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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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Kuhnert E, Collemare J. A genomic journey in the secondary metabolite diversity of fungal plant and insect pathogens: from functional to population genomics. Curr Opin Microbiol 2022; 69:102178. [PMID: 35870224 DOI: 10.1016/j.mib.2022.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/01/2022] [Accepted: 06/23/2022] [Indexed: 11/03/2022]
Abstract
Fungal pathogens produce a broad array of secondary metabolites (SMs), which allow the fungus to thrive in its natural habitat and gain competitive advantage. Analysis of the genetically encoded blueprints for SM assembly highlighted that only a small portion of the SMs these fungi are capable of producing are known, and even fewer have been investigated for their natural function. Using molecular tools, a lot of progress has been made recently in identifying the blueprint products and linking them to their ecological purpose such as the peptide virulence factor fusaoctaxin A released by Fusarium graminearum during infection of wheat or the F. oxysporum polyketide bikaverin that provides competitive advantage against bacteria in tomato. In addition, population genomics have given particularly important insights into the species-specific plasticity of the SM blueprint arsenal, showcasing the ongoing evolution and adaptation of fungal pathogens. This approach holds promise in inferring roles in pathogenicity of many more fungal SMs.
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Affiliation(s)
- Eric Kuhnert
- Centre of Biomolecular Drug Research (BMWZ), Institute for Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany.
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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Ilyukhin E, Markovskaja S, Elgorban AM, Al-Rejaie SS, Maharachchikumbura SS. Genomic Characteristics and Comparative Genomics Analysis of Parafenestella ontariensis sp. nov. J Fungi (Basel) 2022; 8:jof8070732. [PMID: 35887487 PMCID: PMC9318755 DOI: 10.3390/jof8070732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
A new ascomycetous species of Parafenestella was isolated from Acer negundo during the survey of diseased trees in Southern Ontario, Canada. The species is morphologically similar to other taxa of Cucurbitariacea (Pleosporales). The new species is different from the extant species in the morphology of ascospores, culture characteristics and molecular data. The novel species is described as Parafenestella ontariensis sp. nov. based on morphological and multi-gene phylogenetic analyses using a combined set of ITS, LSU, tef1 and tub2 loci. Additionally, the genome of P. ontariensis was sequenced and analyzed. The phylogenomic analysis confirmed the close relationship of the species to the fenestelloid clades of Cucurbitariaceae. The comparative genomics analysis revealed that the species lifestyle appears to be multitrophic (necrotrophic or hemi-biotrophic) with a capability to turn pathogenic on a corresponding plant host.
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Affiliation(s)
- Evgeny Ilyukhin
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
- Correspondence: or
| | | | - Abdallah M. Elgorban
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Salim S. Al-Rejaie
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Sajeewa S.N. Maharachchikumbura
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China;
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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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A New Double-Stranded RNA Mycovirus in Cryphonectria naterciae Is Able to Cross the Species Barrier and Is Deleterious to a New Host. J Fungi (Basel) 2021; 7:jof7100861. [PMID: 34682282 PMCID: PMC8538617 DOI: 10.3390/jof7100861] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 12/25/2022] Open
Abstract
Cryphonectria is a fungal genus associated with economically significant disease of trees. Herein we characterized a novel double-stranded RNA virus from the fungal species Cryphonectria naterciae, a species unexplored as a virus host. De novo assembly of RNA-seq data and Sanger sequencing of RACE (rapid amplification of cDNA ends) clones gave the complete, non-segmented genome (10,164 bp) of the virus termed Cryphonectria naterciae fusagravirus (CnFGV1) that was phylogenetically placed within the previously proposed viral family Fusagraviridae. Of 31 field-collected strains of C. naterciae, 40% tested CnFGV1-positive. Cocultivation resulted in within-species transmission of CnFGV1 to virus-free strains of C. naterciae. Comparison of the mycelium phenotype and the growth rate of CnFGV1-infected and virus-free isogenic strains revealed frequent sectoring and growth reduction in C. naterciae upon virus infection. Co-culturing also led to cross-species transmission of CnFGV1 to Cryphonectria carpinicola and Cryphonectria radicalis, but not to Cryphonectria parasitica. The virus-infected C. naterciae and the experimentally infected Cryphonectria spp. readily transmitted CnFGV1 through asexual spores to the next generation. CnFGV1 strongly reduced conidiation and in some cases vegetative growth of C. carpinicola, which is involved in the European hornbeam disease. This study is the first report of a fusagravirus in the family Cryphonectriaceae and lays the groundwork for assessing a hypovirulence effect of CnFGV1 against the hornbeam decline in Europe.
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Singh NK, Badet T, Abraham L, Croll D. Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen. BMC Genomics 2021; 22:393. [PMID: 34044766 PMCID: PMC8157644 DOI: 10.1186/s12864-021-07691-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors and pathogens have repeatedly escaped recognition due rapid evolutionary change at pathogen virulence loci (i.e. effector genes). The presence of transposable elements (TEs) in close physical proximity of effector genes can have important consequences for gene regulation and sequence evolution. Species-wide investigations of effector gene loci remain rare hindering our ability to predict pathogen evolvability. RESULTS Here, we performed genome-wide association studies (GWAS) on a highly polymorphic mapping population of 120 isolates of Zymoseptoria tritici, the most damaging pathogen of wheat in Europe. We identified a major locus underlying significant variation in reproductive success of the pathogen and damage caused on the wheat cultivar Claro. The most strongly associated locus is intergenic and flanked by genes encoding a predicted effector and a serine-type endopeptidase. The center of the locus contained a highly dynamic region consisting of multiple families of TEs. Based on a large global collection of assembled genomes, we show that the virulence locus has undergone substantial recent sequence evolution. Large insertion and deletion events generated length variation between the flanking genes by a factor of seven (5-35 kb). The locus showed also strong signatures of genomic defenses against TEs (i.e. RIP) contributing to the rapid diversification of the locus. CONCLUSIONS In conjunction, our work highlights the power of combining GWAS and population-scale genome analyses to investigate major effect loci in pathogens.
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Affiliation(s)
- Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000, Neuchâtel, Switzerland.
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Nicoletti R, Beccaro GL, Sekara A, Cirillo C, Di Vaio C. Endophytic Fungi and Ecological Fitness of Chestnuts. PLANTS (BASEL, SWITZERLAND) 2021; 10:542. [PMID: 33805750 PMCID: PMC7999096 DOI: 10.3390/plants10030542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 11/17/2022]
Abstract
Chestnuts (Castanea spp.) are plants of relevant economic interest in the agro-sylvicultural contexts of mountain regions throughout the temperate zone, particularly in the northern hemisphere. In recent years, several biological adversities have repeatedly endangered species belonging to this genus, calling for coordinated actions addressed to contrast their decline. These actions have mainly focused on the control of key pests/pathogens and the improvement of resistance/tolerance by the plant host, while the role of microorganisms as mediators of interactions between plants and the noxious agents has been less considered, essentially by reason of a limited knowledge on their ecological impact. In line with the increasing awareness of the basic importance of microbial symbionts in regulating plant fitness in both natural and crop contexts, this paper offers an overview on the occurrence and effects of endophytic fungi of chestnuts.
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Affiliation(s)
- Rosario Nicoletti
- Research Center for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics, 81100 Caserta, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Gabriele Loris Beccaro
- Department of Agricultural, Forest and Food Sciences, University of Turin, 10095 Grugliasco, Italy;
| | - Agnieszka Sekara
- Department of Horticulture, University of Agriculture, 31-425 Krakow, Poland;
| | - Chiara Cirillo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Claudio Di Vaio
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
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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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Li C, Cheng P, Zheng L, Li Y, Chen Y, Wen S, Yu G. Comparative genomics analysis of two banana Fusarium wilt biocontrol endophytes Bacillus subtilis R31 and TR21 provides insights into their differences on phytobeneficial trait. Genomics 2021; 113:900-909. [PMID: 33592313 DOI: 10.1016/j.ygeno.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 02/08/2021] [Indexed: 01/27/2023]
Abstract
Fusarium wilt of banana is considered one of the most destructive plant diseases. Bacillus subtilis R31 and TR21, isolated from Dendrobium sp. leaves, exhibit different phytobeneficial effects on banana Fusarium wilt bio-controlling. Here, we performed genome sequencing and comparative genomics analysis of R31 and TR21 to enhance our understanding of the different phytobeneficial traits. These results revealed that the strain-specific genes of R31 involved in sporulation, quorum sensing, and antibiotic synthesis allow R31 to present a better capacity of sporulation, rhizosphere adaptation, and quorum sensing than TR21. Selective pressure analysis indicated that the glycosylase and endo-alpha-(1- > 5)-L-arabinanase genes were strong positive selected, which may contribute to the TR21 to colonize well in banana's vascular bundles. Altogether, our findings presented here should advance further agricultural application of R31 and TR21 as two promising resources of plant growth promotion and biological control via genetic engineering.
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Affiliation(s)
- Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
| | - Li Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China
| | - Yongjian Li
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Yanhong Chen
- Zhuhai Modern Agriculture Development Center, Zhuhai 519075, People's Republic of China
| | - Shuheng Wen
- Guangdong Geolong Biotechnology Co., Ltd., Zhuhai 519050, People's Republic of China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, People's Republic of China.
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