51
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Multi-locus phylogeny and pathogenicity of Stemphylium species associated with legumes in Australia. Mycol Prog 2020. [DOI: 10.1007/s11557-020-01566-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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52
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Hybridization and introgression drive genome evolution of Dutch elm disease pathogens. Nat Ecol Evol 2020; 4:626-638. [PMID: 32123324 DOI: 10.1038/s41559-020-1133-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022]
Abstract
Hybridization and the resulting introgression can drive the success of invasive species via the rapid acquisition of adaptive traits. The Dutch elm disease pandemics in the past 100 years were caused by three fungal lineages with permeable reproductive barriers: Ophiostoma ulmi, Ophiostoma novo-ulmi subspecies novo-ulmi and Ophiostoma novo-ulmi subspecies americana. Using whole-genome sequences and growth phenotyping of a worldwide collection of isolates, we show that introgression has been the main driver of genomic diversity and that it impacted fitness-related traits. Introgressions contain genes involved in host-pathogen interactions and reproduction. Introgressed isolates have enhanced growth rate at high temperature and produce different necrosis sizes on an in vivo model for pathogenicity. In addition, lineages diverge in many pathogenicity-associated genes and exhibit differential mycelial growth in the presence of a proxy of a host defence compound, implying an important role of host trees in the molecular and functional differentiation of these pathogens.
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53
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Frantzeskakis L, Di Pietro A, Rep M, Schirawski J, Wu CH, Panstruga R. Rapid evolution in plant-microbe interactions - a molecular genomics perspective. THE NEW PHYTOLOGIST 2020; 225:1134-1142. [PMID: 31134629 DOI: 10.1111/nph.15966] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Rapid (co-)evolution at multiple timescales is a hallmark of plant-microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights into genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathogens. These comprise fresh insights in allelic series of matching pairs of resistance and avirulence genes, the generation of novel pathogen effectors, the recently recognised small RNA warfare, and genomic aspects of secondary metabolite biosynthesis. In addition, we discuss the putative contributions of permissive host environments, transcriptional plasticity and the role of ploidy on the interactions. We conclude that the means underlying the rapid evolution of plant-microbe interactions are multifaceted and depend on the particular nature of each interaction.
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Affiliation(s)
| | - Antonio Di Pietro
- Departamento de Genética and Campus de Excelencia Agroalimentario (ceiA3), Universidad de Córdoba, 14071, Córdoba, Spain
| | - Martijn Rep
- Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94215, 1090 GE, Amsterdam, the Netherlands
| | - Jan Schirawski
- Microbial Genetics, Institute of Applied Microbiology, RWTH Aachen University, Aachen, Germany
| | - Chih-Hang Wu
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, Aachen, 52056, Germany
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54
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Corredor‐Moreno P, Saunders DGO. Expecting the unexpected: factors influencing the emergence of fungal and oomycete plant pathogens. THE NEW PHYTOLOGIST 2020; 225:118-125. [PMID: 31225901 PMCID: PMC6916378 DOI: 10.1111/nph.16007] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/06/2019] [Indexed: 05/12/2023]
Abstract
In recent years, the number of emergent plant pathogens (EPPs) has grown substantially, threatening agroecosystem stability and native biodiversity. Contributing factors include, among others, shifts in biogeography, with EPP spread facilitated by the global unification of monocultures in modern agriculture, high volumes of trade in plants and plant products and an increase in sexual recombination within pathogen populations. The unpredictable nature of EPPs as they move into new territories is a situation that has led to sudden and widespread epidemics. Understanding the underlying causes of pathogen emergence is key to managing the impact of EPPs. Here, we review some factors specifically influencing the emergence of oomycete and fungal EPPs, including new introductions through anthropogenic movement, natural dispersal and weather events, as well as genetic factors linked to shifts in host range.
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55
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Bosch J, Czedik-Eysenberg A, Hastreiter M, Khan M, Güldener U, Djamei A. Two Is Better Than One: Studying Ustilago bromivora- Brachypodium Compatibility by Using a Hybrid Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1623-1634. [PMID: 31657673 DOI: 10.1094/mpmi-05-19-0148-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.
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Affiliation(s)
- Jason Bosch
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Angelika Czedik-Eysenberg
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Maximilian Hastreiter
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Mamoona Khan
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
| | - Ulrich Güldener
- TUM School of Life Sciences, Technical University of Munich, Department of Bioinformatics, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Armin Djamei
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstraße 3, D-06466 Stadt Seeland, Germany
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56
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Feurtey A, Stevens DM, Stephan W, Stukenbrock EH. Interspecific Gene Exchange Introduces High Genetic Variability in Crop Pathogen. Genome Biol Evol 2019; 11:3095-3105. [PMID: 31603209 PMCID: PMC6836716 DOI: 10.1093/gbe/evz224] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2019] [Indexed: 12/27/2022] Open
Abstract
Genome analyses have revealed a profound role of hybridization and introgression in the evolution of many eukaryote lineages, including fungi. The impact of recurrent introgression on fungal evolution however remains elusive. Here, we analyzed signatures of introgression along the genome of the fungal wheat pathogen Zymoseptoria tritici. We applied a comparative population genomics approach, including genome data from five Zymoseptoria species, to characterize the distribution and composition of introgressed regions representing segments with an exceptional haplotype pattern. These regions are found throughout the genome, comprising 5% of the total genome and overlapping with > 1,000 predicted genes. We performed window-based phylogenetic analyses along the genome to distinguish regions which have a monophyletic or nonmonophyletic origin with Z. tritici sequences. A majority of nonmonophyletic windows overlap with the highly variable regions suggesting that these originate from introgression. We verified that incongruent gene genealogies do not result from incomplete lineage sorting by comparing the observed and expected length distribution of haplotype blocks resulting from incomplete lineage sorting. Although protein-coding genes are not enriched in these regions, we identify 18 that encode putative virulence determinants. Moreover, we find an enrichment of transposable elements in these regions implying that hybridization may contribute to the horizontal spread of transposable elements. We detected a similar pattern in the closely related species Zymoseptoria ardabiliae, suggesting that hybridization is widespread among these closely related grass pathogens. Overall, our results demonstrate a significant impact of recurrent hybridization on overall genome evolution of this important wheat pathogen.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Botanical Institute, Christian-Albrechts University of Kiel, Germany
| | - Danielle M Stevens
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Botanical Institute, Christian-Albrechts University of Kiel, Germany
- Department of Plant Pathology, University of California, Davis
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Eva H Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Botanical Institute, Christian-Albrechts University of Kiel, Germany
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57
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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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58
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Thines M. An evolutionary framework for host shifts - jumping ships for survival. THE NEW PHYTOLOGIST 2019; 224:605-617. [PMID: 31381166 DOI: 10.1111/nph.16092] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/04/2019] [Indexed: 06/10/2023]
Abstract
Host jumping is a process by which pathogens settle in new host groups. It is a cornerstone in the evolution of pathogens, as it leads to pathogen diversification. It is unsurprising that host jumping is observed in facultative pathogens, as they can reproduce even if they kill their hosts. However, host jumps were thought to be rare in obligate biotrophic pathogens, but molecular phylogenetics has revealed that the opposite is true. Here, I review some concepts and recent findings and present several hypotheses on the matter. In short, pathogens evolve and diversify via host jumps, followed by radiation, specialisation and speciation. Host jumps are facilitated by, for example, effector innovations, stress, compatible pathogens and physiological similarities. Host jumping, subsequent establishment, and speciation takes place rapidly - within centuries and millennia rather than over millions of years. If pathogens are unable to evolve into neutral or mutualistic interactions with their hosts, they will eventually be removed from the host population, despite balancing trade-offs. Thus, generally, plant pathogens only survive in the course of evolution if they jump hosts. This is also reflected by the diversity patterns observed in many genera of plant pathogens, where it leads to a mosaic pattern of host groups over time, in which the original host group becomes increasingly obscure.
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Affiliation(s)
- Marco Thines
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, D-60486, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, D-60325, Frankfurt am Main, Germany
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59
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Abstract
Strategies to manage plant disease-from use of resistant varieties to crop rotation, elimination of reservoirs, landscape planning, surveillance, quarantine, risk modeling, and anticipation of disease emergences-all rely on knowledge of pathogen host range. However, awareness of the multitude of factors that influence the outcome of plant-microorganism interactions, the spatial and temporal dynamics of these factors, and the diversity of any given pathogen makes it increasingly challenging to define simple, all-purpose rules to circumscribe the host range of a pathogen. For bacteria, fungi, oomycetes, and viruses, we illustrate that host range is often an overlapping continuum-more so than the separation of discrete pathotypes-and that host jumps are common. By setting the mechanisms of plant-pathogen interactions into the scales of contemporary land use and Earth history, we propose a framework to assess the frontiers of host range for practical applications and research on pathogen evolution.
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Affiliation(s)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140, Montfavet, France;
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60
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Ayliffe M, Sørensen CK. Plant nonhost resistance: paradigms and new environments. CURRENT OPINION IN PLANT BIOLOGY 2019; 50:104-113. [PMID: 31075541 DOI: 10.1016/j.pbi.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 03/25/2019] [Indexed: 05/25/2023]
Abstract
Nonhost resistance (NHR) protects plants from a large and diverse array of potential phytopathogens. Each phytopathogen can parasitise some plant species, but most plant species are nonhosts that are innately immune due to a series of physical, chemical and inducible defenses these nonadapted pathogens cannot overcome. New evidence supports the NHR paradigm that posits the inability of potential pathogens to colonise nonhost plants is frequently due to molecular incompatibility between pathogen virulence factors and plant cellular targets. While NHR is durable, it is not insurmountable. Environmental changes can facilitate pathogen host jumps or alternatively result in new encounters between previously isolated plant species and pathogens. Climate change is predicted to substantially alter the current distribution of plants and their pathogens which could result in parasitism of new plant species.
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Affiliation(s)
- Michael Ayliffe
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra, ACT 2601, Australia.
| | - Chris K Sørensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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61
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Bourras S, Kunz L, Xue M, Praz CR, Müller MC, Kälin C, Schläfli M, Ackermann P, Flückiger S, Parlange F, Menardo F, Schaefer LK, Ben-David R, Roffler S, Oberhaensli S, Widrig V, Lindner S, Isaksson J, Wicker T, Yu D, Keller B. The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat. Nat Commun 2019; 10:2292. [PMID: 31123263 PMCID: PMC6533294 DOI: 10.1038/s41467-019-10274-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/03/2019] [Indexed: 12/25/2022] Open
Abstract
The wheat Pm3 resistance gene against the powdery mildew pathogen occurs as an allelic series encoding functionally different immune receptors which induce resistance upon recognition of isolate-specific avirulence (AVR) effectors from the pathogen. Here, we describe the identification of five effector proteins from the mildew pathogens of wheat, rye, and the wild grass Dactylis glomerata, specifically recognized by the PM3B, PM3C and PM3D receptors. Together with the earlier identified AVRPM3A2/F2, the recognized AVRs of PM3B/C, (AVRPM3B2/C2), and PM3D (AVRPM3D3) belong to a large group of proteins with low sequence homology but predicted structural similarities. AvrPm3b2/c2 and AvrPm3d3 are conserved in all tested isolates of wheat and rye mildew, and non-host infection assays demonstrate that Pm3b, Pm3c, and Pm3d are also restricting the growth of rye mildew on wheat. Furthermore, divergent AVR homologues from non-adapted rye and Dactylis mildews are recognized by PM3B, PM3C, or PM3D, demonstrating their involvement in host specificity.
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Affiliation(s)
- Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden.
| | - Lukas Kunz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China
- College of Life Science, Wuhan University, Wuhan, 430072, China
| | - Coraline Rosalie Praz
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Carol Kälin
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Michael Schläfli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Patrick Ackermann
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | | | - Roi Ben-David
- Institute of Plant Science, ARO-Volcani Center, 50250, Bet Dagan, Israel
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Victoria Widrig
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Stefan Lindner
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Jonatan Isaksson
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central China, Wuhan, 430064, China.
- College of Life Science, Wuhan University, Wuhan, 430072, China.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008, Zurich, Switzerland.
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62
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Mohd-Assaad N, McDonald BA, Croll D. The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses. Environ Microbiol 2019; 21:2677-2695. [PMID: 30838748 DOI: 10.1111/1462-2920.14583] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/23/2019] [Accepted: 03/04/2019] [Indexed: 01/28/2023]
Abstract
Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.
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Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH, Zurich, 8092 Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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63
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64
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Sánchez-Martín J, Keller B. Contribution of recent technological advances to future resistance breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:713-732. [PMID: 30756126 DOI: 10.1007/s00122-019-03297-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/02/2019] [Indexed: 05/23/2023]
Abstract
The development of durable host resistance strategies to control crop diseases is a primary need for sustainable agricultural production in the future. This article highlights the potential of recent progress in the understanding of host resistance for future cereal breeding. Much of the novel work is based on advancements in large-scale sequencing and genomics, rapid gene isolation techniques and high-throughput molecular marker technologies. Moreover, emerging applications on the pathogen side like effector identification or field pathogenomics are discussed. The combination of knowledge from both sides of cereal pathosystems will result in new approaches for resistance breeding. We describe future applications and innovative strategies to implement effective and durable strategies to combat diseases of major cereal crops while reducing pesticide dependency.
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Affiliation(s)
- Javier Sánchez-Martín
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zurich, Switzerland
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65
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Müller MC, Praz CR, Sotiropoulos AG, Menardo F, Kunz L, Schudel S, Oberhänsli S, Poretti M, Wehrli A, Bourras S, Keller B, Wicker T. A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew. THE NEW PHYTOLOGIST 2019; 221:2176-2189. [PMID: 30388298 PMCID: PMC6587952 DOI: 10.1111/nph.15529] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 10/02/2018] [Indexed: 05/13/2023]
Abstract
Blumeria graminis f. sp. tritici (B.g. tritici) is the causal agent of the wheat powdery mildew disease. The highly fragmented B.g. tritici genome available so far has prevented a systematic analysis of effector genes that are known to be involved in host adaptation. To study the diversity and evolution of effector genes we produced a chromosome-scale assembly of the B.g. tritici genome. The genome assembly and annotation was achieved by combining long-read sequencing with high-density genetic mapping, bacterial artificial chromosome fingerprinting and transcriptomics. We found that the 166.6 Mb B.g. tritici genome encodes 844 candidate effector genes, over 40% more than previously reported. Candidate effector genes have characteristic local genomic organization such as gene clustering and enrichment for recombination-active regions and certain transposable element families. A large group of 412 candidate effector genes shows high plasticity in terms of copy number variation in a global set of 36 isolates and of transcription levels. Our data suggest that copy number variation and transcriptional flexibility are the main drivers for adaptation in B.g. tritici. The high repeat content may play a role in providing a genomic environment that allows rapid evolution of effector genes with selection as the driving force.
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Affiliation(s)
- Marion C. Müller
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Alexandros G. Sotiropoulos
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Lukas Kunz
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Seraina Schudel
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Simone Oberhänsli
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Manuel Poretti
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Andreas Wehrli
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZurichZollikerstrasse 107ZurichCH‐8008Switzerland
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Saur IML, Bauer S, Kracher B, Lu X, Franzeskakis L, Müller MC, Sabelleck B, Kümmel F, Panstruga R, Maekawa T, Schulze-Lefert P. Multiple pairs of allelic MLA immune receptor-powdery mildew AVR A effectors argue for a direct recognition mechanism. eLife 2019; 8:e44471. [PMID: 30777147 PMCID: PMC6414202 DOI: 10.7554/elife.44471] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 01/03/2023] Open
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR)-containing proteins in plants and animals mediate intracellular pathogen sensing. Plant NLRs typically detect strain-specific pathogen effectors and trigger immune responses often linked to localized host cell death. The barley Mla disease resistance locus has undergone extensive functional diversification in the host population and encodes numerous allelic NLRs each detecting a matching isolate-specific avirulence effector (AVRA) of the fungal pathogen Blumeria graminis f. sp. hordei (Bgh). We report here the isolation of Bgh AVRa7, AVRa9, AVRa10, and AVRa22, which encode small secreted proteins recognized by allelic MLA7, MLA9, MLA10, and MLA22 receptors, respectively. These effectors are sequence-unrelated, except for allelic AVRa10 and AVRa22 that are co-maintained in pathogen populations in the form of a balanced polymorphism. Contrary to numerous examples of indirect recognition of bacterial effectors by plant NLRs, co-expression experiments with matching Mla-AVRa pairs indicate direct detection of the sequence-unrelated fungal effectors by MLA receptors.
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Affiliation(s)
- Isabel ML Saur
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Saskia Bauer
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Barbara Kracher
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Xunli Lu
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lamprinos Franzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Marion C Müller
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Björn Sabelleck
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Florian Kümmel
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology IRWTH Aachen UniversityAachenGermany
| | - Takaki Maekawa
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
| | - Paul Schulze-Lefert
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant SciencesDüsseldorfGermany
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67
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Taylor SA, Larson EL. Insights from genomes into the evolutionary importance and prevalence of hybridization in nature. Nat Ecol Evol 2019; 3:170-177. [DOI: 10.1038/s41559-018-0777-y] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 12/04/2018] [Indexed: 01/27/2023]
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Tedersoo L, Drenkhan R, Anslan S, Morales‐Rodriguez C, Cleary M. High-throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations. Mol Ecol Resour 2019; 19:47-76. [PMID: 30358140 PMCID: PMC7379260 DOI: 10.1111/1755-0998.12959] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/01/2018] [Accepted: 08/28/2018] [Indexed: 12/26/2022]
Abstract
High-throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state-of-the-art high-throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state-of-the-art and still evolving methods for diagnostics and population- and community-level ecological research of pathogens and pests.
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Affiliation(s)
- Leho Tedersoo
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Rein Drenkhan
- Institute of Forestry and Rural EngineeringEstonian University of Life SciencesTartuEstonia
| | - Sten Anslan
- Natural History Museum and Institute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | | | - Michelle Cleary
- Southern Swedish Forest Research CentreSwedish University of Agricultural SciencesAlnarpSweden
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69
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Liang P, Liu S, Xu F, Jiang S, Yan J, He Q, Liu W, Lin C, Zheng F, Wang X, Miao W. Powdery Mildews Are Characterized by Contracted Carbohydrate Metabolism and Diverse Effectors to Adapt to Obligate Biotrophic Lifestyle. Front Microbiol 2018; 9:3160. [PMID: 30619222 PMCID: PMC6305591 DOI: 10.3389/fmicb.2018.03160] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/05/2018] [Indexed: 01/08/2023] Open
Abstract
Powdery mildew is a widespread plant disease caused by obligate biotrophic fungal pathogens involving species-specific interactions between host and parasite. To gain genomic insights into the underlying obligate biotrophic mechanisms, we analyzed 15 microbial genomes covering powdery and downy mildews and rusts. We observed a genome-wide, massive contraction of multiple gene families in powdery mildews, such as enzymes in the carbohydrate metabolism pathway, when compared with ascomycete phytopathogens, while the fatty acid metabolism pathway maintained its integrity. We also observed significant differences in candidate secreted effector protein (CSEP) families between monocot and dicot powdery mildews, perhaps due to different selection forces. While CSEPs in monocot mildews are likely subject to positive selection causing rapid expansion, CSEP families in dicot mildews are shrinking under strong purifying selection. Our results not only illustrate obligate biotrophic mechanisms of powdery mildews driven by gene family evolution in nutrient metabolism, but also demonstrate how the divergence of CSEPs between monocot and dicot lineages might contribute to species-specific adaption.
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Affiliation(s)
- Peng Liang
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China.,Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Songyu Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Feng Xu
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Shuqin Jiang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Jun Yan
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Qiguang He
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Wenbo Liu
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Chunhua Lin
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Fucong Zheng
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing, China
| | - Weiguo Miao
- College of Plant Protection, Hainan University, Haikou, China.,Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests (Hainan University), Ministry of Education, Haikou, China
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70
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Bourras S, Praz CR, Spanu PD, Keller B. Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen. Curr Opin Microbiol 2018; 46:26-33. [DOI: 10.1016/j.mib.2018.01.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/25/2023]
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71
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Wu Y, Ma X, Pan Z, Kale SD, Song Y, King H, Zhang Q, Presley C, Deng X, Wei CI, Xiao S. Comparative genome analyses reveal sequence features reflecting distinct modes of host-adaptation between dicot and monocot powdery mildew. BMC Genomics 2018; 19:705. [PMID: 30253736 PMCID: PMC6156980 DOI: 10.1186/s12864-018-5069-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/11/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Powdery mildew (PM) is one of the most important and widespread plant diseases caused by biotrophic fungi. Notably, while monocot (grass) PM fungi exhibit high-level of host-specialization, many dicot PM fungi display a broad host range. To understand such distinct modes of host-adaptation, we sequenced the genomes of four dicot PM biotypes belonging to Golovinomyces cichoracearum or Oidium neolycopersici. RESULTS We compared genomes of the four dicot PM together with those of Blumeria graminis f.sp. hordei (both DH14 and RACE1 isolates), B. graminis f.sp. tritici, and Erysiphe necator infectious on barley, wheat and grapevine, respectively. We found that despite having a similar gene number (6620-6961), the PM genomes vary from 120 to 222 Mb in size. This high-level of genome size variation is indicative of highly differential transposon activities in the PM genomes. While the total number of genes in any given PM genome is only about half of that in the genomes of closely related ascomycete fungi, most (~ 93%) of the ascomycete core genes (ACGs) can be found in the PM genomes. Yet, 186 ACGs were found absent in at least two of the eight PM genomes, of which 35 are missing in some dicot PM biotypes, but present in the three monocot PM genomes, indicating remarkable, independent and perhaps ongoing gene loss in different PM lineages. Consistent with this, we found that only 4192 (3819 singleton) genes are shared by all the eight PM genomes, the remaining genes are lineage- or biotype-specific. Strikingly, whereas the three monocot PM genomes possess up to 661 genes encoding candidate secreted effector proteins (CSEPs) with families containing up to 38 members, all the five dicot PM fungi have only 116-175 genes encoding CSEPs with limited gene amplification. CONCLUSIONS Compared to monocot (grass) PM fungi, dicot PM fungi have a much smaller effectorome. This is consistent with their contrasting modes of host-adaption: while the monocot PM fungi show a high-level of host specialization, which may reflect an advanced host-pathogen arms race, the dicot PM fungi tend to practice polyphagy, which might have lessened selective pressure for escalating an with a particular host.
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Affiliation(s)
- Ying Wu
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xianfeng Ma
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Hunan Provincial Key Laboratory for Germplasm Innovation and Utilization of Crop, Hunan Agricultural University, Changsha, 410128 China
| | - Zhiyong Pan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shiv D. Kale
- Biocomplexity Institute, Virginia Tech, Blacksburg, VA 24061 USA
| | - Yi Song
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083 China
| | - Harlan King
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Qiong Zhang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Christian Presley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region, Ministry of Agriculture), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cheng-I Wei
- College of Agriculture & Natural Resources, University of Maryland, College Park, MD 20742 USA
| | - Shunyuan Xiao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, MD 20850 USA
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
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72
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Xia C, Wang M, Yin C, Cornejo OE, Hulbert SH, Chen X. Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei). BMC Genomics 2018; 19:664. [PMID: 30208837 PMCID: PMC6134786 DOI: 10.1186/s12864-018-5041-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Plant fungal pathogens can rapidly evolve and adapt to new environmental conditions in response to sudden changes of host populations in agro-ecosystems. However, the genomic basis of their host adaptation, especially at the forma specialis level, remains unclear. RESULTS We sequenced two isolates each representing Puccinia striiformis f. sp. tritici (Pst) and P. striiformis f. sp. hordei (Psh), different formae speciales of the stripe rust fungus P. striiformis highly adapted to wheat and barley, respectively. The divergence of Pst and Psh, estimated to start 8.12 million years ago, has been driven by high nucleotide mutation rates. The high genomic variation within dikaryotic urediniospores of P. striiformis has provided raw genetic materials for genome evolution. No specific gene families have enriched in either isolate, but extensive gene loss events have occurred in both Pst and Psh after the divergence from their most recent common ancestor. A large number of isolate-specific genes were identified, with unique genomic features compared to the conserved genes, including 1) significantly shorter in length; 2) significantly less expressed; 3) significantly closer to transposable elements; and 4) redundant in pathways. The presence of specific genes in one isolate (or forma specialis) was resulted from the loss of the homologues in the other isolate (or forma specialis) by the replacements of transposable elements or losses of genomic fragments. In addition, different patterns and numbers of telomeric repeats were observed between the isolates. CONCLUSIONS Host adaptation of P. striiformis at the forma specialis level is a complex pathogenic trait, involving not only virulence-related genes but also other genes. Gene loss, which might be adaptive and driven by transposable element activities, provides genomic basis for host adaptation of different formae speciales of P. striiformis.
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Affiliation(s)
- Chongjing Xia
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Chuntao Yin
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA 99164-7520 USA
| | - Scot H. Hulbert
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430 USA
- Wheat Health, Genetics, and Quality Research Unit, Agriculture Research Service, U.S. Department of Agriculture, Pullman, WA 99164-6430 USA
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73
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Kusch S, Frantzeskakis L, Thieron H, Panstruga R. Small RNAs from cereal powdery mildew pathogens may target host plant genes. Fungal Biol 2018; 122:1050-1063. [PMID: 30342621 DOI: 10.1016/j.funbio.2018.08.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/25/2018] [Accepted: 08/28/2018] [Indexed: 12/24/2022]
Abstract
Small RNAs (sRNAs) play a key role in eukaryotic gene regulation, for example by gene silencing via RNA interference (RNAi). The biogenesis of sRNAs depends on proteins that are generally conserved in all eukaryotic lineages, yet some species that lack part or all the components of the mechanism exist. Here we explored the presence of the RNAi machinery and its expression as well as the occurrence of sRNA candidates and their putative endogenous as well as host targets in phytopathogenic powdery mildew fungi. We focused on the species Blumeria graminis, which occurs in various specialized forms (formae speciales) that each have a strictly limited host range. B. graminis f. sp. hordei and B. graminis f. sp. tritici, colonizing barley and wheat, respectively, have genomes that are characterized by extensive gene loss. Nonetheless, we find that the RNAi machinery appears to be largely complete and expressed during infection. sRNA sequencing data enabled the identification of putative sRNAs in both pathogens. While a considerable part of the sRNA candidates have predicted target sites in endogenous genes and transposable elements, a small proportion appears to have targets in planta, suggesting potential cross-kingdom RNA transfer between powdery mildew fungi and their respective plant hosts.
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Affiliation(s)
- Stefan Kusch
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Lamprinos Frantzeskakis
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Hannah Thieron
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
| | - Ralph Panstruga
- Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Worringerweg 1, D-52056 Aachen, Germany.
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74
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Feurtey A, Stukenbrock EH. Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi. Annu Rev Microbiol 2018; 72:377-398. [DOI: 10.1146/annurev-micro-090817-062753] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
| | - Eva H. Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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75
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Keller B, Wicker T, Krattinger SG. Advances in Wheat and Pathogen Genomics: Implications for Disease Control. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:67-87. [PMID: 30149791 DOI: 10.1146/annurev-phyto-080516-035419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The gene pool of wheat and its wild and domesticated relatives contains a plethora of resistance genes that can be exploited to make wheat more resilient to pathogens. Only a few of these genes have been isolated and studied at the molecular level. In recent years, we have seen a shift from classical breeding to genomics-assisted breeding, which makes use of the enormous advancements in DNA sequencing and high-throughput molecular marker technologies for wheat improvement. These genomic advancements have the potential to transform wheat breeding in the near future and to significantly increase the speed and precision at which new cultivars can be bred. This review highlights the genomic improvements that have been made in wheat and its pathogens over the past years and discusses their implications for disease-resistance breeding.
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Affiliation(s)
- Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland;
| | - Simon G Krattinger
- Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia;
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76
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Silva DN, Várzea V, Paulo OS, Batista D. Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust. MOLECULAR PLANT PATHOLOGY 2018; 19:1742-1753. [PMID: 29328532 PMCID: PMC6638104 DOI: 10.1111/mpp.12657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 05/30/2023]
Abstract
Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.
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Affiliation(s)
- Diogo Nuno Silva
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Vítor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio Salgueiro Paulo
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Dora Batista
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
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77
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Frantzeskakis L, Kracher B, Kusch S, Yoshikawa-Maekawa M, Bauer S, Pedersen C, Spanu PD, Maekawa T, Schulze-Lefert P, Panstruga R. Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen. BMC Genomics 2018; 19:381. [PMID: 29788921 PMCID: PMC5964911 DOI: 10.1186/s12864-018-4750-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022] Open
Abstract
Background Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). Results The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. Conclusions The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a “one-speed” genome that differs in its architecture and (co-)evolutionary pattern from the “two-speed” genomes reported for several other filamentous phytopathogens. Electronic supplementary material The online version of this article (10.1186/s12864-018-4750-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lamprinos Frantzeskakis
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Barbara Kracher
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Stefan Kusch
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany
| | - Makoto Yoshikawa-Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Saskia Bauer
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Pietro D Spanu
- Imperial College, Department of Life Sciences, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Takaki Maekawa
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant-Microbe Interactions, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
| | - Ralph Panstruga
- Institute for Biology I, Unit of Plant Molecular Cell Biology, RWTH Aachen University, Worringerweg 1, 52056, Aachen, Germany.
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78
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Affiliation(s)
- Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- * E-mail:
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Menardo F, Wicker T, Keller B. Reconstructing the Evolutionary History of Powdery Mildew Lineages (Blumeria graminis) at Different Evolutionary Time Scales with NGS Data. Genome Biol Evol 2018; 9:446-456. [PMID: 28164219 PMCID: PMC5381671 DOI: 10.1093/gbe/evx008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 01/25/2023] Open
Abstract
Blumeria graminis (Ascomycota) includes fungal pathogens that infect numerous grasses and cereals. Despite its economic impact on agriculture and its scientific importance in plant–pathogen interaction studies, the evolution of different lineages with different host ranges is poorly understood. Moreover, the taxonomy of grass powdery mildew is rather exceptional: there is only one described species (B. graminis) subdivided in different formae speciales (ff.spp.), which are defined by their host range. In this study we applied phylogenomic and population genomic methods to whole genome sequence data of 31 isolates of B. graminis belonging to different ff.spp. and reconstructed the evolutionary relationships between different lineages. The results of the phylogenomic analysis support a pattern of co-evolution between some of the ff.spp. and their host plant. In addition, we identified exceptions to this pattern, namely host jump events and the recent radiation of a clade less than 280,000 years ago. Furthermore, we found a high level of gene tree incongruence localized in the youngest clade. To distinguish between incomplete lineage sorting and lateral gene flow, we applied a coalescent-based method of demographic inference and found evidence of horizontal gene flow between recently diverged lineages. Overall we found that different processes shaped the diversification of B. graminis, co-evolution with the host species, host jump and fast radiation. Our study is an example of how genomic data can resolve complex evolutionary histories of cryptic lineages at different time scales, dealing with incomplete lineage sorting and lateral gene flow.
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Abstract
The first eukaryotic genome to be sequenced was fungal, and there continue to be more sequenced genomes in the kingdom Fungi than in any other eukaryotic kingdom. Comparison of these genomes reveals many sources of genetic variation, from single nucleotide polymorphisms to horizontal gene transfer and on to changes in the arrangement and number of chromosomes, not to mention endofungal bacteria and viruses. Population genomics shows that all sources generate variation all the time and implicate natural selection as the force maintaining genome stability. Variation in wild populations is a rich resource for associating genetic variation with phenotypic variation, whether through quantitative trait locus mapping, genome-wide association studies, or reverse ecology. Subjects of studies associating genetic and phenotypic variation include model fungi, e.g., Saccharomyces and Neurospora, but pioneering studies have also been made with fungi pathogenic to plants, e.g., Pyricularia (= Magnaporthe), Zymoseptoria, and Fusarium, and to humans, e.g., Coccidioides, Cryptococcus, and Candida.
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81
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Benevenuto J, Teixeira-Silva NS, Kuramae EE, Croll D, Monteiro-Vitorello CB. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. Front Microbiol 2018; 9:660. [PMID: 29681893 PMCID: PMC5897528 DOI: 10.3389/fmicb.2018.00660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.
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Affiliation(s)
- Juliana Benevenuto
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Natalia S. Teixeira-Silva
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel (UNINE), Neuchâtel, Switzerland
| | - Claudia B. Monteiro-Vitorello
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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82
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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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83
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Ben-David R, Dinoor A, Peleg Z, Fahima T. Reciprocal Hosts' Responses to Powdery Mildew Isolates Originating from Domesticated Wheats and Their Wild Progenitor. FRONTIERS IN PLANT SCIENCE 2018; 9:75. [PMID: 29527213 PMCID: PMC5829517 DOI: 10.3389/fpls.2018.00075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/15/2018] [Indexed: 03/14/2024]
Abstract
The biotroph wheat powdery mildew, Blumeria graminis (DC.) E.O. Speer, f. sp. tritici Em. Marchal (Bgt), has undergone long and dynamic co-evolution with its hosts. In the last 10,000 years, processes involved in plant evolution under domestication, altered host-population structure. Recently both virulence and genomic profiling separated Bgt into two groups based on their origin from domestic host and from wild emmer wheat. While most studies focused on the Bgt pathogen, there is significant knowledge gaps in the role of wheat host diversity in this specification. This study aimed to fill this gap by exploring qualitatively and also quantitatively the disease response of diverse host panel to powdery mildew [105 domesticated wheat genotypes (Triticum turgidum ssp. dicoccum, T. turgidum ssp. durum, and T. aestivum) and 241 accessions of its direct progenitor, wild emmer wheat (T. turgidum ssp. dicoccoides)]. A set of eight Bgt isolates, originally collected from domesticated and wild wheat was used for screening this wheat collection. The isolates from domesticated wheat elicited susceptible to moderate plant responses on domesticated wheat lines and high resistance on wild genotypes (51.7% of the tested lines were resistant). Isolates from wild emmer elicited reciprocal disease responses: high resistance of domesticated germplasm and high susceptibility of the wild material (their original host). Analysis of variance of the quantitative phenotypic responses showed a significant Isolates × Host species interaction [P(F) < 0.0001] and further supported these findings. Furthermore, analysis of the range of disease severity values showed that when the group of host genotypes was inoculated with Bgt isolate from the reciprocal host, coefficient of variation was significantly higher than when inoculated with its own isolates. This trend was attributed to the role of major resistance genes in the latter scenario (high proportion of complete resistance). By testing the association between disease severity and geographical distance from the source of inoculum, we have found higher susceptibility in wild emmer close to the source. Both qualitative and quantitative assays showed a reciprocal resistance pattern in the wheat host and are well aligned with the recent findings of significant differentiation into wild-emmer and domesticated-wheat populations in the pathogen.
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Affiliation(s)
- Roi Ben-David
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization-Volcani Center, Rishon LeZion, Israel
| | - Amos Dinoor
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Zvi Peleg
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem, Rehovot, Israel
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, Institute of Evolution, University of Haifa, Haifa, Israel
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Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B. Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. FRONTIERS IN PLANT SCIENCE 2018; 9:49. [PMID: 29441081 PMCID: PMC5797619 DOI: 10.3389/fpls.2018.00049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 01/10/2018] [Indexed: 05/20/2023]
Abstract
Powdery mildew is an important disease of cereals. It is caused by one species, Blumeria graminis, which is divided into formae speciales each of which is highly specialized to one host. Recently, a new form capable of growing on triticale (B.g. triticale) has emerged through hybridization between wheat and rye mildews (B.g. tritici and B.g. secalis, respectively). In this work, we used RNA sequencing to study the molecular basis of host adaptation in B.g. triticale. We analyzed gene expression in three B.g. tritici isolates, two B.g. secalis isolates and two B.g. triticale isolates and identified a core set of putative effector genes that are highly expressed in all formae speciales. We also found that the genes differentially expressed between isolates of the same form as well as between different formae speciales were enriched in putative effectors. Their coding genes belong to several families including some which contain known members of mildew avirulence (Avr) and suppressor (Svr) genes. Based on these findings we propose that effectors play an important role in host adaptation that is mechanistically based on Avr-Resistance gene-Svr interactions. We also found that gene expression in the B.g. triticale hybrid is mostly conserved with the parent-of-origin, but some genes inherited from B.g. tritici showed a B.g. secalis-like expression. Finally, we identified 11 unambiguous cases of putative effector genes with hybrid-specific, non-parent of origin gene expression, and we propose that they are possible determinants of host specialization in triticale mildew. These data suggest that altered expression of multiple effector genes, in particular Avr and Svr related factors, might play a role in mildew host adaptation based on hybridization.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Mark D. Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Marion C. Müller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- *Correspondence: Salim Bourras
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
- Beat Keller
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85
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Bueno-Sancho V, Persoons A, Hubbard A, Cabrera-Quio LE, Lewis CM, Corredor-Moreno P, Bunting DCE, Ali S, Chng S, Hodson DP, Madariaga Burrows R, Bryson R, Thomas J, Holdgate S, Saunders DGO. Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity. Genome Biol Evol 2017; 9:3282-3296. [PMID: 29177504 PMCID: PMC5730935 DOI: 10.1093/gbe/evx241] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/27/2022] Open
Abstract
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new races that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previous races, leading to wide-scale epidemics. Here, we used field-based genotyping to generate high-resolution data on P. striiformis genetics and carried out global population analysis. We also undertook comparative analysis of the 2014 and 2013 UK populations and assessed the temporal dynamics and host specificity of distinct pathogen genotypes. Our analysis revealed that P. striiformis lineages recently detected in Europe are extremely diverse and in fact similar to globally dispersed populations. In addition, we identified a considerable shift in the UK P. striiformis population structure including the first identification of one infamous race known as Kranich. Next, by establishing the genotype of both the pathogen and host within a single infected field sample, we uncovered evidence for varietal specificity for genetic groups of P. striiformis. Finally, we found potential seasonal specificity for certain genotypes of the pathogen with several lineages identified only in samples collected in late spring and into the summer, whereas one lineage was identified throughout the wheat growing season. Our discovery of which wheat varieties are susceptible to which specific P. striiformis isolates, and when those isolates are prevalent throughout the year, represents a powerful tool for disease management.
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Affiliation(s)
| | - Antoine Persoons
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | - Amelia Hubbard
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Luis Enrique Cabrera-Quio
- Earlham Institute, Norwich Research Park, United Kingdom
- The Sainsbury Laboratory, Norwich Research Park, United Kingdom
| | - Clare M Lewis
- Crop Genetics, John Innes Centre, Norwich Research Park, United Kingdom
| | | | | | - Sajid Ali
- The University of Agriculture, Peshawar, Pakistan
| | - Soonie Chng
- The New Zealand Institute for Plant & Food Research, Lincoln, New Zealand
| | | | | | - Rosie Bryson
- BASF SE, Agricultural Centre, Limburgerhof, Germany
| | - Jane Thomas
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Sarah Holdgate
- ational Institute of Agricultural Botany, Cambridge, United Kingdom
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86
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Sonn JM, Berman S, Richards-Zawacki CL. The Influence of Temperature on Chytridiomycosis In Vivo. ECOHEALTH 2017; 14:762-770. [PMID: 28879516 DOI: 10.1007/s10393-017-1269-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 06/23/2017] [Accepted: 07/11/2017] [Indexed: 06/07/2023]
Abstract
Chytridiomycosis, an amphibian disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), is an ideal system for studying the influence of temperature on host-pathogen relationships because both host and pathogen are ectothermic. Studies of Bd in culture suggest that optimal growth occurs between 17 and 23°C, and death of the fungus occurs above 29 or below 0°C. Amphibian immune systems, however, are also temperature dependent and often more effective at higher temperatures. We therefore hypothesized that pathogen load, probability of infection and mortality in Bd-exposed frogs would peak at a lower temperature than that at which Bd grows best in vitro. To test this, we conducted a study where Bd- and sham-exposed Northern cricket frogs (Acris crepitans) were incubated at six temperatures between 11 and 26°C. While probability of infection did not differ across temperatures, pathogen load and mortality were inversely related to temperature. Survival of infected hosts was greatest between 20 and 26°C, temperatures where Bd grows well in culture. These results demonstrate that the conditions under which a pathogen grows best in culture do not necessarily reflect patterns of pathogenicity, an important consideration for predicting the threat of this and other wildlife pathogens.
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Affiliation(s)
- Julia M Sonn
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs Bldg., New Orleans, LA, 70118, USA.
| | - Scott Berman
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs Bldg., New Orleans, LA, 70118, USA
| | - Corinne L Richards-Zawacki
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs Bldg., New Orleans, LA, 70118, USA
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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87
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Menardo F, Praz CR, Wicker T, Keller B. Rapid turnover of effectors in grass powdery mildew (Blumeria graminis). BMC Evol Biol 2017; 17:223. [PMID: 29089018 PMCID: PMC5664452 DOI: 10.1186/s12862-017-1064-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 10/02/2017] [Indexed: 11/21/2022] Open
Abstract
Background Grass powdery mildew (Blumeria graminis, Ascomycota) is a major pathogen of cereal crops and has become a model organism for obligate biotrophic fungal pathogens of plants. The sequenced genomes of two formae speciales (ff.spp.), B.g. hordei and B.g. tritici (pathogens of barley and wheat), were found to be enriched in candidate effector genes (CEGs). Similar to other filamentous pathogens, CEGs in B. graminis are under positive selection. Additionally, effectors are more likely to have presence-absence polymorphisms than other genes among different strains. Results Here we identified effectors in the genomes of three additional host-specific lineages of B. graminis (B.g. poae, B.g. avenae and B.g. infecting Lolium) which diverged between 24 and 5 million years ago (Mya). We found that most CEGs in B. graminis are clustered in families and that most families are present in both reference genomes (B.g. hordei and B.g. tritici) and in the genomes of all three newly annotated lineages. We identified conserved protein domains including a novel lipid binding domain. The phylogenetic analysis showed that frequent gene duplications and losses shaped the diversity of the effector repertoires of the different lineages through their evolutionary history. We observed several lineage-specific expansions where large clades of CEGs originated in only one lineage from a single gene through repeated gene duplications. When we applied a birth-death model we found that the turnover rate (the rate at which genes are deleted and duplicated) of CEG families is much higher than for non-CEG families. The analysis of genomic context revealed that the immediate surroundings of CEGs are enriched in transposable elements (TE) which could play a role in the duplication and deletion of CEGs. Conclusions The CEG repertoires of related pathogens diverged dramatically in short evolutionary times because of rapid turnover and of positive selection fixing non-synonymous mutations. While signatures of positive selection on effector sequences are the expected outcome of the evolutionary “arms race” between pathogen and plant immune system, it is more difficult to infer the mechanisms and evolutionary forces that maintained an extreme turnover rate in CEG families of B. graminis for several millions of years. Electronic supplementary material The online version of this article (10.1186/s12862-017-1064-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Coraline R Praz
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
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88
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Zhang Y, Ma LJ. Deciphering Pathogenicity of Fusarium oxysporum From a Phylogenomics Perspective. ADVANCES IN GENETICS 2017; 100:179-209. [PMID: 29153400 DOI: 10.1016/bs.adgen.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC. The existence of a diverse array of SP chromosomes determines the broad host range of this species complex, while the conserved core genome maintains essential house-keeping functions. Recognition of these SP chromosomes enables the functional and structural compartmentalization of F. oxysporum genomes. In this review, we examine the impact of this group of cross-kingdom pathogens on agricultural productivity and human health. Focusing on the pathogenicity of F. oxysporum in the phylogenomic framework of the genus Fusarium, we elucidate the evolution of pathogenicity within the FOSC. We conclude that a population genomics approach within a clearly defined phylogenomic framework is essential not only for understanding the evolution of the pathogenicity mechanism but also for identifying informative candidates associated with pathogenicity that can be developed as targets in disease management programs.
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Affiliation(s)
- Yong Zhang
- University of Massachusetts Amherst, Amherst, MA, United States
| | - Li-Jun Ma
- University of Massachusetts Amherst, Amherst, MA, United States.
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89
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Farrer RA, Fisher MC. Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. ADVANCES IN GENETICS 2017; 100:73-140. [PMID: 29153405 DOI: 10.1016/bs.adgen.2017.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.
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90
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Zeng Q, Wang J, Bertels F, Giordano PR, Chilvers MI, Huntley RB, Vargas JM, Sundin GW, Jacobs JL, Yang CH. Recombination of Virulence Genes in Divergent Acidovorax avenae Strains That Infect a Common Host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:813-828. [PMID: 28682158 DOI: 10.1094/mpmi-06-17-0151-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial etiolation and decline (BED), caused by Acidovorax avenae, is an emerging disease of creeping bentgrass on golf courses in the United States. We performed the first comprehensive analysis of A. avenae on a nationwide collection of turfgrass- and maize-pathogenic A. avenae. Surprisingly, our results reveal that the turfgrass-pathogenic A. avenae in North America are not only highly divergent but also belong to two distinct phylogroups. Both phylogroups specifically infect turfgrass but are more closely related to maize pathogens than to each other. This suggests that, although the disease is only recently reported, it has likely been infecting turfgrass for a long time. To identify a genetic basis for the host specificity, we searched for genes closely related among turfgrass strains but distantly related to their homologs from maize strains. We found a cluster of 11 such genes generated by three ancient recombination events within the type III secretion system (T3SS) pathogenicity island. Ever since the recombination, the cluster has been conserved by strong purifying selection, hinting at its selective importance. Together our analyses suggest that BED is an ancient disease that may owe its host specificity to a highly conserved cluster of 11 T3SS genes.
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Affiliation(s)
- Quan Zeng
- 1 Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Jie Wang
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Frederic Bertels
- 3 Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany; and
| | - Paul R Giordano
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Martin I Chilvers
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Regan B Huntley
- 1 Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Joseph M Vargas
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - George W Sundin
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Janette L Jacobs
- 2 Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Ching-Hong Yang
- 4 Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, U.S.A
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91
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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92
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Mehrabi R, Mirzadi Gohari A, Kema GHJ. Karyotype Variability in Plant-Pathogenic Fungi. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:483-503. [PMID: 28777924 DOI: 10.1146/annurev-phyto-080615-095928] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Recent advances in genetic and molecular technologies gradually paved the way for the transition from traditional fungal karyotyping to more comprehensive chromosome biology studies. Extensive chromosomal polymorphisms largely resulting from chromosomal rearrangements (CRs) are widely documented in fungal genomes. These extraordinary CRs in fungi generate substantial genome plasticity compared to other eukaryotic organisms. Here, we review the most recent findings on fungal CRs and their underlying mechanisms and discuss the functional consequences of CRs for adaptation, fungal evolution, host range, and pathogenicity of fungal plant pathogens in the context of chromosome biology. In addition to a complement of permanent chromosomes called core chromosomes, the genomes of many fungal pathogens comprise distinct unstable chromosomes called dispensable chromosomes (DCs) that also contribute to chromosome polymorphisms. Compared to the core chromosomes, the structural features of DCs usually differ for gene density, GC content, housekeeping genes, and recombination frequency. Despite their dispensability for normal growth and development, DCs have important biological roles with respect to pathogenicity in some fungi but not in others. Therefore, their evolutionary origin is also reviewed in relation to overall fungal physiology and pathogenicity.
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Affiliation(s)
- Rahim Mehrabi
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Amir Mirzadi Gohari
- Department of Plant Pathology, Faculty of Agricultural Sciences and Engineering, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
| | - Gert H J Kema
- Wageningen Plant Research, Wageningen University and Research, 6700AA Wageningen, The Netherlands;
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93
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Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet 2017; 13:e1006777. [PMID: 28594822 PMCID: PMC5465968 DOI: 10.1371/journal.pgen.1006777] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.
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94
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McCann HC, Li L, Liu Y, Li D, Pan H, Zhong C, Rikkerink EH, Templeton MD, Straub C, Colombi E, Rainey PB, Huang H. Origin and Evolution of the Kiwifruit Canker Pandemic. Genome Biol Evol 2017; 9:932-944. [PMID: 28369338 PMCID: PMC5388287 DOI: 10.1093/gbe/evx055] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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Affiliation(s)
- Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hui Pan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Erik H.A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Elena Colombi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231 PSL Research University, Paris, France
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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95
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Petit E, Silver C, Cornille A, Gladieux P, Rosenthal L, Bruns E, Yee S, Antonovics J, Giraud T, Hood ME. Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Mol Ecol 2017; 26:1877-1890. [PMID: 28231407 DOI: 10.1111/mec.14073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/13/2017] [Accepted: 02/09/2017] [Indexed: 01/05/2023]
Abstract
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen genus, a range of overlapping host specificities was observed for four delineated Microbotryum lineages on Dianthus hosts, and their frequent co-occurrence within single-host populations was quantified at local and regional scales. In addition to potential consequences for direct pathogen competition, the sympatry of Microbotryum lineages led to hybridization between them in many populations, and these admixed genotypes suffered significant meiotic sterility. Therefore, this investigation of the anther-smut fungi reveals how variation in the degrees of host specificity can have major implications for ecological interactions and genetic integrity of differentiated pathogen lineages.
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Affiliation(s)
- Elsa Petit
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Casey Silver
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Gladieux
- UMR BGPI, INRA, Campus International de Baillarguet, 34398, Montpellier, France
| | - Lisa Rosenthal
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Emily Bruns
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Sarah Yee
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, University of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA, 01002, USA
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96
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Acevedo‐Garcia J, Spencer D, Thieron H, Reinstädler A, Hammond‐Kosack K, Phillips AL, Panstruga R. mlo-based powdery mildew resistance in hexaploid bread wheat generated by a non-transgenic TILLING approach. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:367-378. [PMID: 27565953 PMCID: PMC5316926 DOI: 10.1111/pbi.12631] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 08/12/2016] [Accepted: 08/24/2016] [Indexed: 05/03/2023]
Abstract
Wheat is one of the most widely grown cereal crops in the world and is an important food grain source for humans. However, wheat yields can be reduced by many abiotic and biotic stress factors, including powdery mildew disease caused by Blumeria graminis f.sp. tritici (Bgt). Generating resistant varieties is thus a major effort in plant breeding. Here, we took advantage of the non-transgenic Targeting Induced Lesions IN Genomes (TILLING) technology to select partial loss-of-function alleles of TaMlo, the orthologue of the barley Mlo (Mildew resistance locus o) gene. Natural and induced loss-of-function alleles (mlo) of barley Mlo are known to confer durable broad-spectrum powdery mildew resistance, typically at the expense of pleiotropic phenotypes such as premature leaf senescence. We identified 16 missense mutations in the three wheat TaMlo homoeologues, TaMlo-A1, TaMlo-B1 and TaMlo-D1 that each lead to single amino acid exchanges. Using transient gene expression assays in barley single cells, we functionally analysed the different missense mutants and identified the most promising candidates affecting powdery mildew susceptibility. By stacking of selected mutant alleles we generated four independent lines with non-conservative mutations in each of the three TaMlo homoeologues. Homozygous triple mutant lines and surprisingly also some of the homozygous double mutant lines showed enhanced, yet incomplete, Bgt resistance without the occurrence of discernible pleiotropic phenotypes. These lines thus represent an important step towards the production of commercial non-transgenic, powdery mildew-resistant bread wheat varieties.
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Affiliation(s)
- Johanna Acevedo‐Garcia
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - David Spencer
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Hannah Thieron
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Anja Reinstädler
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
| | - Kim Hammond‐Kosack
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Andrew L. Phillips
- Department of Plant Biology and Crop ScienceRothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQ, UK
| | - Ralph Panstruga
- Unit of Plant Molecular Cell BiologyInstitute for Biology IRWTH Aachen UniversityAachenGermany
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97
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Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S. Codon optimization underpins generalist parasitism in fungi. eLife 2017; 6:e22472. [PMID: 28157073 PMCID: PMC5315462 DOI: 10.7554/elife.22472] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/28/2017] [Indexed: 01/04/2023] Open
Abstract
The range of hosts that parasites can infect is a key determinant of the emergence and spread of disease. Yet, the impact of host range variation on the evolution of parasite genomes remains unknown. Here, we show that codon optimization underlies genome adaptation in broad host range parasites. We found that the longer proteins encoded by broad host range fungi likely increase natural selection on codon optimization in these species. Accordingly, codon optimization correlates with host range across the fungal kingdom. At the species level, biased patterns of synonymous substitutions underpin increased codon optimization in a generalist but not a specialist fungal pathogen. Virulence genes were consistently enriched in highly codon-optimized genes of generalist but not specialist species. We conclude that codon optimization is related to the capacity of parasites to colonize multiple hosts. Our results link genome evolution and translational regulation to the long-term persistence of generalist parasitism.
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Affiliation(s)
- Thomas Badet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Remi Peyraud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Malick Mbengue
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Olivier Navaud
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Mark Derbyshire
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Richard P Oliver
- Centre for Crop and Disease Management, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Adelin Barbacci
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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98
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Praz CR, Bourras S, Zeng F, Sánchez‐Martín J, Menardo F, Xue M, Yang L, Roffler S, Böni R, Herren G, McNally KE, Ben‐David R, Parlange F, Oberhaensli S, Flückiger S, Schäfer LK, Wicker T, Yu D, Keller B. AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus. THE NEW PHYTOLOGIST 2017; 213:1301-1314. [PMID: 27935041 PMCID: PMC5347869 DOI: 10.1111/nph.14372] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 05/20/2023]
Abstract
There is a large diversity of genetically defined resistance genes in bread wheat against the powdery mildew pathogen Blumeria graminis (B. g.) f. sp. tritici. Many confer race-specific resistance to this pathogen, but until now only the mildew avirulence gene AvrPm3a2/f2 that is recognized by Pm3a/f was known molecularly. We performed map-based cloning and genome-wide association studies to isolate a candidate for the mildew avirulence gene AvrPm2. We then used transient expression assays in Nicotiana benthamiana to demonstrate specific and strong recognition of AvrPm2 by Pm2. The virulent AvrPm2 allele arose from a conserved 12 kb deletion, while there is no protein sequence diversity in the gene pool of avirulent B. g. tritici isolates. We found one polymorphic AvrPm2 allele in B. g. triticale and one orthologue in B. g. secalis and both are recognized by Pm2. AvrPm2 belongs to a small gene family encoding structurally conserved RNase-like effectors, including Avra13 from B. g. hordei, the cognate Avr of the barley resistance gene Mla13. These results demonstrate the conservation of functional avirulence genes in two cereal powdery mildews specialized on different hosts, thus providing a possible explanation for successful introgression of resistance genes from rye or other grass relatives to wheat.
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Affiliation(s)
- Coraline R. Praz
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Salim Bourras
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Fansong Zeng
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | | | - Fabrizio Menardo
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Minfeng Xue
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Lijun Yang
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Stefan Roffler
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Rainer Böni
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Gerard Herren
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Kaitlin E. McNally
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Roi Ben‐David
- Institute of Plant ScienceARO‐Volcani CenterBet Dagan50250Israel
| | - Francis Parlange
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simone Oberhaensli
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Simon Flückiger
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Luisa K. Schäfer
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
| | - Dazhao Yu
- Institute of Plant Protection and Soil ScienceHubei Academy of Agricultural SciencesWuhan430064China
- Ministry of Agriculture Key Laboratory of Integrated Pest Management in Crops in Central ChinaWuhan430064China
- College of Life ScienceWuhan UniversityWuhan430072China
| | - Beat Keller
- Department of Plant and Microbial BiologyUniversity of ZürichZürich8008Switzerland
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99
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Abstract
Fungal plant pathogens are ubiquitous and highly diverse. Key to their success is high host density, which notably is the case in agroecosystems. Several hypotheses related to the effects of plant pathogens on plant diversity (the Janzen-Connell hypothesis, the dilution effect hypothesis) and the phenomenon of higher biomass in plant mixtures (i.e., overyielding) can all be explained by the quantitative interplay between host and pathogen density. In many agroecosystems, fungal plant pathogens cause great losses, since in monocultures diseased plants cannot be replaced by healthy plants. On the other hand, in natural ecosystems fungal plant pathogens shape the succession of vegetation and enhance the biodiversity of forests and grasslands. When pathogens are introduced into areas outside their natural range, they may behave differently, causing severe damage. Once introduced, changes may occur such as hybridization with other closely related pathogens or host shifts, host jumps, or horizontal gene transfer. Such changes can be hazardous for both agricultural and natural ecosystems.
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100
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Plissonneau C, Benevenuto J, Mohd-Assaad N, Fouché S, Hartmann FE, Croll D. Using Population and Comparative Genomics to Understand the Genetic Basis of Effector-Driven Fungal Pathogen Evolution. FRONTIERS IN PLANT SCIENCE 2017; 8:119. [PMID: 28217138 PMCID: PMC5289978 DOI: 10.3389/fpls.2017.00119] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/20/2017] [Indexed: 05/20/2023]
Abstract
Epidemics caused by fungal plant pathogens pose a major threat to agro-ecosystems and impact global food security. High-throughput sequencing enabled major advances in understanding how pathogens cause disease on crops. Hundreds of fungal genomes are now available and analyzing these genomes highlighted the key role of effector genes in disease. Effectors are small secreted proteins that enhance infection by manipulating host metabolism. Fungal genomes carry 100s of putative effector genes, but the lack of homology among effector genes, even for closely related species, challenges evolutionary and functional analyses. Furthermore, effector genes are often found in rapidly evolving chromosome compartments which are difficult to assemble. We review how population and comparative genomics toolsets can be combined to address these challenges. We highlight studies that associated genome-scale polymorphisms with pathogen lifestyles and adaptation to different environments. We show how genome-wide association studies can be used to identify effectors and other pathogenicity-related genes underlying rapid adaptation. We also discuss how the compartmentalization of fungal genomes into core and accessory regions shapes the evolution of effector genes. We argue that an understanding of genome evolution provides important insight into the trajectory of host-pathogen co-evolution.
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Affiliation(s)
- Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- UMR, BIOGER, INRA, AgroParisTech, Université Paris-SaclayThiverval-Grignon, France
| | - Juliana Benevenuto
- College of Agriculture “Luiz de Queiroz”, University of São PauloSão Paulo, Brazil
| | - Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan MalaysiaSelangor, Malaysia
| | - Simone Fouché
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
| | - Fanny E. Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurich, Switzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchatelNeuchatel, Switzerland
- *Correspondence: Daniel Croll,
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