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Stauber L, Croll D, Prospero S. Temporal changes in pathogen diversity in a perennial plant-pathogen-hyperparasite system. Mol Ecol 2022; 31:2073-2088. [PMID: 35122694 PMCID: PMC9540319 DOI: 10.1111/mec.16386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 11/27/2022]
Abstract
Hyperparasites can affect the evolution of pathosystems by influencing the stability of both pathogen and host populations. However, how pathogens of perennial hosts evolve in the presence of a hyperparasite has rarely been studied. Here, we investigated temporal changes in genetic diversity of the invasive chestnut blight pathogen Cryphonectria parasitica in the presence of its parasitic mycovirus Cryphonectria hypovirus 1 (CHV1). The virus reduces fungal virulence and represents an effective natural biocontrol agent against chestnut blight in Europe. We analysed genome‐wide diversity and CHV1 prevalence in C. parasitica populations in southern Switzerland that were sampled twice at an interval of about 30 years. Overall, we found that both pathogen population structure and CHV1 prevalence were retained over time. The results suggest that recent bottlenecks have influenced the structure of C. parasitica populations in southern Switzerland. Strong balancing selection signals were found at a single vegetative incompatibility (vic) locus, consistent with negative frequency‐dependent selection imposed by the vegetative incompatibility system. High levels of mating among related individuals (i.e., inbreeding) and genetic drift are probably at the origin of imbalanced allele ratios at vic loci and subsequently low vc type diversity. Virus infection rates were stable at ~30% over the study period and we found no significant impact of the virus on fungal population diversity. Consequently, the efficacy of CHV1‐mediated biocontrol was probably retained.
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Affiliation(s)
- Lea Stauber
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland.,Department of Environmental Sciences, University of Basel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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Leigh DM, Peranić K, Prospero S, Cornejo C, Ćurković-Perica M, Kupper Q, Nuskern L, Rigling D, Ježić M. Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections. Virus Evol 2021; 7:veab101. [PMID: 35299787 PMCID: PMC8923234 DOI: 10.1093/ve/veab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus Cryphonectria hypovirus 1 (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (Cryphonectria parasitica), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
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Affiliation(s)
- Deborah M Leigh
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Karla Peranić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Simone Prospero
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Carolina Cornejo
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | | | | | - Lucija Nuskern
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Daniel Rigling
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Marin Ježić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
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Škorić D, Černi S, Ćurković-Perica M, Ježić M, Krajačić M, Šeruga Musić M. Legacy of Plant Virology in Croatia-From Virus Identification to Molecular Epidemiology, Evolution, Genomics and Beyond. Viruses 2021; 13:2339. [PMID: 34960609 PMCID: PMC8707422 DOI: 10.3390/v13122339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 11/16/2022] Open
Abstract
This paper showcases the development of plant virology in Croatia at the University of Zagreb, Faculty of Science, from its beginning in the 1950s until today, more than 70 years later. The main achievements of the previous and current group members are highlighted according to various research topics and fields. Expectedly, some of those accomplishments remained within the field of plant virology, but others make part of a much-extended research spectrum exploring subviral pathogens, prokaryotic plant pathogens, fungi and their viruses, as well as their interactions within ecosystems. Thus, the legacy of plant virology in Croatia continues to contribute to the state of the art of microbiology far beyond virology. Research problems pertinent for directing the future research endeavors are also proposed in this review.
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Affiliation(s)
- Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia; (S.Č.); (M.Ć.-P.); (M.J.); (M.K.); (M.Š.M.)
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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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Vuković R, Liber Z, Ježić M, Sotirovski K, Ćurković-Perica M. Link between epigenetic diversity and invasive status of south-eastern European populations of phytopathogenic fungus Cryphonectria parasitica. Environ Microbiol 2019; 21:4521-4536. [PMID: 31314941 DOI: 10.1111/1462-2920.14742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications may play an important role in invasion and adaptation of clonal and invasive populations to different environments. The aim of this study was to analyse epigenetic diversity and structure within and among populations of invasive pathogenic fungus Cryphonectria parasitica from south-eastern Europe, where one haplotype S12 dominates. The highest level of epigenetic diversity was found in haplotype S1, followed by S2, while the lowest level of epigenetic diversity was found in haplotype S12. Similar pattern of epigenetic diversity was detected in the control, genetically diverse Croatian population where S1 haplotype dominates. In four south-eastern European populations, the highest level of epigenetic diversity was observed in the Italian population, the oldest population in the studied area, while the lowest diversity was found in most recently established Bulgarian population. This relationship between epigenetic diversity and population age implies the important role of epigenetic modifications on the process of invasion. Our data suggest that epigenetic differences might affect the success of expansion of certain haplotype into new regions. Understanding the role of epigenetic processes in expansion and (pre)adaptation of fungal plant pathogens, besides fundamental knowledge, can contribute to development of strategies for control of fungal spread and pathogenesis.
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Affiliation(s)
- Rosemary Vuković
- Department of Biology, J. J. Strossmayer University of Osijek, Osijek, Croatia
| | - Zlatko Liber
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.,Centre of Excellence for Biodiversity and Molecular Plant Breeding, Zagreb, Croatia
| | - Marin Ježić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Kiril Sotirovski
- Faculty of Forestry, Ss. Cyril and Methodius University of Skopje, Skopje, North Macedonia
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