1
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Lambou K, Tag A, Lassagne A, Collemare J, Clergeot PH, Barbisan C, Perret P, Tharreau D, Millazo J, Chartier E, De Vries RP, Hirsch J, Morel JB, Beffa R, Kroj T, Thomas T, Lebrun MH. The bZIP transcription factor BIP1 of the rice blast fungus is essential for infection and regulates a specific set of appressorium genes. PLoS Pathog 2024; 20:e1011945. [PMID: 38252628 PMCID: PMC10833574 DOI: 10.1371/journal.ppat.1011945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 02/01/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The rice blast fungus Magnaporthe oryzae differentiates specialized cells called appressoria that are required for fungal penetration into host leaves. In this study, we identified the novel basic leucine zipper (bZIP) transcription factor BIP1 (B-ZIP Involved in Pathogenesis-1) that is essential for pathogenicity. BIP1 is required for the infection of plant leaves, even if they are wounded, but not for appressorium-mediated penetration of artificial cellophane membranes. This phenotype suggests that BIP1 is not implicated in the differentiation of the penetration peg but is necessary for the initial establishment of the fungus within plant cells. BIP1 expression was restricted to the appressorium by both transcriptional and post-transcriptional control. Genome-wide transcriptome analysis showed that 40 genes were down regulated in a BIP1 deletion mutant. Most of these genes were specifically expressed in the appressorium. They encode proteins with pathogenesis-related functions such as enzymes involved in secondary metabolism including those encoded by the ACE1 gene cluster, small secreted proteins such as SLP2, BAS2, BAS3, and AVR-Pi9 effectors, as well as plant cuticle and cell wall degrading enzymes. Interestingly, this BIP1 network is different from other known infection-related regulatory networks, highlighting the complexity of gene expression control during plant-fungal interactions. Promoters of BIP1-regulated genes shared a GCN4/bZIP-binding DNA motif (TGACTC) binding in vitro to BIP1. Mutation of this motif in the promoter of MGG_08381.7 from the ACE1 gene cluster abolished its appressorium-specific expression, showing that BIP1 behaves as a transcriptional activator. In summary, our findings demonstrate that BIP1 is critical for the expression of early invasion-related genes in appressoria. These genes are likely needed for biotrophic invasion of the first infected host cell, but not for the penetration process itself. Through these mechanisms, the blast fungus strategically anticipates the host plant environment and responses during appressorium-mediated penetration.
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Affiliation(s)
- Karine Lambou
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Andrew Tag
- Department of Biology, Texas A&M University. College Station, Texas, United States of America
| | - Alexandre Lassagne
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Jérôme Collemare
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Pierre-Henri Clergeot
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- ASP Bourgogne Franche-Comté, Dijon, France
| | | | - Philippe Perret
- Biochemistry Department, Bayer Crop Science SAS, Lyon, France
- Bayer S.A.S. Crop Science Division Global Toxicology- Sophia Antipolis Cedex, France
| | - Didier Tharreau
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Joelle Millazo
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Elia Chartier
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Ronald P. De Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Judith Hirsch
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- Pathologie Végétale, INRAE, Montfavet, France
| | - Jean-Benoit Morel
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Roland Beffa
- Biochemistry Department, Bayer Crop Science SAS, Lyon, France
| | - Thomas Kroj
- Plant Health Institute of Montpellier (PHIM), Montpellier University, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Terry Thomas
- Department of Biology, Texas A&M University. College Station, Texas, United States of America
| | - Marc-Henri Lebrun
- CNRS-Bayer Crop Science, UMR 5240 MAP, Lyon, France
- Université Paris-Saclay, INRAE, UR 1290 BIOGER, Palaiseau, France
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Kaboré KH, Kassankogno AI, Adreit H, Ravel S, Charriat F, Diagne D, Lebrun MH, Tharreau D. Whole-genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum isolated from rice in Burkina Faso, France, Mali, and Pakistan. Microbiol Resour Announc 2023; 12:e0013423. [PMID: 37812008 PMCID: PMC10652970 DOI: 10.1128/mra.00134-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/23/2023] [Indexed: 10/10/2023] Open
Abstract
Different fungal species of the Pleosporaceae family infect rice, causing similar symptoms. Reference genomic sequences are useful tools to study the evolution of these species and to develop accurate molecular diagnostic tools. Here, we report the complete genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum.
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Affiliation(s)
- Kouka Hilaire Kaboré
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- CIRAD, UMR PHIM, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier, Montpellier, France
| | - Sebastien Ravel
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier, Montpellier, France
| | - Florian Charriat
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier, Montpellier, France
| | - Diariatou Diagne
- Laboratoire de Biologie Moléculaire Appliquée (LBMA)/Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | | | - Didier Tharreau
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier, Montpellier, France
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3
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Feurtey A, Lorrain C, McDonald MC, Milgate A, Solomon PS, Warren R, Puccetti G, Scalliet G, Torriani SFF, Gout L, Marcel TC, Suffert F, Alassimone J, Lipzen A, Yoshinaga Y, Daum C, Barry K, Grigoriev IV, Goodwin SB, Genissel A, Seidl MF, Stukenbrock EH, Lebrun MH, Kema GHJ, McDonald BA, Croll D. A thousand-genome panel retraces the global spread and adaptation of a major fungal crop pathogen. Nat Commun 2023; 14:1059. [PMID: 36828814 PMCID: PMC9958100 DOI: 10.1038/s41467-023-36674-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Human activity impacts the evolutionary trajectories of many species worldwide. Global trade of agricultural goods contributes to the dispersal of pathogens reshaping their genetic makeup and providing opportunities for virulence gains. Understanding how pathogens surmount control strategies and cope with new climates is crucial to predicting the future impact of crop pathogens. Here, we address this by assembling a global thousand-genome panel of Zymoseptoria tritici, a major fungal pathogen of wheat reported in all production areas worldwide. We identify the global invasion routes and ongoing genetic exchange of the pathogen among wheat-growing regions. We find that the global expansion was accompanied by increased activity of transposable elements and weakened genomic defenses. Finally, we find significant standing variation for adaptation to new climates encountered during the global spread. Our work shows how large population genomic panels enable deep insights into the evolutionary trajectory of a major crop pathogen.
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Affiliation(s)
- Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Cécile Lorrain
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Megan C McDonald
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
- School of Biosciences, Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - Andrew Milgate
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Pine Gully Road, Wagga Wagga, NSW, 2650, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rachael Warren
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332, Stein, Switzerland
| | | | | | - Lilian Gout
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Thierry C Marcel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Frédéric Suffert
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | | | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher Daum
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 9472, USA
| | | | - Anne Genissel
- Université Paris Saclay, INRAE, UR BIOGER, 91120, Palaiseau, France
| | - Michael F Seidl
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
- Utrecht University, Theoretical Biology and Bioinformatics, Utrecht, The Netherlands
| | - Eva H Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | | | - Gert H J Kema
- Wageningen University and Research, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Bruce A McDonald
- Plant Pathology, D-USYS, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland.
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Fernandez O, Lemaître-Guillier C, Songy A, Robert-Siegwald G, Lebrun MH, Schmitt-Kopplin P, Larignon P, Adrian M, Fontaine F. The Combination of Both Heat and Water Stresses May Worsen Botryosphaeria Dieback Symptoms in Grapevine. Plants (Basel) 2023; 12:plants12040753. [PMID: 36840101 PMCID: PMC9961737 DOI: 10.3390/plants12040753] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 06/12/2023]
Abstract
(1) Background: Grapevine trunk diseases (GTDs) have become a global threat to vineyards worldwide. These diseases share three main common features. First, they are caused by multiple pathogenic micro-organisms. Second, these pathogens often maintain a long latent phase, which makes any research in pathology and symptomatology challenging. Third, a consensus is raising to pinpoint combined abiotic stresses as a key factor contributing to disease symptom expression. (2) Methods: We analyzed the impact of combined abiotic stresses in grapevine cuttings artificially infected by two fungi involved in Botryosphaeria dieback (one of the major GTDs), Neofusicoccum parvum and Diplodia seriata. Fungal-infected and control plants were subjected to single or combined abiotic stresses (heat stress, drought stress or both). Disease intensity was monitored thanks to the measurement of necrosis area size. (3) Results and conclusions: Overall, our results suggest that combined stresses might have a stronger impact on disease intensity upon infection by the less virulent pathogen Diplodia seriata. This conclusion is discussed through the impact on plant physiology using metabolomic and transcriptomic analyses of leaves sampled for the different conditions.
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Affiliation(s)
- Olivier Fernandez
- Unité Résistance Induite et Bioprotection des Plantes EA 4707, USC INRAE 1488, SFR Condorcet FR CNRS 3417, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | | | - Aurélie Songy
- Unité Résistance Induite et Bioprotection des Plantes EA 4707, USC INRAE 1488, SFR Condorcet FR CNRS 3417, Université de Reims Champagne-Ardenne, 51100 Reims, France
| | | | - Marc-Henri Lebrun
- Research Group Genomics of Plant-Pathogen Interactions, Research Unit Biologie et Gestion des Risques en Agriculture, UR 1290 BIOGER, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | - Philippe Schmitt-Kopplin
- Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | | | - Marielle Adrian
- Agroécologie, Institut Agro Dijon, CNRS, INRAE, Université Bourgogne Franche-Comté, 21000 Dijon, France
| | - Florence Fontaine
- Unité Résistance Induite et Bioprotection des Plantes EA 4707, USC INRAE 1488, SFR Condorcet FR CNRS 3417, Université de Reims Champagne-Ardenne, 51100 Reims, France
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5
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Oliveira L, Chevrollier N, Dallery JF, O'Connell RJ, Lebrun MH, Viaud M, Lespinet O. CusProSe: a customizable protein annotation software with an application to the prediction of fungal secondary metabolism genes. Sci Rep 2023; 13:1417. [PMID: 36697464 PMCID: PMC9876896 DOI: 10.1038/s41598-023-27813-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
We report here a new application, CustomProteinSearch (CusProSe), whose purpose is to help users to search for proteins of interest based on their domain composition. The application is customizable. It consists of two independent tools, IterHMMBuild and ProSeCDA. IterHMMBuild allows the iterative construction of Hidden Markov Model (HMM) profiles for conserved domains of selected protein sequences, while ProSeCDA scans a proteome of interest against an HMM profile database, and annotates identified proteins using user-defined rules. CusProSe was successfully used to identify, in fungal genomes, genes encoding key enzyme families involved in secondary metabolism, such as polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), hybrid PKS-NRPS and dimethylallyl tryptophan synthases (DMATS), as well as to characterize distinct terpene synthases (TS) sub-families. The highly configurable characteristics of this application makes it a generic tool, which allows the user to refine the function of predicted proteins, to extend detection to new enzymes families, and may also be applied to biological systems other than fungi and to other proteins than those involved in secondary metabolism.
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Affiliation(s)
- Leonor Oliveira
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.
| | - Nicolas Chevrollier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France.,Orphanet-INSERM, US14, Plateforme des Maladies Rares, Paris, France
| | - Jean-Felix Dallery
- Université Paris-Saclay, INRAE, UR BIOGER, 78850, Thiverval-Grignon, France
| | | | - Marc-Henri Lebrun
- Université Paris-Saclay, INRAE, UR BIOGER, 78850, Thiverval-Grignon, France
| | - Muriel Viaud
- Université Paris-Saclay, INRAE, UR BIOGER, 78850, Thiverval-Grignon, France
| | - Olivier Lespinet
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
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Kaboré KH, Kassankogno AI, Adreit H, Milazzo J, Guillou S, Blondin L, Chopin L, Ravel S, Charriat F, Barro M, Tollenaere C, Lebrun MH, Tharreau D. Genetic diversity and structure of Bipolaris oryzae and Exserohilum rostratum populations causing brown spot of rice in Burkina Faso based on genotyping-by-sequencing. Front Plant Sci 2022; 13:1022348. [PMID: 36507371 PMCID: PMC9732276 DOI: 10.3389/fpls.2022.1022348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
In recent years, Brown spot disease of rice (BSR) has been observed on leaves and seeds of rice in all rice-growing areas of Burkina Faso. Bipolaris oryzae and Exserohilum rostratum are the main fungal species isolated from BSR infected tissues and they are frequently observed in the same field. However, we are lacking information on the genetic diversity and population structure of these fungi in Burkina Faso. The mode of reproduction is also unknown. The genetic diversity of isolates of B. oryzae (n=61) and E. rostratum (n=151), collected from major rice-growing areas of Burkina Faso, was estimated using genotyping-by-sequencing (GBS). The mean values for nucleotide diversity (π) were 1.9 x10-4 for B. oryzae and 4.8 x10-4 for E. rostratum. There is no genetic differentiation between the geographical populations of each species. The analysis of molecular variance revealed that 89% and 94% of the genetic variances were within the populations of B. oryzae and E. rostratum, respectively. For each species, four genetic clusters were identified by two clustering methods (DAPC and sNMF). The distribution of these genetic groups was independent of the geographical origin of the isolates. Evidence of recombination was detected in the populations of B. oryzae and E. rostratum. For B. oryzae balanced mating type ratios were supporting sexual reproduction. For E. rostratum overrepresentation of MAT1-2 isolates (79%) suggested a predominant asexual reproduction. This study provides important information on the biology and genetics of the two major fungi causing brown spot disease of rice in Burkina Faso.
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Affiliation(s)
- Kouka Hilaire Kaboré
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- CIRAD, UMR PHIM, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Joëlle Milazzo
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Sonia Guillou
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Laurence Blondin
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Laurie Chopin
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Sébastien Ravel
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Florian Charriat
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Mariam Barro
- CNRST/INERA, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | | | | | - Didier Tharreau
- CIRAD, UMR PHIM, Montpellier, France
- PHIM, Univ Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
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7
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Kaboré KH, Diagne D, Milazzo J, Adreit H, Lebrun MH, Tharreau D. First Report of Rice Brown Spot Caused by Exserohilum rostratum in Mali. Plant Dis 2022; 106:PDIS03210662PDN. [PMID: 34784745 DOI: 10.1094/pdis-03-21-0662-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Kouka Hilaire Kaboré
- UMR BIOGER, Université Paris-Saclay, INRAE, AgroParisTech, 78850 Thiverval-Grignon, France
- CIRAD, PHIM, 34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Diariatou Diagne
- CIRAD, PHIM, 34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
- Laboratoire de Biologie Moléculaire Appliquée (LBMA)/Université des Sciences des Techniques et des Technologies de Bamako (USTTB), Mali
| | - Joëlle Milazzo
- CIRAD, PHIM, 34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Henri Adreit
- CIRAD, PHIM, 34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
| | - Marc-Henri Lebrun
- UMR BIOGER, Université Paris-Saclay, INRAE, AgroParisTech, 78850 Thiverval-Grignon, France
| | - Didier Tharreau
- CIRAD, PHIM, 34398 Montpellier, France
- PHIM, Université Montpellier, CIRAD, INRAE, IRD, Montpellier SupAgro, Montpellier, France
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Battache M, Lebrun MH, Sakai K, Soudière O, Cambon F, Langin T, Saintenac C. Blocked at the Stomatal Gate, a Key Step of Wheat Stb16q-Mediated Resistance to Zymoseptoria tritici. Front Plant Sci 2022; 13:921074. [PMID: 35832231 PMCID: PMC9271956 DOI: 10.3389/fpls.2022.921074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/03/2022] [Indexed: 05/11/2023]
Abstract
Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is among the most threatening wheat diseases in Europe. Genetic resistance remains one of the main environmentally sustainable strategies to efficiently control STB. However, the molecular and physiological mechanisms underlying resistance are still unknown, limiting the implementation of knowledge-driven management strategies. Among the 22 known major resistance genes (Stb), the recently cloned Stb16q gene encodes a cysteine-rich receptor-like kinase conferring a full broad-spectrum resistance against Z. tritici. Here, we showed that an avirulent Z. tritici inoculated on Stb16q quasi near isogenic lines (NILs) either by infiltration into leaf tissues or by brush inoculation of wounded tissues partially bypasses Stb16q-mediated resistance. To understand this bypass, we monitored the infection of GFP-labeled avirulent and virulent isolates on Stb16q NILs, from germination to pycnidia formation. This quantitative cytological analysis revealed that 95% of the penetration attempts were unsuccessful in the Stb16q incompatible interaction, while almost all succeeded in compatible interactions. Infectious hyphae resulting from the few successful penetration events in the Stb16q incompatible interaction were arrested in the sub-stomatal cavity of the primary-infected stomata. These results indicate that Stb16q-mediated resistance mainly blocks the avirulent isolate during its stomatal penetration into wheat tissue. Analyses of stomatal aperture of the Stb16q NILs during infection revealed that Stb16q triggers a temporary stomatal closure in response to an avirulent isolate. Finally, we showed that infiltrating avirulent isolates into leaves of the Stb6 and Stb9 NILs also partially bypasses resistances, suggesting that arrest during stomatal penetration might be a common major mechanism for Stb-mediated resistances.
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Affiliation(s)
- Mélissa Battache
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
| | - Marc-Henri Lebrun
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Kaori Sakai
- Université Paris-Saclay, INRAE, UR BIOGER, Thiverval-Grignon, France
| | - Olivier Soudière
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
| | - Florence Cambon
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
| | - Thierry Langin
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
| | - Cyrille Saintenac
- Université Clermont Auvergne, INRAE, GDEC, Clermont-Ferrand, France
- *Correspondence: Cyrille Saintenac,
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9
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Bruez E, Vallance J, Gautier A, Laval V, Compant S, Maurer W, Sessitsch A, Lebrun MH, Rey P. Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease. Environ Microbiol 2020; 22:5189-5206. [PMID: 32755016 DOI: 10.1111/1462-2920.15180] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 11/27/2022]
Abstract
Esca, a major grapevine trunk disease in old grapevines, is associated with the colonization of woody tissues by a broad range of plant pathogenic fungi. To identify which fungal and bacterial species are involved in the onset of this disease, we analysed the microbiota from woody tissues of young (10-year-old) grapevines at an early stage of esca. Using meta-barcoding, 515 fungal and 403 bacterial operational taxonomic units (OTUs) were identified in woody tissues. In situ hybridization showed that these fungi and bacteria co-inhabited in grapevine woody tissues. In non-necrotic woody tissues, fungal and bacterial microbiota varied according to organs and seasons but not diseased plant status. Phaeomoniella chlamydospora, involved in the Grapevine trunk disease, was the most abundant species in non-necrotic tissues from healthy plants, suggesting a possible non-pathogenic endophytic behaviour. Most diseased plants (70%) displayed cordons, with their central white-rot necrosis colonized essentially by two plant pathogenic fungi (Fomitiporia mediterranea: 60%-90% and P. chlamydospora: 5%-15%) and by a few bacterial taxa (Sphingomonas spp. and Mycobacterium spp.). The occurrence of a specific association of fungal and bacterial species in cordons from young grapevines expressing esca-foliar symptoms strongly suggests that that microbiota is involved in the onset of this complex disease.
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Affiliation(s)
- Emilie Bruez
- INRAE, ISVV, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, Villenave d'Ornon, F-33140, France.,Bordeaux Sciences Agro, INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Gradignan, F-33130, France.,Université de Bordeaux, Unité de recherche Œnologie, EA 4577, USC 1366 INRAE, Villenave d'Ornon, F-33882, France
| | - Jessica Vallance
- INRAE, ISVV, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, Villenave d'Ornon, F-33140, France.,Bordeaux Sciences Agro, INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Gradignan, F-33130, France
| | - Angélique Gautier
- INRAE, AgroParisTech, UMR 1290 Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, F-78850, France
| | - Valérie Laval
- INRAE, AgroParisTech, UMR 1290 Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, F-78850, France
| | - Stéphane Compant
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Tulln, 3430, Austria
| | - Wolfgang Maurer
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Tulln, 3430, Austria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Bioresources Unit, Center for Health & Bioresources, Tulln, 3430, Austria
| | - Marc-Henri Lebrun
- INRAE, AgroParisTech, UMR 1290 Biologie et gestion des risques en agriculture (BIOGER), Thiverval-Grignon, F-78850, France
| | - Patrice Rey
- INRAE, ISVV, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Bordeaux Sciences Agro, Villenave d'Ornon, F-33140, France.,Bordeaux Sciences Agro, INRAE, UMR1065 Santé et Agroécologie du Vignoble (SAVE), Gradignan, F-33130, France
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10
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Phan HTT, Jones DAB, Rybak K, Dodhia KN, Lopez-Ruiz FJ, Valade R, Gout L, Lebrun MH, Brunner PC, Oliver RP, Tan KC. Low Amplitude Boom-and-Bust Cycles Define the Septoria Nodorum Blotch Interaction. Front Plant Sci 2020; 10:1785. [PMID: 32082346 PMCID: PMC7005668 DOI: 10.3389/fpls.2019.01785] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/20/2019] [Indexed: 05/30/2023]
Abstract
INTRODUCTION Septoria nodorum blotch (SNB) is a complex fungal disease of wheat caused by the Dothideomycete fungal pathogen Parastagonospora nodorum. The fungus infects through the use of necrotrophic effectors (NEs) that cause necrosis on hosts carrying matching dominant susceptibility genes. The Western Australia (WA) wheatbelt is a SNB "hot spot" and experiences significant under favorable conditions. Consequently, SNB has been a major target for breeders in WA for many years. MATERIALS AND METHODS In this study, we assembled a panel of 155 WA P. nodorum isolates collected over a 44-year period and compared them to 23 isolates from France and the USA using 28 SSR loci. RESULTS The WA P. nodorum population was clustered into five groups with contrasting properties. 80% of the studied isolates were assigned to two core groups found throughout the collection location and time. The other three non-core groups that encompassed transient and emergent populations were found in restricted locations and time. Changes in group genotypes occurred during periods that coincided with the mass adoption of a single or a small group of widely planted wheat cultivars. When introduced, these cultivars had high scores for SNB resistance. However, the field resistance of these new cultivars often declined over subsequent seasons prompting their replacement with new, more resistant varieties. Pathogenicity assays showed that newly emerged isolates non-core are more pathogenic than old isolates. It is likely that the non-core groups were repeatedly selected for increased virulence on the contemporary popular cultivars. DISCUSSION The low level of genetic diversity within the non-core groups, difference in virulence, low abundance, and restriction to limited locations suggest that these populations more vulnerable to a population crash when the cultivar was replaced by one that was genetically different and more resistant. We characterize the observed pattern as a low-amplitude boom-and-bust cycle in contrast with the classical high amplitude boom-and-bust cycles seen for biotrophic pathogens where the contrast between resistance and susceptibility is typically much greater. Implications of the results are discussed relating to breeding strategies for more sustainable SNB resistance and more generally for pathogens with NEs.
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Affiliation(s)
- Huyen T. T. Phan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Darcy A. B. Jones
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kasia Rybak
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kejal N. Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Francisco J. Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Romain Valade
- ARVALIS Institut du Végétal Avenue Lucien Brétignières, Bâtiment INRA Bioger, Thiverval-Grignon, France
| | - Lilian Gout
- UMR INRA Bioger Agro-ParisTech, Thiverval-Grignon, France
| | | | - Patrick C. Brunner
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Richard P. Oliver
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Kar-Chun Tan
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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11
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Collemare J, O'Connell R, Lebrun MH. Nonproteinaceous effectors: the terra incognita of plant-fungal interactions. New Phytol 2019; 223:590-596. [PMID: 30851201 DOI: 10.1111/nph.15785] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/22/2019] [Indexed: 05/27/2023]
Abstract
Molecular plant-fungal interaction studies have mainly focused on small secreted protein effectors. However, accumulating evidence shows that numerous fungal secondary metabolites are produced at all stages of plant colonization, especially during early asymptomatic/biotrophic phases. The discovery of fungal small RNAs targeting plant transcripts has expanded the fungal repertoire of nonproteinaceous effectors even further. The challenge now is to develop specific functional methods to fully understand the biological roles of these effectors. Studies on fungal extracellular vesicles are also needed because they could be the universal carriers of all kinds of fungal effectors. With this review, we aim to stimulate the nonproteinaceous effector research field to move from descriptive to functional studies, which should bring a paradigm shift in plant-fungal interactions.
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Affiliation(s)
- Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
| | - Richard O'Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, F78850, Thiverval-Grignon, France
| | - Marc-Henri Lebrun
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, F78850, Thiverval-Grignon, France
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12
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Anasontzis GE, Lebrun MH, Haon M, Champion C, Kohler A, Lenfant N, Martin F, O'Connell RJ, Riley R, Grigoriev IV, Henrissat B, Berrin JG, Rosso MN. Broad-specificity GH131 β-glucanases are a hallmark of fungi and oomycetes that colonize plants. Environ Microbiol 2019; 21:2724-2739. [PMID: 30887618 DOI: 10.1111/1462-2920.14596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/17/2019] [Accepted: 03/17/2019] [Indexed: 12/21/2022]
Abstract
Plant-tissue-colonizing fungi fine-tune the deconstruction of plant-cell walls (PCW) using different sets of enzymes according to their lifestyle. However, some of these enzymes are conserved among fungi with dissimilar lifestyles. We identified genes from Glycoside Hydrolase family GH131 as commonly expressed during plant-tissue colonization by saprobic, pathogenic and symbiotic fungi. By searching all the publicly available genomes, we found that GH131-coding genes were widely distributed in the Dikarya subkingdom, except in Taphrinomycotina and Saccharomycotina, and in phytopathogenic Oomycetes, but neither other eukaryotes nor prokaryotes. The presence of GH131 in a species was correlated with its association with plants as symbiont, pathogen or saprobe. We propose that GH131-family expansions and horizontal-gene transfers contributed to this adaptation. We analysed the biochemical activities of GH131 enzymes whose genes were upregulated during plant-tissue colonization in a saprobe (Pycnoporus sanguineus), a plant symbiont (Laccaria bicolor) and three hemibiotrophic-plant pathogens (Colletotrichum higginsianum, C. graminicola, Zymoseptoria tritici). These enzymes were all active on substrates with β-1,4, β-1,3 and mixed β-1,4/1,3 glucosidic linkages. Combined with a cellobiohydrolase, GH131 enzymes enhanced cellulose degradation. We propose that secreted GH131 enzymes unlock the PCW barrier and allow further deconstruction by other enzymes during plant tissue colonization by symbionts, pathogens and saprobes.
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Affiliation(s)
- George E Anasontzis
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.,CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Marc-Henri Lebrun
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Mireille Haon
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Charlotte Champion
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Annegret Kohler
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Nicolas Lenfant
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France
| | - Francis Martin
- INRA, University of Lorraine, Laboratory of Excellence Advanced Research on the Biology of Tree and Forest Ecosystems (ARBRE), UMR 1136, Champenoux, France
| | - Richard J O'Connell
- INRA, AgroParisTech, Université Paris-Saclay, BIOGER, Thiverval-Grignon, France
| | - Robert Riley
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA, 94598, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94598, USA
| | - Bernard Henrissat
- CNRS, Aix-Marseille Univ, UMR7257, Architecture et Fonction des Macromolecules Biologiques, Marseille, France.,INRA, USC 1408, AFMB, Marseille, France
| | - Jean-Guy Berrin
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
| | - Marie-Noëlle Rosso
- INRA, Aix-Marseille Univ, UMR1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France
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13
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018. [PMID: 29487238 DOI: 10.01210.01128/mbio] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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14
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018; 9:e01219-17. [PMID: 29487238 PMCID: PMC5829825 DOI: 10.1128/mbio.01219-17] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/20/2017] [Indexed: 11/25/2022] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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15
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Robert-Siegwald G, Vallet J, Abou-Mansour E, Xu J, Rey P, Bertsch C, Rego C, Larignon P, Fontaine F, Lebrun MH. Draft Genome Sequence of Diplodia seriata F98.1, a Fungal Species Involved in Grapevine Trunk Diseases. Genome Announc 2017; 5:e00061-17. [PMID: 28385831 PMCID: PMC5383879 DOI: 10.1128/genomea.00061-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/02/2017] [Indexed: 12/03/2022]
Abstract
The ascomycete Diplodia seriata is a causal agent of grapevine trunk diseases. Here, we present the draft genome sequence of D. seriata isolate F98.1 (37.27 Mb, 512 contigs, 112 scaffolds, and 8,087 predicted protein-coding genes).
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Affiliation(s)
| | - Julie Vallet
- Université de Reims Champagne-Ardenne, URVVC EA 4707, Laboratoire Stress, Défenses et Reproduction des Plantes, Reims, France
| | | | | | - Patrice Rey
- UMR1065 SAVE, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, Villenave d'Ornon, France
| | - Christophe Bertsch
- Université Haute Alsace, Laboratoire Vigne Biotechnologie et Environnement EA 3991, Colmar, France
| | - Cecilia Rego
- Institut Supérieur d'Agronomie, Tapada da Ajuda, Lisbon, Portugal
| | - Philippe Larignon
- Institut Français de la Vigne et du Vin Pôle Rhône-Méditerranée, Rodilhan, France
| | - Florence Fontaine
- Université de Reims Champagne-Ardenne, URVVC EA 4707, Laboratoire Stress, Défenses et Reproduction des Plantes, Reims, France
| | - Marc-Henri Lebrun
- UMR 1290 BIOGER, INRA, AgroParisTech, Campus AgroParistech, Thiverval-Grignon, France
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16
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Genissel A, Confais J, Lebrun MH, Gout L. Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function. Front Plant Sci 2017; 8:1301. [PMID: 28791038 PMCID: PMC5524819 DOI: 10.3389/fpls.2017.01301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/11/2017] [Indexed: 05/05/2023]
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17
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Vincent D, Plummer KM, Solomon PS, Lebrun MH, Job D, Rafiqi M. Editorial: How Can Secretomics Help Unravel the Secrets of Plant-Microbe Interactions? Front Plant Sci 2016; 7:1777. [PMID: 27965687 PMCID: PMC5127848 DOI: 10.3389/fpls.2016.01777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Delphine Vincent
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Kim M. Plummer
- Animal, Plant and Soil Sciences Department, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of Biology, The Australian National UniversityCanberra, ACT, Australia
| | - Marc-Henri Lebrun
- Institut National de la Recherche Agronomique-AgroParisTech, UMR INRA1290, Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des PlantesThiverval-Grignon, France
| | - Dominique Job
- Centre National de la Recherche-Scientifique, UMR5240 Centre Nationnal de la Recherche Scientifique/University Claude Bernard Lyon 1/INSA/Bayer CropScience Joint Laboratory, Bayer CropScienceLyon, France
| | - Maryam Rafiqi
- Jodrell Laboratory, Royal Botanic GardensKew, London, UK
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18
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Islam MT, Croll D, Gladieux P, Soanes DM, Persoons A, Bhattacharjee P, Hossain MS, Gupta DR, Rahman MM, Mahboob MG, Cook N, Salam MU, Surovy MZ, Sancho VB, Maciel JLN, NhaniJúnior A, Castroagudín VL, Reges JTDA, Ceresini PC, Ravel S, Kellner R, Fournier E, Tharreau D, Lebrun MH, McDonald BA, Stitt T, Swan D, Talbot NJ, Saunders DGO, Win J, Kamoun S. Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae. BMC Biol 2016; 14:84. [PMID: 27716181 PMCID: PMC5047043 DOI: 10.1186/s12915-016-0309-7] [Citation(s) in RCA: 204] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/12/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated wheat area in Bangladesh, with yield losses reaching up to 100 %. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. RESULTS Reinoculation of seedlings with strains isolated from infected wheat grains showed wheat blast symptoms on leaves of wheat but not rice. Our phylogenomic and population genomic analyses revealed that the wheat blast outbreak in Bangladesh was most likely caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. CONCLUSION Our findings suggest that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.
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Affiliation(s)
- M Tofazzal Islam
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Pierre Gladieux
- INRA, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Darren M Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | | | - Pallab Bhattacharjee
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Shaid Hossain
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Dipali Rani Gupta
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - Md Mahbubur Rahman
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | - M Golam Mahboob
- Argo-Environmental Remote Sensing and Modeling Lab, Bangladesh Agricultural Research Institute, Joydebpur 1701, Gazipur, Bangladesh
| | - Nicola Cook
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Moin U Salam
- Directorate of Grains Industry, Department of Agriculture and Food Western Australia (DAFWA), 3 Baron-Hay Court, South Perth, WA, 6151, Australia
| | - Musrat Zahan Surovy
- Department of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh
| | | | - João Leodato Nunes Maciel
- Brazilian Agricultural Research Enterprise - EMBRAPA Wheat/Trigo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Antonio NhaniJúnior
- Brazilian Agricultural Research Enterprise - EMBRAPA Wheat/Trigo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Vanina Lilián Castroagudín
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Juliana T de Assis Reges
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Paulo Cezar Ceresini
- Department of Crop Protection, Rural Engineering, and Soil Science, University of São Paulo State - UNESP, IlhaSolteira Campus, São Paulo, Brazil
| | - Sebastien Ravel
- CIRAD, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Ronny Kellner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Elisabeth Fournier
- INRA, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Didier Tharreau
- CIRAD, UMR 385 Biologie et génétique des interactions plantes-pathogènes BGPI, Montpellier, France
| | - Marc-Henri Lebrun
- INRA, UMR 1290 Biologie et Gestion des Risques en agriculture BIOGER, Thiverval-Grignon, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, 8092, Zurich, Switzerland
| | - Timothy Stitt
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Daniel Swan
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Diane G O Saunders
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Joe Win
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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19
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Zhang N, Luo J, Rossman AY, Aoki T, Chuma I, Crous PW, Dean R, de Vries RP, Donofrio N, Hyde KD, Lebrun MH, Talbot NJ, Tharreau D, Tosa Y, Valent B, Wang Z, Xu JR. Generic names in Magnaporthales. IMA Fungus 2016; 7:155-9. [PMID: 27433445 PMCID: PMC4941683 DOI: 10.5598/imafungus.2016.07.01.09] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/15/2016] [Indexed: 11/04/2022] Open
Abstract
The order Magnaporthales comprises about 200 species and includes the economically and scientifically important rice blast fungus and the take-all pathogen of cereals, as well as saprotrophs and endophytes. Recent advances in phylogenetic analyses of these fungi resulted in taxonomic revisions. In this paper we list the 28 currently accepted genera in Magnaporthales with their type species and available gene and genome resources. The polyphyletic Magnaporthe 1972 is proposed for suppression, and Pyricularia 1880 and Nakataea 1939 are recommended for protection as the generic names for the rice blast fungus and the rice stem rot fungus, respectively. The rationale for the recommended names is also provided. These recommendations are made by the Pyricularia/Magnaporthe Working Group established under the auspices of the International Commission on the Taxonomy of Fungi (ICTF).
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Affiliation(s)
- Ning Zhang
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jing Luo
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Amy Y Rossman
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Izumi Chuma
- Kobe University, 1-1 Rokkodai cho, Nada-ku, Kobe 657-8501, Japan
| | - Pedro W Crous
- CBS-KNAW Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Ralph Dean
- Department of Plant Pathology, 2510 Thomas Hall, Raleigh, NC 27695, North Carolina State University, USA
| | - Ronald P de Vries
- CBS-KNAW Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands; Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Nicole Donofrio
- Department of Plant and Soil Sciences, University of Delaware, 531 S. College Ave, 152 Townsend Hall, Newark, DE 19711, USA
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Marc-Henri Lebrun
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, 78850 Thiverval-Grignon, France
| | | | | | - Yukio Tosa
- Kobe University, 1-1 Rokkodai cho, Nada-ku, Kobe 657-8501, Japan
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA
| | - Zonghua Wang
- Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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20
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Klaubauf S, Zhou M, Lebrun MH, de Vries RP, Battaglia E. A novel L-arabinose-responsive regulator discovered in the rice-blast fungus Pyricularia oryzae (Magnaporthe oryzae). FEBS Lett 2016; 590:550-8. [PMID: 26790567 DOI: 10.1002/1873-3468.12070] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/19/2015] [Accepted: 01/04/2016] [Indexed: 11/12/2022]
Abstract
In this study we identified the L-arabinose-responsive regulator of Pyricularia oryzae that regulates L-arabinose release and catabolism. Previously we identified the Zn2Cys6 transcription factor (TF), AraR, that has this role in the Trichocomaceae family (Eurotiales), but is absent in other fungi. Candidate Zn2Cys6 TF genes were selected according to their transcript profiles on L-arabinose. Deletion mutants of these genes were screened for their growth phenotype on L-arabinose. One mutant, named Δara1, was further analyzed. Our analysis demonstrated that Ara1 from P. oryzae is the functional analog of AraR from A. niger, while there is no significant sequence similarity between them.
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Affiliation(s)
- Sylvia Klaubauf
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Miaomiao Zhou
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Marc-Henri Lebrun
- MPA, UMR 2847 CNRS-Bayer Crop science, Lyon, France.,UMR 1290 BIOGER-CPP, INRA, AgroParisTech, Campus AgroParisTech, Ave Louis Bretignières, F75850 Thiverval-Grignon, France
| | - Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
| | - Evy Battaglia
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre & Fungal Molecular Physiology, Utrecht University, The Netherlands
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21
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Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, Ortega-Abboud E, Lebrun MH, Henrissat B, Gendrault A, Rodolphe F, Tharreau D, Fournier E. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol 2015; 7:2896-912. [PMID: 26454013 PMCID: PMC4684704 DOI: 10.1093/gbe/evv187] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
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Affiliation(s)
- Hélène Chiapello
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Ludovic Mallet
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Cyprien Guérin
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Gabriela Aguileta
- CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain
| | - Joëlle Amselem
- INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Thomas Kroj
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Enrique Ortega-Abboud
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Marc-Henri Lebrun
- INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annie Gendrault
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - François Rodolphe
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Didier Tharreau
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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22
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Song Z, Bakeer W, Marshall JW, Yakasai AA, Khalid RM, Collemare J, Skellam E, Tharreau D, Lebrun MH, Lazarus CM, Bailey AM, Simpson TJ, Cox RJ. Heterologous expression of the avirulence gene ACE1 from the fungal rice pathogen Magnaporthe oryzae. Chem Sci 2015; 6:4837-4845. [PMID: 29142718 PMCID: PMC5667575 DOI: 10.1039/c4sc03707c] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 06/01/2015] [Indexed: 01/07/2023] Open
Abstract
The ACE1 and RAP1 genes from the avirulence signalling gene cluster of the rice blast fungus Magnaporthe oryzae were expressed in Aspergillus oryzae and M. oryzae itself. Expression of ACE1 alone produced a polyenyl pyrone (magnaporthepyrone), which is regioselectively epoxidised and hydrolysed to give different diols, 6 and 7, in the two host organisms. Analysis of the three introns present in ACE1 determined that A. oryzae does not process intron 2 correctly, while M. oryzae processes all introns correctly in both appressoria and mycelia. Co-expression of ACE1 and RAP1 in A. oryzae produced an amide 8 which is similar to the PKS-NRPS derived backbone of the cytochalasans. Biological testing on rice leaves showed that neither the diols 6 and 7, nor amide 8 was responsible for the observed ACE1 mediated avirulence, however, gene cluster analysis suggests that the true avirulence signalling compound may be a tyrosine-derived cytochalasan compound.
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Affiliation(s)
- Zhongshu Song
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Walid Bakeer
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK.,Microbiology Department , Faculty of Pharmacy , Beni Suef University , Egypt
| | - James W Marshall
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Ahmed A Yakasai
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Rozida Mohd Khalid
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | | | - Elizabeth Skellam
- Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany .
| | - Didier Tharreau
- UMR BGPI , CIRAD , Campus International de Baillarguet , 34398 Montpellier Cedex 5 , France
| | - Marc-Henri Lebrun
- UR 1290 BIOGER-CPP , INRA , Campus AgroParisTech , 78850 Thiverval-Grignon , France.,UMR 5240 MAP , CNRS , UCB , INSA , Bayer CropScience , 69263 Lyon Cedex 09 , France
| | - Colin M Lazarus
- School of Biological Sciences , University of Bristol , 24 Tyndall Avenue , Bristol BS8 1TQ , UK
| | - Andrew M Bailey
- School of Biological Sciences , University of Bristol , 24 Tyndall Avenue , Bristol BS8 1TQ , UK
| | - Thomas J Simpson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK
| | - Russell J Cox
- School of Chemistry , University of Bristol , Cantock's Close , Bristol , BS8 1TS , UK.,Institute for Organic Chemistry , Leibniz University of Hannover , Schneiderberg 1B , 30167 , Hannover , Germany .
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23
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Crous PW, Carris LM, Giraldo A, Groenewald JZ, Hawksworth DL, Hernández-Restrepo M, Jaklitsch WM, Lebrun MH, Schumacher RK, Stielow JB, van der Linde EJ, Vilcāne J, Voglmayr H, Wood AR. The Genera of Fungi - fixing the application of the type species of generic names - G 2: Allantophomopsis, Latorua, Macrodiplodiopsis, Macrohilum, Milospium, Protostegia, Pyricularia, Robillarda, Rotula, Septoriella, Torula, and Wojnowicia. IMA Fungus 2015; 6:163-98. [PMID: 26203422 PMCID: PMC4500082 DOI: 10.5598/imafungus.2015.06.01.11] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/05/2015] [Indexed: 11/03/2022] Open
Abstract
The present paper represents the second contribution in the Genera of Fungi series, linking type species of fungal genera to their morphology and DNA sequence data, and where possible, ecology. This paper focuses on 12 genera of microfungi, 11 of which the type species are neo- or epitypified here: Allantophomopsis (A. cytisporea, Phacidiaceae, Phacidiales, Leotiomycetes), Latorua gen. nov. (Latorua caligans, Latoruaceae, Pleosporales, Dothideomycetes), Macrodiplodiopsis (M. desmazieri, Macrodiplodiopsidaceae, Pleosporales, Dothideomycetes), Macrohilum (M. eucalypti, Macrohilaceae, Diaporthales, Sordariomycetes), Milospium (M. graphideorum, incertae sedis, Pezizomycotina), Protostegia (P. eucleae, Mycosphaerellaceae, Capnodiales, Dothideomycetes), Pyricularia (P. grisea, Pyriculariaceae, Magnaporthales, Sordariomycetes), Robillarda (R. sessilis, Robillardaceae, Xylariales, Sordariomycetes), Rutola (R. graminis, incertae sedis, Pleosporales, Dothideomycetes), Septoriella (S. phragmitis, Phaeosphaeriaceae, Pleosporales, Dothideomycetes), Torula (T. herbarum, Torulaceae, Pleosporales, Dothideomycetes) and Wojnowicia (syn. of Septoriella, S. hirta, Phaeosphaeriaceae, Pleosporales, Dothideomycetes). Novel species include Latorua grootfonteinensis, Robillarda africana, R. roystoneae, R. terrae, Torula ficus, T. hollandica, and T. masonii spp. nov., and three new families: Macrodiplodiopsisceae, Macrohilaceae, and Robillardaceae. Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed for the major groups of fungi on the List of Protected Generic Names for Fungi (www.generaoffungi.org).
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Affiliation(s)
- Pedro W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lori M. Carris
- Department of Plant Pathology, Washington State University, Pullman WA 99164-6430, USA
| | - Alejandra Giraldo
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | | | - David L. Hawksworth
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, Madrid 28040, Spain
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
- Mycology Section, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK
| | - Margarita Hernández-Restrepo
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Walter M. Jaklitsch
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
- Institute of Forest Entomology, Forest Pathology and Forest Protection, Dept. of Forest and Soil Sciences, BOKU-University of Natural Resources and Life Sciences, Peter Jordan-Straße 82, 1190 Vienna, Austria
| | - Marc-Henri Lebrun
- UR1290 INRA BIOGER-CPP, Campus AgroParisTech, F-78850 Thiverval-Grignon, France
| | | | - J. Benjamin Stielow
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Elna J. van der Linde
- ARC – Plant Protection Research Institute, Biosystematics Division – Mycology, P. Bag X134, Queenswood 0121, South Africa
| | - Jūlija Vilcāne
- Horticulture Crop pathology, Latvian Plant Protection research centre Ltd., Struktoru 14A, Riga, LATVIA, LV-1039
| | - Hermann Voglmayr
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Alan R. Wood
- ARC – Plant Protection Research Institute, P. Bag X5017, Stellenbosch 7599, South Africa
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24
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Amselem J, Lebrun MH, Quesneville H. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics 2015. [PMID: 25766680 DOI: 10.1186/s12864-015-1347-1341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas MIP only methylates TEs at C residues. Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1 superfamily. RESULTS We annotated TE sequences from 10 fungal genomes with different TE content (1-70%). We then used these TE sequences to carry out a genome-wide analysis of C to T mutations biases. Genomes from either Ascomycota or Basidiomycota that were massively invaded by TEs (Blumeria, Melampsora, Puccinia) were characterized by a low frequency of C to T mutation bias (10-20%), whereas other genomes displayed intermediate to high frequencies (25-75%). We identified several dinucleotide signatures at these C to T mutation sites (CpA, CpT, and CpG). Phylogenomic analysis of fungal Dnmt1 MTases revealed a previously unreported association between these dinucleotide signatures and the presence/absence of sub-classes of Dnmt1. CONCLUSIONS We identified fungal genomes containing large numbers of TEs with many C to T mutations associated with species-specific dinucleotide signatures. This bias suggests that a basic defense mechanism against TE invasion similar to RIP is widespread in fungi, although the efficiency and specificity of this mechanism differs between species. Our analysis revealed that dinucleotide signatures are associated with the presence/absence of specific Dnmt1 subfamilies. In particular, an RID1-dependent RIP mechanism was found only in Ascomycota.
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Affiliation(s)
- Joëlle Amselem
- INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France.
- INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France.
| | - Marc-Henri Lebrun
- INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France.
| | - Hadi Quesneville
- INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France.
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Amselem J, Lebrun MH, Quesneville H. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics 2015; 16:141. [PMID: 25766680 PMCID: PMC4352252 DOI: 10.1186/s12864-015-1347-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) and Quelling (RNA interference). RIP inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas MIP only methylates TEs at C residues. Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1 superfamily. RESULTS We annotated TE sequences from 10 fungal genomes with different TE content (1-70%). We then used these TE sequences to carry out a genome-wide analysis of C to T mutations biases. Genomes from either Ascomycota or Basidiomycota that were massively invaded by TEs (Blumeria, Melampsora, Puccinia) were characterized by a low frequency of C to T mutation bias (10-20%), whereas other genomes displayed intermediate to high frequencies (25-75%). We identified several dinucleotide signatures at these C to T mutation sites (CpA, CpT, and CpG). Phylogenomic analysis of fungal Dnmt1 MTases revealed a previously unreported association between these dinucleotide signatures and the presence/absence of sub-classes of Dnmt1. CONCLUSIONS We identified fungal genomes containing large numbers of TEs with many C to T mutations associated with species-specific dinucleotide signatures. This bias suggests that a basic defense mechanism against TE invasion similar to RIP is widespread in fungi, although the efficiency and specificity of this mechanism differs between species. Our analysis revealed that dinucleotide signatures are associated with the presence/absence of specific Dnmt1 subfamilies. In particular, an RID1-dependent RIP mechanism was found only in Ascomycota.
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Affiliation(s)
- Joëlle Amselem
- INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France. .,INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France.
| | - Marc-Henri Lebrun
- INRA, UR1290 BIOGER, Biologie et gestion des risques en agriculture, Campus AgroParisTech, F-78850, Thiverval-Grignon, France.
| | - Hadi Quesneville
- INRA, UR1164 URGI Research Unit in Genomics-Info, F-78026, Versailles, France.
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26
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Perez-Nadales E, Nogueira MFA, Baldin C, Castanheira S, El Ghalid M, Grund E, Lengeler K, Marchegiani E, Mehrotra PV, Moretti M, Naik V, Oses-Ruiz M, Oskarsson T, Schäfer K, Wasserstrom L, Brakhage AA, Gow NAR, Kahmann R, Lebrun MH, Perez-Martin J, Di Pietro A, Talbot NJ, Toquin V, Walther A, Wendland J. Fungal model systems and the elucidation of pathogenicity determinants. Fungal Genet Biol 2014; 70:42-67. [PMID: 25011008 PMCID: PMC4161391 DOI: 10.1016/j.fgb.2014.06.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/23/2014] [Accepted: 06/25/2014] [Indexed: 12/05/2022]
Abstract
Fungi have the capacity to cause devastating diseases of both plants and animals, causing significant harvest losses that threaten food security and human mycoses with high mortality rates. As a consequence, there is a critical need to promote development of new antifungal drugs, which requires a comprehensive molecular knowledge of fungal pathogenesis. In this review, we critically evaluate current knowledge of seven fungal organisms used as major research models for fungal pathogenesis. These include pathogens of both animals and plants; Ashbya gossypii, Aspergillus fumigatus, Candida albicans, Fusarium oxysporum, Magnaporthe oryzae, Ustilago maydis and Zymoseptoria tritici. We present key insights into the virulence mechanisms deployed by each species and a comparative overview of key insights obtained from genomic analysis. We then consider current trends and future challenges associated with the study of fungal pathogenicity.
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Affiliation(s)
- Elena Perez-Nadales
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain.
| | | | - Clara Baldin
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutembergstr. 11a, 07745 Jena, Germany; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Sónia Castanheira
- Instituto de Biología Funcional y GenómicaCSIC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Mennat El Ghalid
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Elisabeth Grund
- Functional Genomics of Plant Pathogenic Fungi, UMR 5240 CNRS-UCB-INSA-Bayer SAS, Bayer CropScience, 69263 Lyon, France
| | - Klaus Lengeler
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Elisabetta Marchegiani
- Evolution and Genomics of Plant Pathogen Interactions, UR 1290 INRA, BIOGER-CPP, Campus AgroParisTech, 78850 Thiverval-Grignon, France
| | - Pankaj Vinod Mehrotra
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Marino Moretti
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Vikram Naik
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Miriam Oses-Ruiz
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK
| | - Therese Oskarsson
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Katja Schäfer
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Lisa Wasserstrom
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Beutembergstr. 11a, 07745 Jena, Germany; Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Neil A R Gow
- Aberdeen Fungal Group, School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Regine Kahmann
- Max-Planck-Institute for Terrestrial Microbiology, Department of Organismic Interactions, Karl-von-Frisch-Strasse 10, D-35043 Marburg, Germany
| | - Marc-Henri Lebrun
- Evolution and Genomics of Plant Pathogen Interactions, UR 1290 INRA, BIOGER-CPP, Campus AgroParisTech, 78850 Thiverval-Grignon, France
| | - José Perez-Martin
- Instituto de Biología Funcional y GenómicaCSIC, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Antonio Di Pietro
- Department of Genetics, Edificio Gregor Mendel, Planta 1. Campus de Rabanales, University of Cordoba, 14071 Cordoba, Spain
| | - Nicholas J Talbot
- School of Biosciences, Geoffrey Pope Building, University of Exeter, Exeter EX4 4QD, UK
| | - Valerie Toquin
- Biochemistry Department, Bayer SAS, Bayer CropScience, CRLD, 69263 Lyon, France
| | - Andrea Walther
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
| | - Jürgen Wendland
- Carlsberg Laboratory, Department of Yeast Genetics, Gamle Carlsberg Vej 10, DK-1799, Copenhagen V, Denmark
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Vayssier-Taussat M, Albina E, Citti C, Cosson JF, Jacques MA, Lebrun MH, Le Loir Y, Ogliastro M, Petit MA, Roumagnac P, Candresse T. Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics. Front Cell Infect Microbiol 2014; 4:29. [PMID: 24634890 PMCID: PMC3942874 DOI: 10.3389/fcimb.2014.00029] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/15/2014] [Indexed: 01/10/2023] Open
Abstract
The concept of pathogenesis has evolved considerably over recent years, and the scenario "a microbe + virulence factors = disease" is probably far from reality in a number of cases. Actual pathogens have extremely broad biological diversity and are found in all major groups of microorganisms (viruses, bacteria, fungi, protozoa…). Their pathogenicity results from strong and often highly specific interactions they have with either their microbial environment, hosts and/or arthropod vectors. In this review, we explore the contribution of metagenomic approaches toward understanding pathogens within the context of microbial communities. With this broader view, we discussed the concept of "pathobiome" and the research questions that this raises.
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Affiliation(s)
| | - Emmanuel Albina
- CIRAD, UMR CMAEE Petit-Bourg, Guadeloupe, France ; INRA, UMR 1309 CMAEE Montpellier, France ; INRA, Université de Toulouse, INP, ENVT, UMR 1225, IHAP Toulouse, France
| | - Christine Citti
- INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro) Montferrier-sur-Lez, France
| | - Jean-Franҫois Cosson
- INRA, Institut de Recherche en Horticulture et Semences, UMR 1345 Angers, France
| | | | | | - Yves Le Loir
- Agrocampus Ouest, UMR 1253 STLO Rennes, France ; INRA, UMR 1333 DGIMI Montpellier, France
| | | | | | - Philippe Roumagnac
- UMR 1332 Biologie du Fruit et Pathologie, INRA Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Université de Bordeaux Villenave d'Ornon Cedex, France
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28
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Battaglia E, Klaubauf S, Vallet J, Ribot C, Lebrun MH, de Vries RP. Xlr1 is involved in the transcriptional control of the pentose catabolic pathway, but not hemi-cellulolytic enzymes in Magnaporthe oryzae. Fungal Genet Biol 2013; 57:76-84. [PMID: 23810898 DOI: 10.1016/j.fgb.2013.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/14/2013] [Accepted: 06/15/2013] [Indexed: 10/26/2022]
Abstract
Magnaporthe oryzae is a fungal plant pathogen of many grasses including rice. Since arabinoxylan is one of the major components of the plant cell wall of grasses, M. oryzae is likely to degrade this polysaccharide for supporting its growth in infected leaves. D-Xylose is released from arabinoxylan by fungal depolymerising enzymes and catabolized through the pentose pathway. The expression of genes involved in these pathways is under control of the transcriptional activator XlnR/Xlr1, conserved among filamentous ascomycetes. In this study, we identified M. oryzae genes involved in the pentose catabolic pathway (PCP) and their function during infection, including the XlnR homolog, XLR1, through the phenotypic analysis of targeted null mutants. Growth of the Δxlr1 strain was reduced on D-xylose and xylan, but unaffected on L-arabinose and arabinan. A strong reduction of PCP gene expression was observed in the Δxlr1 strain on D-xylose and L-arabinose. However, there was no significant difference in xylanolytic and cellulolytic enzyme activities between the Δxlr1 mutant and the reference strain. These data demonstrate that XLR1 encodes the transcriptional activator of the PCP in M. oryzae, but does not appear to play a role in the regulation of the (hemi-) cellulolytic system in this fungus. This indicates only partial similarity in function between Xlr1 and A. niger XlnR. The deletion mutant of D-xylulose kinase encoding gene (XKI1) is clearly unable to grow on either D-xylose or L-arabinose and showed reduced growth on xylitol, L-arabitol and xylan. Δxki1 displayed an interesting molecular phenotype as it over-expressed other PCP genes as well as genes encoding (hemi-) cellulolytic enzymes. However, neither Δxlr1 nor Δxki1 showed significant differences in their pathogeny on rice and barley compared to the wild type, suggesting that D-xylose catabolism is not required for fungal growth in infected leaves.
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Affiliation(s)
- Evy Battaglia
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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29
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Ribot C, Césari S, Abidi I, Chalvon V, Bournaud C, Vallet J, Lebrun MH, Morel JB, Kroj T. The Magnaporthe oryzae effector AVR1-CO39 is translocated into rice cells independently of a fungal-derived machinery. Plant J 2013; 74:1-12. [PMID: 23279638 DOI: 10.1111/tpj.12099] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 12/10/2012] [Accepted: 12/17/2012] [Indexed: 05/06/2023]
Abstract
Effector proteins are key elements in plant-fungal interactions. The rice blast fungus Magnaporthe oryzae secretes numerous effectors that are suspected to be translocated inside plant cells. However, their cellular targets and the mechanisms of translocation are still unknown. Here, we have identified the open reading frame (ORF3) corresponding to the M. oryzae avirulence gene AVR1-CO39 that interacts with the rice resistance gene Pi-CO39 and encodes a small secreted protein without homology to other proteins. We demonstrate that AVR1-CO39 is specifically expressed and secreted at the plant-fungal interface during the biotrophic phase of infection. Live-cell imaging with M. oryzae transformants expressing a translational fusion between AVR1-CO39 and the monomeric red fluorescent protein (mRFP) indicated that AVR1-CO39 is translocated into the cytoplasm of infected rice cells. Transient expression of an AVR1-CO39 isoform without a signal peptide in rice protoplasts triggers a Pi-CO39-specific hypersensitive response, suggesting that recognition of AVR1-CO39 by the Pi-CO39 gene product occurs in the cytoplasm of rice cells. The native AVR1-CO39 protein enters the secretory pathway of rice protoplasts as demonstrated by the ER localization of AVR1-CO39:mRFP:HDEL translational fusions, and is correctly processed as shown by Western blotting. However, this secreted AVR1-CO39 isoform triggers a Pi-CO39-specific hypersensitive response and accumulates inside rice protoplasts as shown by Western blotting and localization of AVR1-CO39:mRFP translational fusions. This indicates that AVR1-CO39 is secreted by rice protoplasts and re-enters into the cytoplasm by unknown mechanisms, suggesting that translocation of AVR1-CO39 into rice cells occurs independently of fungal factors.
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Affiliation(s)
- Cécile Ribot
- INRA UMR385 Biologie et Génétique des Interactions Plante-Pathogène, F-34398 Montpellier, France
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30
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Klaubauf S, Ribot C, Melayah D, Lagorce A, Lebrun MH, de Vries RP. The pentose catabolic pathway of the rice-blast fungus Magnaporthe oryzae
involves a novel pentose reductase restricted to few fungal species. FEBS Lett 2013; 587:1346-52. [DOI: 10.1016/j.febslet.2013.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 03/02/2013] [Indexed: 11/26/2022]
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31
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Malagnac F, Bidard F, Lalucque H, Brun S, Lambou K, Lebrun MH, Silar P. Convergent evolution of morphogenetic processes in fungi: Role of tetraspanins and NADPH oxidases 2 in plant pathogens and saprobes. Commun Integr Biol 2012; 1:180-1. [PMID: 19704887 DOI: 10.4161/cib.1.2.7198] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 10/15/2008] [Indexed: 01/27/2023] Open
Abstract
Convergent evolution of trophic life style and morphological characters are very common in the fungal kingdom. Recently, we have shown that the same molecular machinery containing a tetraspanin and a NADPH oxidase has been recruited in two different fungal species for the same purpose (exiting from a melanized re-enforced cell at a focal weakened point), but at different stages of their development (ascospore germination and appressorium mediated penetration). Although this molecular machinery is required at these key developmental steps, it is also likely involved in specialized cellular functions at other stages of fungal development, as shown here for nutrient acquisition by Podospora anserina.
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Affiliation(s)
- Fabienne Malagnac
- UFR des Sciences du Vivant; Université de Paris 7 Diderot; Paris France
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32
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O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ. Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nat Genet 2012; 44:1060-5. [PMID: 22885923 DOI: 10.1038/ng.2372] [Citation(s) in RCA: 561] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 07/05/2012] [Indexed: 11/09/2022]
Abstract
Colletotrichum species are fungal pathogens that devastate crop plants worldwide. Host infection involves the differentiation of specialized cell types that are associated with penetration, growth inside living host cells (biotrophy) and tissue destruction (necrotrophy). We report here genome and transcriptome analyses of Colletotrichum higginsianum infecting Arabidopsis thaliana and Colletotrichum graminicola infecting maize. Comparative genomics showed that both fungi have large sets of pathogenicity-related genes, but families of genes encoding secreted effectors, pectin-degrading enzymes, secondary metabolism enzymes, transporters and peptidases are expanded in C. higginsianum. Genome-wide expression profiling revealed that these genes are transcribed in successive waves that are linked to pathogenic transitions: effectors and secondary metabolism enzymes are induced before penetration and during biotrophy, whereas most hydrolases and transporters are upregulated later, at the switch to necrotrophy. Our findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
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Affiliation(s)
- Richard J O'Connell
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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33
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Vincent D, Kohler A, Claverol S, Solier E, Joets J, Gibon J, Lebrun MH, Plomion C, Martin F. Secretome of the Free-living Mycelium from the Ectomycorrhizal Basidiomycete Laccaria bicolor. J Proteome Res 2011; 11:157-71. [DOI: 10.1021/pr200895f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Annegret Kohler
- INRA, UMR1136 Interactions Arbres/Micro-Organismes, Nancy, France
| | | | - Emilie Solier
- Plate-forme Protéomique, Université Bordeaux 2, Bordeaux, France
| | - Johann Joets
- UMR Génétique Végétale du Moulon, Gif-sur-Yvette, France
| | - Julien Gibon
- INRA, UMR1136 Interactions Arbres/Micro-Organismes, Nancy, France
| | | | | | - Francis Martin
- INRA, UMR1136 Interactions Arbres/Micro-Organismes, Nancy, France
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34
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Amselem J, Cuomo CA, van Kan JAL, Viaud M, Benito EP, Couloux A, Coutinho PM, de Vries RP, Dyer PS, Fillinger S, Fournier E, Gout L, Hahn M, Kohn L, Lapalu N, Plummer KM, Pradier JM, Quévillon E, Sharon A, Simon A, ten Have A, Tudzynski B, Tudzynski P, Wincker P, Andrew M, Anthouard V, Beever RE, Beffa R, Benoit I, Bouzid O, Brault B, Chen Z, Choquer M, Collémare J, Cotton P, Danchin EG, Da Silva C, Gautier A, Giraud C, Giraud T, Gonzalez C, Grossetete S, Güldener U, Henrissat B, Howlett BJ, Kodira C, Kretschmer M, Lappartient A, Leroch M, Levis C, Mauceli E, Neuvéglise C, Oeser B, Pearson M, Poulain J, Poussereau N, Quesneville H, Rascle C, Schumacher J, Ségurens B, Sexton A, Silva E, Sirven C, Soanes DM, Talbot NJ, Templeton M, Yandava C, Yarden O, Zeng Q, Rollins JA, Lebrun MH, Dickman M. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet 2011; 7:e1002230. [PMID: 21876677 PMCID: PMC3158057 DOI: 10.1371/journal.pgen.1002230] [Citation(s) in RCA: 647] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 06/22/2011] [Indexed: 12/03/2022] Open
Abstract
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
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Affiliation(s)
- Joelle Amselem
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Christina A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Muriel Viaud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Ernesto P. Benito
- Departamento de Microbiología y Genética, Centro Hispano-Luso de Investigaciones Agrarias, Universidad de Salamanca, Salamanca, Spain
| | | | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | - Ronald P. de Vries
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
- CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
| | - Paul S. Dyer
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Sabine Fillinger
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Elisabeth Fournier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Biologie et Génétique des Interactions Plante-Parasite, CIRAD – INRA – SupAgro, Montpellier, France
| | - Lilian Gout
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Matthias Hahn
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Linda Kohn
- Biology Department, University of Toronto, Mississauga, Canada
| | - Nicolas Lapalu
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Kim M. Plummer
- Botany Department, La Trobe University, Melbourne, Australia
| | - Jean-Marc Pradier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Emmanuel Quévillon
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Amir Sharon
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Adeline Simon
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Arjen ten Have
- Instituto de Investigaciones Biologicas – CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Bettina Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Paul Tudzynski
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Marion Andrew
- Biology Department, University of Toronto, Mississauga, Canada
| | | | | | - Rolland Beffa
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Isabelle Benoit
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Ourdia Bouzid
- Microbiology and Kluyver Centre for Genomics of Industrial Fermentations, Utrecht, The Netherlands
| | - Baptiste Brault
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Zehua Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mathias Choquer
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Jérome Collémare
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Pascale Cotton
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Etienne G. Danchin
- Interactions Biotiques et Santé Plantes, UMR5240, INRA – Université de Nice Sophia-Antipolis – CNRS, Sophia-Antipolis, France
| | | | - Angélique Gautier
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Corinne Giraud
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Tatiana Giraud
- Laboratoire d'Ecologie, Systématique et Evolution, Université Paris-Sud – CNRS – AgroParisTech, Orsay, France
| | - Celedonio Gonzalez
- Departamento de Bioquímica y Biología Molecular, Universidad de La Laguna, Tenerife, Spain
| | - Sandrine Grossetete
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Ulrich Güldener
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS – Université de la Méditerranée et Université de Provence, Marseille, France
| | | | - Chinnappa Kodira
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Anne Lappartient
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Michaela Leroch
- Faculty of Biology, Kaiserslautern University, Kaiserslautern, Germany
| | - Caroline Levis
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
| | - Evan Mauceli
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Cécile Neuvéglise
- Biologie Intégrative du Métabolisme Lipidique Microbien, UMR1319, INRA – Micalis – AgroParisTech, Thiverval-Grignon, France
| | - Birgitt Oeser
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | - Matthew Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Julie Poulain
- GENOSCOPE, Centre National de Séquençage, Evry, France
| | - Nathalie Poussereau
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Hadi Quesneville
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
| | - Christine Rascle
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Julia Schumacher
- Molekularbiologie und Biotechnologie der Pilze, Institut für Biologie und Biotechnologie der Pflanzen, Münster, Germany
| | | | - Adrienne Sexton
- School of Botany, University of Melbourne, Melbourne, Australia
| | - Evelyn Silva
- Fundacion Ciencia para la Vida and Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | - Catherine Sirven
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Darren M. Soanes
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Matt Templeton
- Plant and Food Research, Mt. Albert Research Centre, Auckland, New Zealand
| | - Chandri Yandava
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, Hebrew University Jerusalem, Rehovot, Israel
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey A. Rollins
- Department of Plant Pathology, University of Florida, Gainesville, Florida, United States of America
| | - Marc-Henri Lebrun
- Unité de Recherche Génomique – Info, UR1164, INRA, Versailles, France
- Biologie et Gestion des Risques en Agriculture – Champignons Pathogènes des Plantes, UR1290, INRA, Grignon, France
- Laboratoire de Génomique Fonctionnelle des Champignons Pathogènes de Plantes, UMR5240, Université de Lyon 1 – CNRS – BAYER S.A.S., Lyon, France
| | - Marty Dickman
- Institute for Plant Genomics and Biotechnology, Borlaug Genomics and Bioinformatics Center, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
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de Vries RP, Benoit I, Doehlemann G, Kobayashi T, Magnuson JK, Panisko EA, Baker SE, Lebrun MH. Post-genomic approaches to understanding interactions between fungi and their environment. IMA Fungus 2011; 2:81-6. [PMID: 22679591 PMCID: PMC3317359 DOI: 10.5598/imafungus.2011.02.01.11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 05/18/2011] [Indexed: 01/22/2023] Open
Abstract
Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of post-genomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments.
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Affiliation(s)
- Ronald P de Vries
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Spanu PD, Abbott JC, Amselem J, Burgis TA, Soanes DM, Stüber K, Ver Loren van Themaat E, Brown JKM, Butcher SA, Gurr SJ, Lebrun MH, Ridout CJ, Schulze-Lefert P, Talbot NJ, Ahmadinejad N, Ametz C, Barton GR, Benjdia M, Bidzinski P, Bindschedler LV, Both M, Brewer MT, Cadle-Davidson L, Cadle-Davidson MM, Collemare J, Cramer R, Frenkel O, Godfrey D, Harriman J, Hoede C, King BC, Klages S, Kleemann J, Knoll D, Koti PS, Kreplak J, López-Ruiz FJ, Lu X, Maekawa T, Mahanil S, Micali C, Milgroom MG, Montana G, Noir S, O'Connell RJ, Oberhaensli S, Parlange F, Pedersen C, Quesneville H, Reinhardt R, Rott M, Sacristán S, Schmidt SM, Schön M, Skamnioti P, Sommer H, Stephens A, Takahara H, Thordal-Christensen H, Vigouroux M, Wessling R, Wicker T, Panstruga R. Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism. Science 2010; 330:1543-6. [PMID: 21148392 DOI: 10.1126/science.1194573] [Citation(s) in RCA: 600] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
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Affiliation(s)
- Pietro D Spanu
- Department of Life Sciences, Imperial College London, London, UK.
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Abstract
Plant secretomics is a newly emerging area of the plant proteomics field. It basically describes the global study of secreted proteins into the extracellular space of plant cell or tissue at any given time and under certain conditions through various secretory mechanisms. A combination of biochemical, proteomics and bioinformatics approaches has been developed to isolate, identify and profile secreted proteins using complementary in vitro suspension-cultured cells and in planta systems. Developed inventories of secreted proteins under normal, biotic and abiotic conditions revealed several different types of novel secreted proteins, including the leaderless secretory proteins (LSPs). On average, LSPs can account for more than 50% of the total identified secretome, supporting, as in other eukaryotes, the existence of novel secretory mechanisms independent of the classical endoplasmic reticulum-Golgi secretory pathway, and suggesting that this non-classical mechanism of protein expression is, for as yet unknown reasons, more massively used than in other eukaryotic systems. Plants LSPs, which seem to be potentially involved in the defense/stress responses, might have dual (extracellular and/or intracellular) roles as most of them have established intracellular functions, yet presently unknown extracellular functions. Evidence is emerging on the role of glycosylation in the apical sorting and trafficking of secretory proteins. These initial secretome studies in plants have considerably advanced our understanding on secretion of different types of proteins and their underlying mechanisms, and opened a door for comparative analyses of plant secretomes with those of other organisms. In this first review on plant secretomics, we summarize and discuss the secretome definition, the applied approaches for unlocking secrets of the secreted proteins in the extracellular fluid, the possible functional significance and secretory mechanisms of LSPs, as well as glycosylation of secreted proteins and challenges involved ahead. Further improvements in existing and developing strategies and techniques will continue to drive forward plant secretomics research to building comprehensive and confident data sets of secreted proteins. This will lead to an increased understanding on how cells couple the concerted action of secreted protein networks to their internal and external environments.
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Ding SL, Liu W, Iliuk A, Ribot C, Vallet J, Tao A, Wang Y, Lebrun MH, Xu JR. The tig1 histone deacetylase complex regulates infectious growth in the rice blast fungus Magnaporthe oryzae. Plant Cell 2010; 22:2495-508. [PMID: 20675574 PMCID: PMC2929099 DOI: 10.1105/tpc.110.074302] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Magnaporthe oryzae is the most damaging fungal pathogen of rice (Oryza sativa). In this study, we characterized the TIG1 transducin beta-like gene required for infectious growth and its interacting genes that are required for plant infection in this model phytopathogenic fungus. Tig1 homologs in yeast and mammalian cells are part of a conserved histone deacetylase (HDAC) transcriptional corepressor complex. The tig1 deletion mutant was nonpathogenic and defective in conidiogenesis. It had an increased sensitivity to oxidative stress and failed to develop invasive hyphae in plant cells. Using affinity purification and coimmunoprecipitation assays, we identified several Tig1-associated proteins, including two HDACs that are homologous to components of the yeast Set3 complex. Functional analyses revealed that TIG1, SET3, SNT1, and HOS2 were core components of the Tig1 complex in M. oryzae. The set3, snt1, and hos2 deletion mutants displayed similar defects as those observed in the tig1 mutant, but deletion of HST1 or HOS4 had no detectable phenotypes. Deletion of any of these core components of the Tig1 complex resulted in a significant reduction in HDAC activities. Our results showed that TIG1, like its putative yeast and mammalian orthologs, is one component of a conserved HDAC complex that is required for infectious growth and conidiogenesis in M. oryzae and highlighted that chromatin modification is an essential regulatory mechanism during plant infection.
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Affiliation(s)
- Sheng-Li Ding
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Wende Liu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
| | - Anton Iliuk
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Cecile Ribot
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
| | - Julie Vallet
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
| | - Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Yang Wang
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Marc-Henri Lebrun
- Université Lyon-1, Centre National de la Recherche Scientifique, Bayer CropScience, 69263 Lyon Cedex 09, France
- Institut National de la Recherche Agronomique, 78850 Thiverval-Grignon, France
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- College of Plant Protection and Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
- Address correspondence to
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Affiliation(s)
- Marc-Henri Lebrun
- BIOGER, UMR INRA-APT, Campus Agroparistech, 78850 Thiverval Grignon, France
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Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury JM, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun MH, Paolocci F, Bonfante P, Ottonello S, Wincker P. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 2010; 464:1033-8. [PMID: 20348908 DOI: 10.1038/nature08867] [Citation(s) in RCA: 436] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Accepted: 01/28/2010] [Indexed: 11/09/2022]
Abstract
The Périgord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.
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Affiliation(s)
- Francis Martin
- INRA, UMR 1136, INRA-Nancy Université, Interactions Arbres/Microorganismes, 54280 Champenoux, France.
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Vincent D, Balesdent MH, Gibon J, Claverol S, Lapaillerie D, Lomenech AM, Blaise F, Rouxel T, Martin F, Bonneu M, Amselem J, Dominguez V, Howlett BJ, Wincker P, Joets J, Lebrun MH, Plomion C. Hunting down fungal secretomes using liquid-phase IEF prior to high resolution 2-DE. Electrophoresis 2010; 30:4118-36. [PMID: 19960477 DOI: 10.1002/elps.200900415] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The secreted proteins (secretome) of fungi play a key role in interactions of pathogenic and symbiotic fungi with plants. Using the plant pathogenic fungus Leptosphaeria maculans and symbiont Laccaria bicolor grown in culture, we have established a proteomic protocol for extraction, concentration and resolution of the fungal secretome. As no proteomic data were available on mycelium tissues from both L. maculans and L. bicolor, mycelial proteins were studied; they also helped verifying the purity of secretome samples. The quality of protein extracts was initially assessed by both 1-DE and 2-DE using first a broad pH range for IEF, and then narrower acidic and basic pH ranges, prior to 2-DE. Compared with the previously published protocols for which only dozens of 2-D spots were recovered from fungal secretome samples, up to approximately 2000 2-D spots were resolved by our method. MS identification of proteins along several pH gradients confirmed this high resolution, as well as the presence of major secretome markers such as endopolygalacturonases, beta-glucanosyltransferases, pectate lyases and endoglucanases. Shotgun proteomic experiments evidenced the enrichment of secreted protein within the liquid medium. This is the first description of the proteome of L. maculans and L. bicolor, and the first application of liquid-phase IEF to any fungal extracts.
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Heupel S, Roser B, Kuhn H, Lebrun MH, Villalba F, Requena N. Erl1, a novel era-like GTPase from Magnaporthe oryzae, is required for full root virulence and is conserved in the mutualistic symbiont Glomus intraradices. Mol Plant Microbe Interact 2010; 23:67-81. [PMID: 19958140 DOI: 10.1094/mpmi-23-1-0067] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Comparative analyses of genome sequences from several plant-infecting fungi have shown conservation and expansion of protein families with plant disease-related functions. Here, we show that this hypothesis can be extended to mutualistic symbiotic fungi. We have identified a gene encoding an Era (Escherichia coli Ras)-like GTPase in the rice blast fungus Magnaporthe oryzae and found that it is orthologous to the mature amino terminal part of the Gin1 protein from the arbuscular mycorrhizal (AM) fungus Glomus intraradices. M. oryzae Erl1 is required for full root virulence. Appressoria formation was not severely affected in Deltaerl1 strains, but invasive hyphae grew slower than in the wild type. Root browning defect of Deltaerl1 strains could be complemented by the AM gene under the control of the ERL1 promoter. Erl1 and Gin-N localized to the nucleus when carboxy-terminally labeled with green fluorescent protein (GFP). However, amino-terminal GFP-tagged versions of the proteins expressed in Aspergillus nidulans were shown to localize in the cytoplasm and to cause polarity defects. These data suggest that Erl1 and Gin-N are orthologs and might be involved in the control of hyphal growth in planta. This is the first characterization of an Era-like GTPase in filamentous fungi.
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Affiliation(s)
- Stephanie Heupel
- Plant-Microbe Interactions, Botanical Institute, University of Karlsruhe, Hertzstrasse 16, D-76187 Karlsruhe, Germany
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Rispail N, Soanes DM, Ant C, Czajkowski R, Grünler A, Huguet R, Perez-Nadales E, Poli A, Sartorel E, Valiante V, Yang M, Beffa R, Brakhage AA, Gow NAR, Kahmann R, Lebrun MH, Lenasi H, Perez-Martin J, Talbot NJ, Wendland J, Di Pietro A. Comparative genomics of MAP kinase and calcium-calcineurin signalling components in plant and human pathogenic fungi. Fungal Genet Biol 2009; 46:287-98. [PMID: 19570501 DOI: 10.1016/j.fgb.2009.01.002] [Citation(s) in RCA: 230] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 01/16/2009] [Accepted: 01/17/2009] [Indexed: 01/22/2023]
Abstract
Mitogen-activated protein kinase (MAPK) cascades and the calcium-calcineurin pathway control fundamental aspects of fungal growth, development and reproduction. Core elements of these signalling pathways are required for virulence in a wide array of fungal pathogens of plants and mammals. In this review, we have used the available genome databases to explore the structural conservation of three MAPK cascades and the calcium-calcineurin pathway in ten different fungal species, including model organisms, plant pathogens and human pathogens. While most known pathway components from the model yeast Saccharomyces cerevisiae appear to be widely conserved among taxonomically and biologically diverse fungi, some of them were found to be restricted to the Saccharomycotina. The presence of multiple paralogues in certain species such as the zygomycete Rhizopus oryzae and the incorporation of new functional domains that are lacking in S. cerevisiae signalling proteins, most likely reflect functional diversification or adaptation as filamentous fungi have evolved to occupy distinct ecological niches.
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Affiliation(s)
- Nicolas Rispail
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
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Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H. FUNYBASE: a FUNgal phYlogenomic dataBASE. BMC Bioinformatics 2008; 9:456. [PMID: 18954438 PMCID: PMC2600828 DOI: 10.1186/1471-2105-9-456] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Accepted: 10/27/2008] [Indexed: 11/10/2022] Open
Abstract
Background The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotation and the difficulty of retrieving true orthologs, makes such investigations challenging. The aim of this study was to provide a reliable and integrated resource of orthologous gene families to perform comparative and phylogenetic analyses in fungi. Description FUNYBASE is a database dedicated to the analysis of fungal single-copy genes extracted from available fungal genomes sequences, their classification into reliable clusters of orthologs, and the assessment of their informative value for phylogenetic reconstruction based on amino acid sequences. The current release of FUNYBASE contains two types of protein data: (i) a complete set of protein sequences extracted from 30 public fungal genomes and classified into clusters of orthologs using a robust automated procedure, and (ii) a subset of 246 reliable ortholog clusters present as single copy genes in 21 fungal genomes. For each of these 246 ortholog clusters, phylogenetic trees were reconstructed based on their amino acid sequences. To assess the informative value of each ortholog cluster, each was compared to a reference species tree constructed using a concatenation of roughly half of the 246 sequences that are best approximated by the WAG evolutionary model. The orthologs were classified according to a topological score, which measures their ability to recover the same topology as the reference species tree. The full results of these analyses are available on-line with a user-friendly interface that allows for searches to be performed by species name, the ortholog cluster, various keywords, or using the BLAST algorithm. Examples of fruitful utilization of FUNYBASE for investigation of fungal phylogenetics are also presented. Conclusion FUNYBASE constitutes a novel and useful resource for two types of analyses: (i) comparative studies can be greatly facilitated by reliable clusters of orthologs across sets of user-defined fungal genomes, and (ii) phylogenetic reconstruction can be improved by identifying genes with the highest informative value at the desired taxonomic level.
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Affiliation(s)
- Sylvain Marthey
- UR MIG, INRA, Bâtiment 233 Domaine de Vilvert 78350, Cedex, France.
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Collemare J, Pianfetti M, Houlle AE, Morin D, Camborde L, Gagey MJ, Barbisan C, Fudal I, Lebrun MH, Böhnert HU. Magnaporthe grisea avirulence gene ACE1 belongs to an infection-specific gene cluster involved in secondary metabolism. New Phytol 2008; 179:196-208. [PMID: 18433432 DOI: 10.1111/j.1469-8137.2008.02459.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The avirulence gene ACE1 from the rice blast fungus Magnaporthe grisea encodes a polyketide synthase (PKS) fused to a nonribosomal peptide synthetase (NRPS) probably involved in the biosynthesis of a secondary metabolite recognized by Pi33 resistant rice (Oryza sativa) cultivars. Analysis of the M. grisea genome revealed that ACE1 is located in a cluster of 15 genes, of which 14 are potentially involved in secondary metabolism as they encode enzymes such as a second PKS-NRPS (SYN2), two enoyl reductases (RAP1 and RAP2) and a putative Zn(II)(2)Cys(6) transcription factor (BC2). These 15 genes are specifically expressed during penetration into the host plant, defining an infection-specific gene cluster. A pORF3-GFP transcriptional fusion showed that the highly expressed ORF3 gene from the ACE1 cluster is only expressed in appressoria, as is ACE1. Phenotypic analysis of deletion or disruption mutants of SYN2 and RAP2 showed that they are not required for avirulence in Pi33 rice cultivars, unlike ACE1. Inactivation of other genes was unsuccessful because targeted gene replacement and disruption were inefficient at this locus. Overall, the ACE1 gene cluster displays an infection-specific expression pattern restricted to the penetration stage which is probably controlled at the transcriptional level and reflects regulatory networks specific to early stages of infection.
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Affiliation(s)
- Jérôme Collemare
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Mikaël Pianfetti
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Anne-Elodie Houlle
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Damien Morin
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Laurent Camborde
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Marie-Josèphe Gagey
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Crystel Barbisan
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Isabelle Fudal
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Marc-Henri Lebrun
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
| | - Heidi U Böhnert
- UMR5240 CNRS/UCB/INSA/BAYER CropScience, 14-20 Rue Pierre Baizet, 69263 Lyon cedex 09, France
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Lambou K, Tharreau D, Kohler A, Sirven C, Marguerettaz M, Barbisan C, Sexton AC, Kellner EM, Martin F, Howlett BJ, Orbach MJ, Lebrun MH. Fungi have three tetraspanin families with distinct functions. BMC Genomics 2008; 9:63. [PMID: 18241352 PMCID: PMC2278132 DOI: 10.1186/1471-2164-9-63] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Accepted: 02/03/2008] [Indexed: 01/16/2023] Open
Abstract
Background Tetraspanins are small membrane proteins that belong to a superfamily encompassing 33 members in human and mouse. These proteins act as organizers of membrane-signalling complexes. So far only two tetraspanin families have been identified in fungi. These are Pls1, which is required for pathogenicity of the plant pathogenic ascomycetes, Magnaporthe grisea, Botrytis cinerea and Colletotrichum lindemuthianum, and Tsp2, whose function is unknown. In this report, we describe a third family of tetraspanins (Tsp3) and a new family of tetraspanin-like proteins (Tpl1) in fungi. We also describe expression of some of these genes in M. grisea and a basidiomycete, Laccaria bicolor, and also their functional analysis in M. grisea. Results The exhaustive search for tetraspanins in fungal genomes reveals that higher fungi (basidiomycetes and ascomycetes) contain three families of tetraspanins (Pls1, Tsp2 and Tsp3) with different distribution amongst phyla. Pls1 is found in ascomycetes and basidiomycetes, whereas Tsp2 is restricted to basidiomycetes and Tsp3 to ascomycetes. A unique copy of each of PLS1 and TSP3 was found in ascomycetes in contrast to TSP2, which has several paralogs in the basidiomycetes, Coprinus cinereus and Laccaria bicolor. A tetraspanin-like family (Tpl1) was also identified in ascomycetes. Transcriptional analyses in various tissues of L. bicolor and M. grisea showed that PLS1 and TSP2 are expressed in all tissues in L. bicolor and that TSP3 and TPL1 are overexpressed in the sexual fruiting bodies (perithecia) and mycelia of M. grisea, suggesting that these genes are not pseudogenes. Phenotypic analysis of gene replacementmutants Δtsp3 and Δtpl1 of M. grisea revealed a reduction of the pathogenicity only on rice, in contrast to Δpls1 mutants, which are completely non-pathogenic on barley and rice. Conclusion A new tetraspanin family (Tsp3) and a tetraspanin-like protein family (Tpl1) have been identified in fungi. Functional analysis by gene replacement showed that these proteins, as well as Pls1, are involved in the infection process of the plant pathogenic fungus M. grisea. The next challenge will be to decipher the role(s) of tetraspanins in a range of symbiotic, saprophytic and human pathogenic fungi.
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Affiliation(s)
- Karine Lambou
- UMR 5240 CNRS-UCB-INSA-Bayer CropScience, Microbiologie, Adaptation et Pathogénie, Bayer CropScience, 14-20 rue Pierre Baizet, 69263 Lyon Cedex 09, France.
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Collemare J, Billard A, Böhnert HU, Lebrun MH. Biosynthesis of secondary metabolites in the rice blast fungus Magnaporthe grisea: the role of hybrid PKS-NRPS in pathogenicity. ACTA ACUST UNITED AC 2008; 112:207-15. [DOI: 10.1016/j.mycres.2007.08.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Accepted: 08/09/2007] [Indexed: 01/22/2023]
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Ribot C, Hirsch J, Balzergue S, Tharreau D, Nottéghem JL, Lebrun MH, Morel JB. Susceptibility of rice to the blast fungus, Magnaporthe grisea. J Plant Physiol 2008; 165:114-24. [PMID: 17905473 DOI: 10.1016/j.jplph.2007.06.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 06/25/2007] [Accepted: 06/26/2007] [Indexed: 05/17/2023]
Abstract
The interaction between rice and the blast fungus Magnaporthe grisea is the focus of extensive studies on rice disease resistance and fungal infection mechanisms. Here, we review the characteristics of susceptible rice blast infections in terms of physiology, cytology and both host and pathogen transcriptional responses. The success of the infection and the type of disease symptoms strongly depend on environmental and developmental cues. After its penetration into a host cell, the fungus differentiates invasive hyphae that fill up the plant cell lumen and are in direct contact with the membrane of the infected cell. The infected plant cell is alive, displaying considerable vesicle accumulation near the fungus, which is consistent with the establishment of a biotrophic phase at this stage of the infection. Colonization of host tissues by the fungus occurs through the perforation of cell walls from adjacent cells, likely using plasmodesmata as breaking points, or through hyphal growth in the apoplasm. After a few days of biotrophic growth within rice tissues, the fungus switches to a necrotrophic-like phase associated with the onset of sporulation, leading to visible lesions. Genome-wide transcriptomic studies have shown that classical plant defence responses are triggered during a susceptible infection, although the kinetics and amplitude of these responses are slower and lower than in resistant interactions. Infected rice cells are submitted to an intense transcriptional reprogramming, where responses to hormones such as auxins, abscissic acid and jasmonates are likely involved. Consistent with the extensive plant-fungal exchanges during the biotrophic phase, many rice genes expressed during infection encode plasma membrane proteins. At the onset of lesion formation (5 days after the start of infection), M. grisea is actively reprogramming its transcription towards active DNA, RNA and protein syntheses to sustain its rapid growth in infected tissues. A striking characteristic of M. grisea genes expressed at this stage of the infection is the over-representation of genes encoding secreted proteins, mainly of unknown function. However, some of these secreted proteins are enzymes involved in cell wall, protein and lipid degradation, suggesting that the fungus is starting to degrade host polymers and cell walls or is remodelling its own cell wall. The next challenge will be to decipher the role of these induced plant and fungal genes in the susceptible interaction.
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Affiliation(s)
- Cécile Ribot
- UMR 5240 CNRS-UCB-INSA-BCS, Bayer CropScience, 14-20 rue Pierre Baizet BP9163, 69263 Lyon Cedex 09, France
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Faivre-Rampant O, Thomas J, Allègre M, Morel JB, Tharreau D, Nottéghem JL, Lebrun MH, Schaffrath U, Piffanelli P. Characterization of the model system rice--Magnaporthe for the study of nonhost resistance in cereals. New Phytol 2008; 180:899-910. [PMID: 19138233 DOI: 10.1111/j.1469-8137.2008.02621.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The best characterized form of resistance is gene-for-gene resistance. Less well characterized is nonhost resistance in which an entire plant species is resistant to an entire pathogen species. Here, different rice genotypes were inoculated with host and nonhost strains of Magnaporthe isolated from rice, wheat and crabgrass. The different types of interactions were characterized at a cytological level using a 3,3'-diaminobenzidine (DAB) stain to investigate the occurrence of reactive oxygen intermediates or by observing the occurrence of cellular autofluorescence. Gene expression of a set of selected PR-genes was analysed using quantitative real-time polymerase chain reaction. Inoculation with the isolate from crabgrass resulted in a lack of penetration. The wheat isolate induced a hypersensitive response with varying degrees of pathogen growth inside the invaded cell according to the rice genotype. Expression analysis of our PR-gene set revealed clear differences between the different types of interactions in both kinetic and magnitude of gene induction. Our integrated study opens the way to the dissection of molecular components leading to nonhost reactions to Magnaporthe grisea in rice and points to novel sources of durable resistance to fungal plant pathogens in other cereal crops.
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Khaldi N, Collemare J, Lebrun MH, Wolfe KH. Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi. Genome Biol 2008; 9:R18. [PMID: 18218086 PMCID: PMC2395248 DOI: 10.1186/gb-2008-9-1-r18] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Revised: 12/21/2007] [Accepted: 01/24/2008] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Filamentous fungi synthesize many secondary metabolites and are rich in genes encoding proteins involved in their biosynthesis. Genes from the same pathway are often clustered and co-expressed in particular conditions. Such secondary metabolism gene clusters evolve rapidly through multiple rearrangements, duplications and losses. It has long been suspected that clusters can be transferred horizontally between species, but few concrete examples have been described so far. RESULTS In the rice blast fungus Magnaporthe grisea, the avirulence gene ACE1 that codes for a hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) belongs to a cluster of 15 genes involved in secondary metabolism. Additional related clusters were detected in the ascomycetes Chaetomium globosum, Stagonospora nodorum and Aspergillus clavatus. Gene-by-gene phylogenetic analysis showed that in C. globosum and M. grisea, the evolution of these ACE1-like clusters is characterized by successive complex duplication events including tandem duplication within the M. grisea cluster. The phylogenetic trees also present evidence that at least five of the six genes in the homologous ACE1 gene cluster in A. clavatus originated by horizontal transfer from a donor closely related to M. grisea. CONCLUSION The ACE1 cluster originally identified in M. grisea is shared by only few fungal species. Its sporadic distribution within euascomycetes is mainly explained by multiple events of duplication and losses. However, because A. clavatus contains an ACE1 cluster of only six genes, we propose that horizontal transfer from a relative of M. grisea into an ancestor of A. clavatus provides a much simpler explanation of the observed data than the alternative of multiple events of duplication and losses of parts of the cluster.
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Affiliation(s)
- Nora Khaldi
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jérôme Collemare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Marc-Henri Lebrun
- 2UMR5240 CNRS/UCB/INSA/BCS, Bayer Cropscience, 69263 Lyon cedex 09, France
| | - Kenneth H Wolfe
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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