101
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Petit E, Silver C, Cornille A, Gladieux P, Rosenthal L, Bruns E, Yee S, Antonovics J, Giraud T, Hood ME. Co-occurrence and hybridization of anther-smut pathogens specialized on Dianthus hosts. Mol Ecol 2017; 26:1877-1890. [PMID: 28231407 DOI: 10.1111/mec.14073] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/13/2017] [Accepted: 02/09/2017] [Indexed: 01/05/2023]
Abstract
Host specialization has important consequences for the diversification and ecological interactions of obligate pathogens. The anther-smut disease of natural plant populations, caused by Microbotryum fungi, has been characterized by specialized host-pathogen interactions, which contribute in part to the isolation among these numerous fungal species. This study investigated the molecular variation of Microbotryum pathogens within the geographic and host-specific distributions on wild Dianthus species in southern European Alps. In contrast to prior studies on this pathogen genus, a range of overlapping host specificities was observed for four delineated Microbotryum lineages on Dianthus hosts, and their frequent co-occurrence within single-host populations was quantified at local and regional scales. In addition to potential consequences for direct pathogen competition, the sympatry of Microbotryum lineages led to hybridization between them in many populations, and these admixed genotypes suffered significant meiotic sterility. Therefore, this investigation of the anther-smut fungi reveals how variation in the degrees of host specificity can have major implications for ecological interactions and genetic integrity of differentiated pathogen lineages.
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Affiliation(s)
- Elsa Petit
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, MA, USA
| | - Casey Silver
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
| | - Pierre Gladieux
- UMR BGPI, INRA, Campus International de Baillarguet, 34398, Montpellier, France
| | - Lisa Rosenthal
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Emily Bruns
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Sarah Yee
- Biology Department, Amherst College, Amherst, MA, 01002, USA
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA, 22903, USA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, CNRS, University of Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA, 01002, USA
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102
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Teixeira M, Moreno L, Stielow B, Muszewska A, Hainaut M, Gonzaga L, Abouelleil A, Patané J, Priest M, Souza R, Young S, Ferreira K, Zeng Q, da Cunha M, Gladki A, Barker B, Vicente V, de Souza E, Almeida S, Henrissat B, Vasconcelos A, Deng S, Voglmayr H, Moussa T, Gorbushina A, Felipe M, Cuomo C, de Hoog GS. Exploring the genomic diversity of black yeasts and relatives ( Chaetothyriales, Ascomycota). Stud Mycol 2017; 86:1-28. [PMID: 28348446 PMCID: PMC5358931 DOI: 10.1016/j.simyco.2017.01.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The order Chaetothyriales (Pezizomycotina, Ascomycetes) harbours obligatorily melanised fungi and includes numerous etiologic agents of chromoblastomycosis, phaeohyphomycosis and other diseases of vertebrate hosts. Diseases range from mild cutaneous to fatal cerebral or disseminated infections and affect humans and cold-blooded animals globally. In addition, Chaetothyriales comprise species with aquatic, rock-inhabiting, ant-associated, and mycoparasitic life-styles, as well as species that tolerate toxic compounds, suggesting a high degree of versatile extremotolerance. To understand their biology and divergent niche occupation, we sequenced and annotated a set of 23 genomes of main the human opportunists within the Chaetothyriales as well as related environmental species. Our analyses included fungi with diverse life-styles, namely opportunistic pathogens and closely related saprobes, to identify genomic adaptations related to pathogenesis. Furthermore, ecological preferences of Chaetothyriales were analysed, in conjuncture with the order-level phylogeny based on conserved ribosomal genes. General characteristics, phylogenomic relationships, transposable elements, sex-related genes, protein family evolution, genes related to protein degradation (MEROPS), carbohydrate-active enzymes (CAZymes), melanin synthesis and secondary metabolism were investigated and compared between species. Genome assemblies varied from 25.81 Mb (Capronia coronata) to 43.03 Mb (Cladophialophora immunda). The bantiana-clade contained the highest number of predicted genes (12 817 on average) as well as larger genomes. We found a low content of mobile elements, with DNA transposons from Tc1/Mariner superfamily being the most abundant across analysed species. Additionally, we identified a reduction of carbohydrate degrading enzymes, specifically many of the Glycosyl Hydrolase (GH) class, while most of the Pectin Lyase (PL) genes were lost in etiological agents of chromoblastomycosis and phaeohyphomycosis. An expansion was found in protein degrading peptidase enzyme families S12 (serine-type D-Ala-D-Ala carboxypeptidases) and M38 (isoaspartyl dipeptidases). Based on genomic information, a wide range of abilities of melanin biosynthesis was revealed; genes related to metabolically distinct DHN, DOPA and pyomelanin pathways were identified. The MAT (MAting Type) locus and other sex-related genes were recognized in all 23 black fungi. Members of the asexual genera Fonsecaea and Cladophialophora appear to be heterothallic with a single copy of either MAT-1-1 or MAT-1-2 in each individual. All Capronia species are homothallic as both MAT1-1 and MAT1-2 genes were found in each single genome. The genomic synteny of the MAT-locus flanking genes (SLA2-APN2-COX13) is not conserved in black fungi as is commonly observed in Eurotiomycetes, indicating a unique genomic context for MAT in those species. The heterokaryon (het) genes expansion associated with the low selective pressure at the MAT-locus suggests that a parasexual cycle may play an important role in generating diversity among those fungi.
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Affiliation(s)
- M.M. Teixeira
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - L.F. Moreno
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - B.J. Stielow
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - A. Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - M. Hainaut
- Université Aix-Marseille (CNRS), Marseille, France
| | - L. Gonzaga
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | | | - J.S.L. Patané
- Department of Biochemistry, University of São Paulo, Brazil
| | - M. Priest
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - R. Souza
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Young
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - K.S. Ferreira
- Department of Biological Sciences, Federal University of São Paulo, Diadema, SP, Brazil
| | - Q. Zeng
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - M.M.L. da Cunha
- Núcleo Multidisciplinar de Pesquisa em Biologia UFRJ-Xerém-NUMPEX-BIO, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - A. Gladki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - B. Barker
- Division of Pathogen Genomics, Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - V.A. Vicente
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
| | - E.M. de Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, PR, Brazil
| | - S. Almeida
- Department of Clinical and Toxicological Analysis, University of São Paulo, São Paulo, SP, Brazil
| | - B. Henrissat
- Université Aix-Marseille (CNRS), Marseille, France
| | - A.T.R. Vasconcelos
- The National Laboratory for Scientific Computing (LNCC), Petropolis, Brazil
| | - S. Deng
- Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - H. Voglmayr
- Department of Systematic and Evolutionary Botany, University of Vienna, Vienna, Austria
| | - T.A.A. Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza, Egypt
| | - A. Gorbushina
- Federal Institute for Material Research and Testing (BAM), Berlin, Germany
| | - M.S.S. Felipe
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - C.A. Cuomo
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - G. Sybren de Hoog
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
- Department of Basic Pathology, Federal University of Paraná State, Curitiba, PR, Brazi1
- Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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103
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Badouin H, Gladieux P, Gouzy J, Siguenza S, Aguileta G, Snirc A, Le Prieur S, Jeziorski C, Branca A, Giraud T. Widespread selective sweeps throughout the genome of model plant pathogenic fungi and identification of effector candidates. Mol Ecol 2017; 26:2041-2062. [DOI: 10.1111/mec.13976] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 12/11/2022]
Affiliation(s)
- H. Badouin
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - P. Gladieux
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR BGPI; Campus International de Baillarguet; INRA; 34398 Montpellier France
| | - J. Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - S. Siguenza
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR441; INRA; 31326 Castanet-Tolosan France
- Laboratoire des Interactions Plantes-Microorganismes (LIPM); UMR2594; CNRS; 31326 Castanet-Tolosan France
| | - G. Aguileta
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - A. Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - S. Le Prieur
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - C. Jeziorski
- Genotoul; GeT-PlaGe; INRA Auzeville 31326 Castanet-Tolosan France
- UAR1209; INRA Auzeville 31326 Castanet-Tolosan France
| | - A. Branca
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - T. Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech; Université Paris-Saclay; 91400 Orsay France
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104
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Liao J, Huang H, Meusnier I, Adreit H, Ducasse A, Bonnot F, Pan L, He X, Kroj T, Fournier E, Tharreau D, Gladieux P, Morel JB. Pathogen effectors and plant immunity determine specialization of the blast fungus to rice subspecies. eLife 2016; 5. [PMID: 28008850 PMCID: PMC5182064 DOI: 10.7554/elife.19377] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/01/2016] [Indexed: 12/02/2022] Open
Abstract
Understanding how fungi specialize on their plant host is crucial for developing sustainable disease control. A traditional, centuries-old rice agro-system of the Yuanyang terraces was used as a model to show that virulence effectors of the rice blast fungus Magnaporthe oryzaeh play a key role in its specialization on locally grown indica or japonica local rice subspecies. Our results have indicated that major differences in several components of basal immunity and effector-triggered immunity of the japonica and indica rice varieties are associated with specialization of M. oryzae. These differences thus play a key role in determining M. oryzae host specificity and may limit the spread of the pathogen within the Yuanyang agro-system. Specifically, the AVR-Pia effector has been identified as a possible determinant of the specialization of M. oryzae to local japonica rice. DOI:http://dx.doi.org/10.7554/eLife.19377.001 Microbes that cause diseases in plants are a threat to food security. For example, the rice blast fungus Magnaporthe oryzae causes the loss of enough rice to feed 60 million people each year. Disease-causing microbes must overcome the plant’s first line of defense, which includes preformed barriers and antimicrobial responses that are triggered by characteristic molecules found in many different microbes. The microbes that can overcome this first line of defense typically do so with an arsenal of proteins called effectors that interfere with specific biological processes in the plant. To counteract this interference, some plants have evolved genes that encode proteins that detect these effectors and trigger stronger antimicrobial responses. For centuries, farmers and plant breeders have selected for these resistance genes when trying to breed crops that are more resistant to disease. However, over time, disease-causing microbes have lost effectors, which means that several resistance genes have rapidly become ineffective. Some researchers predicted that growing a mixture of varieties of a given crop together might be a better way of protecting crop yields. Over 16 years ago, this idea was proved successful against the rice blast fungus for rice plants grown in China. However, the exact reasons why this strategy worked and its effects on the fungus were not clear. Now Liao, Huang et al. have taken another look at rice varieties grown via the traditional method of terraces of rice paddies in Yuanyang. Some of these varieties had a strong first line of defense and few resistance genes, while others relied much more on resistance genes to protect themselves again the rice blast fungus. Liao, Huang et al. found that growing rice varieties with such different immune systems forces some of the rice blast fungi to accumulate effector proteins to combat the first line of defense, whereas other fungi had to get rid of these effectors to avoid being recognized by the major resistance genes. These two forces led to the evolution of two specialized populations of fungi that can infect specific rice varieties but not others. This means that the fungi cannot spread in the landscape, and so the fields of rice become resistant as a whole. These new findings demonstrate the importance of diversity in rice for sustainable crop protection. The next challenge will be to demonstrate if a similar approach can also protect other major crops grown in different agricultural settings. DOI:http://dx.doi.org/10.7554/eLife.19377.002
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Affiliation(s)
- Jingjing Liao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Isabelle Meusnier
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| | - Henri Adreit
- Centre de coopération internationale en recherche agronomique pour le développement, UMR BGPI, Montpellier, France
| | - Aurélie Ducasse
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| | - François Bonnot
- Centre de coopération internationale en recherche agronomique pour le développement, UMR BGPI, Montpellier, France
| | - Lei Pan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.,Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Thomas Kroj
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| | - Elisabeth Fournier
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| | - Didier Tharreau
- Centre de coopération internationale en recherche agronomique pour le développement, UMR BGPI, Montpellier, France
| | - Pierre Gladieux
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
| | - Jean-Benoit Morel
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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105
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Croll D, McDonald BA. The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems. Mol Ecol 2016; 26:2027-2040. [DOI: 10.1111/mec.13870] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/13/2016] [Accepted: 09/26/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel Croll
- Plant Pathology; Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
| | - Bruce A. McDonald
- Plant Pathology; Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
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106
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The famous cultivated mushroom Bailinggu is a separate species of the Pleurotus eryngii species complex. Sci Rep 2016; 6:33066. [PMID: 27629112 PMCID: PMC5024158 DOI: 10.1038/srep33066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/21/2016] [Indexed: 12/02/2022] Open
Abstract
The mushroom of the genus Pleurotus in western China, called Bailinggu, is a precious edible fungus with high economic value. However, its taxonomical position is unclear. Some researchers regard it as a variety of P. eryngii, namely P. eryngii var. tuoliensis, whereas others consider it to be a subspecies of P. eryngii, viz. P. eryngii subsp. tuoliensis. A total of 51 samples representing seven genetic groups of the genus Pleurotus were subjected to a phylogenetic analysis of partial sequences of the translation elongation factor 1 alpha gene (ef1a), the RNA polymerase II largest subunit gene (rpb1), the RNA polymerase II second largest subunit gene (rpb2) and nuc rDNA internal transcribed spacers (ITS). Our data indicate that the mushroom Bailinggu is a lineage independent of P. eryngii and should be lifted as its own species, namely P. tuoliensis. In addition, its known distribution range consists of both western China and Iran.
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107
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Ropars J, Lo YC, Dumas E, Snirc A, Begerow D, Rollnik T, Lacoste S, Dupont J, Giraud T, López-Villavicencio M. Fertility depression among cheese-making Penicillium roqueforti strains suggests degeneration during domestication. Evolution 2016; 70:2099-109. [PMID: 27470007 PMCID: PMC5129480 DOI: 10.1111/evo.13015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 06/20/2016] [Accepted: 07/09/2016] [Indexed: 11/28/2022]
Abstract
Genetic differentiation occurs when gene flow is prevented, due to reproductive barriers or asexuality. Investigating the early barriers to gene flow is important for understanding the process of speciation. Here, we therefore investigated reproductive isolation between different genetic clusters of the fungus Penicillium roqueforti, used for maturing blue cheeses, and also occurring as food spoiler or in silage. We investigated premating and postmating fertility between and within three genetic clusters (two from cheese and one from other substrates), and we observed sexual structures under scanning electron microscopy. All intercluster types of crosses showed some fertility, suggesting that no intersterility has evolved between domesticated and wild populations despite adaptation to different environments and lack of gene flow. However, much lower fertility was found in crosses within the cheese clusters than within the noncheese cluster, suggesting reduced fertility of cheese strains, which may constitute a barrier to gene flow. Such degeneration may be due to bottlenecks during domestication and/or to the exclusive clonal replication of the strains in industry. This study shows that degeneration has occurred rapidly and independently in two lineages of a domesticated species. Altogether, these results inform on the processes and tempo of degeneration and speciation.
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Affiliation(s)
- Jeanne Ropars
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.,Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Ying-Chu Lo
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Emilie Dumas
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Dominik Begerow
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Tanja Rollnik
- Ruhr-Universität Bochum, AG Geobotanik Gebäude ND 03/174 Universitätsstraße 150 44780 Bochum, Germany
| | - Sandrine Lacoste
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Joëlle Dupont
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, F-91405, Orsay cedex, France
| | - Manuela López-Villavicencio
- Origine, Structure, Evolution de la Biodiversité, UMR 7205 CNRS-MNHN, Muséum National d'Histoire Naturelle, CP39, 57 rue Cuvier, 75231, Paris Cedex 05, France.
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108
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Poloni A, Schirawski J. Host specificity in Sporisorium reilianum is determined by distinct mechanisms in maize and sorghum. MOLECULAR PLANT PATHOLOGY 2016; 17:741-54. [PMID: 26419898 PMCID: PMC6638427 DOI: 10.1111/mpp.12326] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Smut fungi are biotrophic plant pathogens that exhibit a very narrow host range. The smut fungus Sporisorium reilianum exists in two host-adapted formae speciales: S. reilianum f. sp. reilianum (SRS), which causes head smut of sorghum, and S. reilianum f. sp. zeae (SRZ), which induces disease on maize. It is unknown why the two formae speciales cannot form spores on their respective non-favoured hosts. By fungal DNA quantification and fluorescence microscopy of stained plant samples, we followed the colonization behaviour of both SRS and SRZ on sorghum and maize. Both formae speciales were able to penetrate and multiply in the leaves of both hosts. In sorghum, the hyphae of SRS reached the apical meristems, whereas the hyphae of SRZ did not. SRZ strongly induced several defence responses in sorghum, such as the generation of H2 O2 , callose and phytoalexins, whereas the hyphae of SRS did not. In maize, both SRS and SRZ were able to spread through the plant to the apical meristem. Transcriptome analysis of colonized maize leaves revealed more genes induced by SRZ than by SRS, with many of them being involved in defence responses. Amongst the maize genes specifically induced by SRS were 11 pentatricopeptide repeat proteins. Together with the microscopic analysis, these data indicate that SRZ succumbs to plant defence after sorghum penetration, whereas SRS proliferates in a relatively undisturbed manner, but non-efficiently, on maize. This shows that host specificity is determined by distinct mechanisms in sorghum and maize.
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Affiliation(s)
- Alana Poloni
- Albrecht-von-Haller Institute for Plant Sciences, Department for Molecular Biology of Plant-Microbe Interaction, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
- Institute of Applied Microbiology, Department of Microbial Genetics, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Jan Schirawski
- Albrecht-von-Haller Institute for Plant Sciences, Department for Molecular Biology of Plant-Microbe Interaction, Georg-August-University Göttingen, Julia-Lermontowa-Weg 3, 37077, Göttingen, Germany
- Institute of Applied Microbiology, Department of Microbial Genetics, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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109
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Leroy T, Caffier V, Celton JM, Anger N, Durel CE, Lemaire C, Le Cam B. When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis. THE NEW PHYTOLOGIST 2016; 210:1443-1452. [PMID: 26853715 DOI: 10.1111/nph.13873] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/21/2015] [Indexed: 06/05/2023]
Abstract
In pathogens, introgressions through secondary contacts between divergent populations from agricultural and nonagricultural disease reservoirs are expected to have crucial evolutionary and epidemiological implications. Despite the importance of this question for disease management, experimental demonstrations of these implications remain scarce. Recently, we identified a virulent population of the apple scab pathogen Venturia inaequalis that migrated from nonagricultural hosts to European domestic apple orchards. Here, we investigated the occurrence of gene flow between agricultural and nonagricultural populations sampled in two orchards, and thereafter its consequences on the pathogenicity of hybrids. Population genetic structure and demographic inferences based on the genotypes of 104 strains revealed a high amount of gene flow between the two populations in one orchard. In this site, mating between populations was made possible by the presence of a common host. Our results revealed an invasion of the virulent trait in the agricultural population; a main direction of introgression in hybrids from the agricultural to nonagricultural genetic backgrounds; and a population of hybrids with transgressive traits. We demonstrate a secondary contact with gene flow between divergent populations of pathogens. Our findings highlight evolutionary and epidemiological changes in pathogens and have concrete implications for sustainable disease management.
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Affiliation(s)
- Thibault Leroy
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Valérie Caffier
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Jean-Marc Celton
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Nicolas Anger
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Charles-Eric Durel
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Christophe Lemaire
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
| | - Bruno Le Cam
- INRA, ACO, Université d'Angers - UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES LUNAM, Beaucouze, France
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110
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The genetic landscape of Ceratocystis albifundus populations in South Africa reveals a recent fungal introduction event. Fungal Biol 2016; 120:690-700. [PMID: 27109366 DOI: 10.1016/j.funbio.2016.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/27/2022]
Abstract
Geographical range expansion or host shifts is amongst the various evolutionary forces that underlie numerous emerging diseases caused by fungal pathogens. In this regard, Ceratocystis albifundus, the causal agent of a serious wilt disease of Acacia mearnsii trees in Africa, was recently identified killing cultivated Protea cynaroides in the Western Cape (WC) Province of South Africa. Protea cynaroides is an important native plant in the area and a key component of the Cape Floristic Region. The appearance of this new disease outbreak, together with isolates of C. albifundus from natural ecosystems as well as plantations of nonnative trees, provided an opportunity to consider questions relating to the possible origin and movement of the pathogen in South Africa. Ten microsatellite markers were used to determine the genetic diversity, population structure, and possible gene flow in a collection of 193 C. albifundus isolates. All populations, other than those from the WC, showed high levels of genetic diversity. An intermediate level of gene flow was found amongst populations of the pathogen. The results suggest that a limited number of individuals have recently been introduced into the WC, resulting in a novel disease problem in the area.
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111
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Delmas CEL, Fabre F, Jolivet J, Mazet ID, Richart Cervera S, Delière L, Delmotte F. Adaptation of a plant pathogen to partial host resistance: selection for greater aggressiveness in grapevine downy mildew. Evol Appl 2016; 9:709-25. [PMID: 27247621 PMCID: PMC4869412 DOI: 10.1111/eva.12368] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 01/27/2016] [Indexed: 01/29/2023] Open
Abstract
An understanding of the evolution of pathogen quantitative traits in response to host selective pressures is essential for the development of durable management strategies for resistant crops. However, we still lack experimental data on the effects of partial host resistance on multiple phenotypic traits (aggressiveness) and evolutionary strategies in pathogens. We performed a cross‐inoculation experiment with four grapevine hosts and 103 isolates of grapevine downy mildew (Plasmopara viticola) sampled from susceptible and partially resistant grapevine varieties. We analysed the neutral and adaptive genetic differentiation of five quantitative traits relating to pathogen transmission. Isolates from resistant hosts were more aggressive than isolates from susceptible hosts, as they had a shorter latency period and higher levels of spore production. This pattern of adaptation contrasted with the lack of neutral genetic differentiation, providing evidence for directional selection. No specificity for a particular host variety was detected. Adapted isolates had traits that were advantageous on all resistant varieties. There was no fitness cost associated with this genetic adaptation, but several trade‐offs between pathogen traits were observed. These results should improve the accuracy of prediction of fitness trajectories for this biotrophic pathogen, an essential element for the modelling of durable deployment strategies for resistant varieties.
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Affiliation(s)
- Chloé E L Delmas
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Frédéric Fabre
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Jérôme Jolivet
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Isabelle D Mazet
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Sylvie Richart Cervera
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - Laurent Delière
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
| | - François Delmotte
- UMR 1065 Santé et Agroécologie du VignobleINRAVillenave d'OrnonFrance; Bordeaux Science AgroUMR 1065 SAVEISVVUniversité de BordeauxVillenave d'OrnonFrance
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112
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Dutheil JY, Mannhaupt G, Schweizer G, M K Sieber C, Münsterkötter M, Güldener U, Schirawski J, Kahmann R. A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi. Genome Biol Evol 2016; 8:681-704. [PMID: 26872771 PMCID: PMC4824034 DOI: 10.1093/gbe/evw026] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Smut fungi are plant pathogens mostly parasitizing wild species of grasses as well as domesticated cereal crops. Genome analysis of several smut fungi including Ustilago maydis revealed a singular clustered organization of genes encoding secreted effectors. In U. maydis, many of these clusters have a role in virulence. Reconstructing the evolutionary history of clusters of effector genes is difficult because of their intrinsically fast evolution, which erodes the phylogenetic signal and homology relationships. Here, we describe the use of comparative evolutionary analyses of quality draft assemblies of genomes to study the mechanisms of this evolution. We report the genome sequence of a South African isolate of Sporisorium scitamineum, a smut fungus parasitizing sugar cane with a phylogenetic position intermediate to the two previously sequenced species U. maydis and Sporisorium reilianum. We show that the genome of S. scitamineum contains more and larger gene clusters encoding secreted effectors than any previously described species in this group. We trace back the origin of the clusters and find that their evolution is mainly driven by tandem gene duplication. In addition, transposable elements play a major role in the evolution of the clustered genes. Transposable elements are significantly associated with clusters of genes encoding fast evolving secreted effectors. This suggests that such clusters represent a case of genome compartmentalization that restrains the activity of transposable elements on genes under diversifying selection for which this activity is potentially beneficial, while protecting the rest of the genome from its deleterious effect.
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Affiliation(s)
- Julien Y Dutheil
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Gertrud Mannhaupt
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gabriel Schweizer
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christian M K Sieber
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Münsterkötter
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ulrich Güldener
- German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jan Schirawski
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Regine Kahmann
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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113
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Lemaire C, De Gracia M, Leroy T, Michalecka M, Lindhard-Pedersen H, Guerin F, Gladieux P, Le Cam B. Emergence of new virulent populations of apple scab from nonagricultural disease reservoirs. THE NEW PHYTOLOGIST 2016; 209:1220-9. [PMID: 26428268 DOI: 10.1111/nph.13658] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/15/2015] [Indexed: 05/11/2023]
Abstract
Plant pathogens adapt readily to new crop varieties in agrosystems, and it is crucial to understand the factors underlying the epidemic spread of new virulent strains if we are to develop more efficient strategies to control them. In this study we used multilocus microsatellite typing, molecular epidemiology tools and a large collection of isolates from cultivated, wild and ornamental apples to investigate the origin of new virulent populations of Venturia inaequalis, an ascomycete fungus causing apple scab on varieties carrying the Rvi6 resistance gene. We demonstrated a common origin at the European scale of populations infecting apples (Malus × domestica) carrying the Rvi6 resistance and Malus floribunda, the progenitor of the Rvi6 resistance. Demographic modeling indicated that the Rvi6-virulent lineage separated several thousands of years ago from populations infecting non-Rvi6 hosts, without detectable gene flow between the two lineages. These findings show that 'breakdowns' of plant resistance genes can be caused by the selection and migration of virulent genotypes from standing genetic variation maintained in environmental disease reservoirs, here ornamental crabapples. This work stresses the need to take better account of pathogen diversity in resistance screenings of breeding lines and in resistance deployment strategies, in order to enhance sustainable disease management.
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Affiliation(s)
- Christophe Lemaire
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France
| | - Marie De Gracia
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
| | - Thibault Leroy
- Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), SFR4207 QUASAV, PRES L'UNAM, Angers, 49075, France
- INRA, UMR 1202 BIOGECO, Cestas, 33612, France
| | - Monika Michalecka
- Department of Plant Pathology, Institute of Horticulture, Skierniewice, 96-100, Poland
| | | | - Fabien Guerin
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
- Université de la Réunion, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Saint Pierre, 97715, La Réunion, France
| | - Pierre Gladieux
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
- INRA, UMR BGPI, Montpellier, 34398, France
- CIRAD, UMR BGPI, Montpellier, 34398, France
| | - Bruno Le Cam
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, 49071, France
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114
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Stukenbrock EH. The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens. PHYTOPATHOLOGY 2016; 106:104-12. [PMID: 26824768 DOI: 10.1094/phyto-08-15-0184-rvw] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Hybridization in fungi has recently been recognized as a major force in the generation of new fungal plant pathogens. These include the grass pathogen Zymoseptoria pseudotritici and the powdery mildew pathogen Blumeria graminis triticale of triticale. Hybridization also plays an important role in the transfer of genetic material between species. This process is termed introgressive hybridization and involves extensive backcrossing between hybrid and the parental species. Introgressive hybridization has contributed substantially to the successful spread of plant pathogens such as Ophiostoma ulmi and O. novo-ulmi, the causal agents of Dutch elm disease, and other tree pathogens such as the rust pathogen Melampsora. Hybridization occurs more readily between species that have previously not coexisted, so-called allopatric species. Reproductive barriers between allopatric species are likely to be more permissive allowing interspecific mating to occur. The bringing together of allopatric species of plant pathogens by global agricultural trade consequently increases the potential for hybridization between pathogen species. In light of global environmental changes, agricultural development, and the facilitated long-distance spread of fungal plant pathogens, hybridization should be considered an important mechanism whereby new pathogens may emerge. Recent studies have gained insight into the genetics and biology of fungal hybrids. Here I summarize current knowledge about hybrid speciation and introgressive hybridization. I propose that future studies will benefit greatly from the availability of large genome data sets and that genome data provide a powerful resource in combination with experimental approaches for analyses of hybrid species.
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Affiliation(s)
- Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118 Kiel, Germany and Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
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115
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Thomas GE, Geetha KA, Augustine L, Mamiyil S, Thomas G. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality. FRONTIERS IN PLANT SCIENCE 2016; 7:1913. [PMID: 28066470 PMCID: PMC5167741 DOI: 10.3389/fpls.2016.01913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/02/2016] [Indexed: 05/09/2023]
Abstract
Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller's ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller's ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically diverse, but were susceptible, whereas populations inhabiting the revenue land were fragmented and monoclonal, but were resistant. It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by habitat fragmentation or pathogen pressure, Z. zerumbet.
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Affiliation(s)
| | - Kiran A. Geetha
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
| | - Lesly Augustine
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
| | - Sabu Mamiyil
- Department of Botany, University of CalicutMalappuram, India
| | - George Thomas
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
- *Correspondence: George Thomas,
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116
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Tollenaere C, Susi H, Laine AL. Evolutionary and Epidemiological Implications of Multiple Infection in Plants. TRENDS IN PLANT SCIENCE 2016; 21:80-90. [PMID: 26651920 DOI: 10.1016/j.tplants.2015.10.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 10/02/2015] [Accepted: 10/20/2015] [Indexed: 05/04/2023]
Abstract
Recent methodological advances have uncovered tremendous microbial diversity cohabiting in the same host plant, and many of these microbes cause disease. In this review we highlight how the presence of other pathogen species, or other pathogen genotypes, within a plant can affect key components of host-pathogen interactions: (i) within-plant virulence and pathogen accumulation, through direct and host-mediated mechanisms; (ii) evolutionary trajectories of pathogen populations, through virulence evolution, generation of novel genetic combinations, and maintenance of genetic diversity; and (iii) disease dynamics, with multiple infection likely to render epidemics more devastating. The major future challenges are to couple a community ecology approach with a molecular investigation of the mechanisms operating under coinfection and to evaluate the evolution and effectiveness of resistance within a coinfection framework.
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Affiliation(s)
- Charlotte Tollenaere
- Interactions Plantes-Microorganismes et Environnement (IPME), Institut de Recherches pour le Développement (IRD) - Cirad - Université de Montpellier, 34394 Montpellier, France; Laboratoire Mixte International Patho-Bios, IRD-INERA (Institut de l'Environnement et de Recherches Agricoles), BP171, Bobo-Dioulasso, Burkina Faso
| | - Hanna Susi
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Helsinki, Finland
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, PO Box 65 (Viikinkaari 1), FI-00014 University of Helsinki, Helsinki, Finland.
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117
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Jimu L, Chen S, Wingfield MJ, Mwenje E, Roux J. Three genetic groups of the Eucalyptus stem canker pathogen Teratosphaeria zuluensis introduced into Africa from an unknown source. Antonie Van Leeuwenhoek 2016; 109:21-33. [PMID: 26499489 DOI: 10.1111/efp.12095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/05/2015] [Indexed: 05/28/2023]
Abstract
The Eucalyptus stem canker pathogen Teratosphaeria zuluensis was discovered in South Africa in 1988 and it has subsequently been found in several other African countries as well as globally. In this study, the population structure, genetic diversity and evolutionary history of T. z uluensis were analysed using microsatellite markers to gain an enhanced understanding of its movement in Africa. Isolates were collected from several sites in Malawi, Mozambique, Uganda and Zambia. Data obtained were compared with those previously published for a South African population. The data obtained from 334 isolates, amplified across eight microsatellite loci, were used for assignment, differentiation and genetic diversity tests. STRUCTURE analyses, θ st and genetic distances revealed the existence of two clusters, one dominated by isolates from South Africa and the other by isolates from the Zambezi basin including Malawi, Mozambique and Zambia. High levels of admixture were found within and among populations, dominated by the Mulanje population in Malawi. Moderate to low genetic diversity of the populations supports the previously held view that the pathogen was introduced into Africa. The clonal nature of the Ugandan population suggests a very recent introduction, most likely from southern Africa.
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Affiliation(s)
- Luke Jimu
- Department of Plant Production and Soil Science, Forest Science Postgraduate Programme, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa.
| | - ShuaiFei Chen
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eddie Mwenje
- Bindura University of Science Education (BUSE), P. Bag 1020, Bindura, Zimbabwe
| | - Jolanda Roux
- Department of Microbiology and Plant Pathology, FABI, University of Pretoria, Private Bag X20, Hatfield, Pretoria, 0028, South Africa
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118
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Gladieux P, Wilson BA, Perraudeau F, Montoya LA, Kowbel D, Hann-Soden C, Fischer M, Sylvain I, Jacobson DJ, Taylor JW. Genomic sequencing reveals historical, demographic and selective factors associated with the diversification of the fire-associated fungus Neurospora discreta. Mol Ecol 2015; 24:5657-75. [PMID: 26453896 DOI: 10.1111/mec.13417] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/30/2022]
Abstract
Delineating microbial populations, discovering ecologically relevant phenotypes and identifying migrants, hybrids or admixed individuals have long proved notoriously difficult, thereby limiting our understanding of the evolutionary forces at play during the diversification of microbial species. However, recent advances in sequencing and computational methods have enabled an unbiased approach whereby incipient species and the genetic correlates of speciation can be identified by examining patterns of genomic variation within and between lineages. We present here a population genomic study of a phylogenetic species in the Neurospora discreta species complex, based on the resequencing of full genomes (~37 Mb) for 52 fungal isolates from nine sites in three continents. Population structure analyses revealed two distinct lineages in South-East Asia, and three lineages in North America/Europe with a broad longitudinal and latitudinal range and limited admixture between lineages. Genome scans for selective sweeps and comparisons of the genomic landscapes of diversity and recombination provided no support for a role of selection at linked sites on genomic heterogeneity in levels of divergence between lineages. However, demographic inference indicated that the observed genomic heterogeneity in divergence was generated by varying rates of gene flow between lineages following a period of isolation. Many putative cases of exchange of genetic material between phylogenetically divergent fungal lineages have been discovered, and our work highlights the quantitative importance of genetic exchanges between more closely related taxa to the evolution of fungal genomes. Our study also supports the role of allopatric isolation as a driver of diversification in saprobic microbes.
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Affiliation(s)
- Pierre Gladieux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecologie Systematique Evolution, Université Paris Sud, Batiment 360, 91405, Orsay, France
| | | | - Fanny Perraudeau
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Ecole Polytechnique, Route de Saclay, 91128, Palaiseau, France
| | - Liliam A Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | | | - Monika Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Iman Sylvain
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - David J Jacobson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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119
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Ding X, Yang M, Huang H, Chuan Y, He X, Li C, Zhu Y, Zhu S. Priming maize resistance by its neighbors: activating 1,4-benzoxazine-3-ones synthesis and defense gene expression to alleviate leaf disease. FRONTIERS IN PLANT SCIENCE 2015; 6:830. [PMID: 26528303 PMCID: PMC4600908 DOI: 10.3389/fpls.2015.00830] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/22/2015] [Indexed: 05/23/2023]
Abstract
Plant disease can be effectively suppressed in intercropping systems. Our previous study demonstrated that neighboring maize plants can restrict the spread of soil-borne pathogens of pepper plants by secreting defense compounds into the soil. However, whether maize plant can receive benefits from its neighboring pepper plants in an intercropping system is little attention. We examined the effects of maize roots treated with elicitors from the pepper pathogen Phytophthora capsici and pepper root exudates on the synthesis of 1,4-benzoxazine-3-ones (BXs), the expression of defense-related genes in maize, and their ability to alleviate the severity of southern corn leaf blight (SCLB) caused by Bipolaris maydis. We found that SCLB was significantly reduced after the above treatments. The contents of 1,4-benzoxazine-3-ones (BXs: DIBOA, DIMBOA, and MBOA) and the expression levels of BX synthesis and defense genes in maize roots and shoots were up-regulated. DIMBOA and MBOA effectively inhibited the mycelium growth of Bipolaris maydis at physiological concentrations in maize shoots. Further studies suggested that the defense related pathways or genes in maize roots and shoots were activated by elicitors from the P. capsici or pepper root exudates. In conclusion, maize increased the levels of BXs and defense gene expression both in roots and shoots after being triggered by root exudates and pathogen from neighboring pepper plants, eventually enhancing its resistance.
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Affiliation(s)
| | | | | | | | | | | | | | - Shusheng Zhu
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural UniversityKunming, China
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120
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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] [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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Poppe S, Dorsheimer L, Happel P, Stukenbrock EH. Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola). PLoS Pathog 2015. [PMID: 26225424 PMCID: PMC4520584 DOI: 10.1371/journal.ppat.1005055] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The speciation of pathogens can be driven by divergent host specialization. Specialization to a new host is possible via the acquisition of advantageous mutations fixed by positive selection. Comparative genome analyses of closely related species allows for the identification of such key substitutions via inference of genome-wide signatures of positive selection. We previously used a comparative genomics framework to identify genes that have evolved under positive selection during speciation of the prominent wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola). In this study, we conducted functional analyses of four genes exhibiting strong signatures of positive selection in Z. tritici. We deleted the four genes in Z. tritici and confirm a virulence-related role of three of the four genes ΔZt80707, ΔZt89160 and ΔZt103264. The two mutants ΔZt80707 and ΔZt103264 show a significant reduction in virulence during infection of wheat; the ΔZt89160 mutant causes a hypervirulent phenotype in wheat. Mutant phenotypes of ΔZt80707, ΔZt89160 and ΔZt103264 can be restored by insertion of the wild-type genes. However, the insertion of the Zt80707 and Zt89160 orthologs from Z. pseudotritici and Z. ardabiliae do not restore wild-type levels of virulence, suggesting that positively selected substitutions in Z. tritici may relate to divergent host specialization. Interestingly, the gene Zt80707 encodes also a secretion signal that targets the protein for cell secretion. This secretion signal is however only transcribed in Z. tritici, suggesting that Z. tritici-specific substitutions relate to a new function of the protein in the extracellular space of the wheat-Z. tritici interaction. Together, the results presented here highlight that Zt80707, Zt103264 and Zt89160 represent key genes involved in virulence and host-specific disease development of Z. tritici. Our findings illustrate that evolutionary predictions provide a powerful tool for the identification of novel traits crucial for host adaptation and pathogen evolution. Zymoseptoria spp provides a unique model system to study the underlying genetics of host specialization of plant pathogens. Closely related Zymoseptoria species, including the prominent wheat pathogen Z. tritici, have recently specialized to distinct grass hosts. Positively selected substitutions have played a central role in the acquisition of new host specificities. We have identified a small set of genes showing signatures of positive selection. We demonstrate that three of these four candidate genes play an important role during host infection. Two mutants of Z. tritici were impaired in virulence; a third mutant showed a hypervirulent phenotype. New protein specificities not only include changes at the amino acid sequence level but also at the level of the protein structure. We conducted a gene replacement experiment to test if mutant phenotypes in Z. tritici could be complemented by the insertion of orthologous genes from the two closely related species Z. pseudotritici and Z. ardabiliae. For two genes, we confirm that the species-specific protein changes are essential for proper protein functioning in Z. tritici; key traits involved in the evolution of virulence and host specificity of this prominent pathogen can be characterized via a combination of evolutionary predictions and functional analyses.
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Affiliation(s)
- Stephan Poppe
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lena Dorsheimer
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Petra Happel
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Holtgrewe Stukenbrock
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
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Stewart JE, Brooks K, Brannen PM, Cline WO, Brewer MT. Elevated Genetic Diversity in the Emerging Blueberry Pathogen Exobasidium maculosum. PLoS One 2015; 10:e0132545. [PMID: 26207812 PMCID: PMC4514876 DOI: 10.1371/journal.pone.0132545] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/17/2015] [Indexed: 01/26/2023] Open
Abstract
Emerging diseases caused by fungi are increasing at an alarming rate. Exobasidium leaf and fruit spot of blueberry, caused by the fungus Exobasidium maculosum, is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA, severely reducing fruit quality in some plantings. The objectives of this study were to determine the genetic diversity of E. maculosum in the southeastern USA to elucidate the basis of disease emergence and to investigate if populations of E. maculosum are structured by geography, host species, or tissue type. We sequenced three conserved loci from 82 isolates collected from leaves and fruit of rabbiteye blueberry (Vaccinium virgatum), highbush blueberry (V. corymbosum), and southern highbush blueberry (V. corymbosum hybrids) from commercial fields in Georgia and North Carolina, USA, and 6 isolates from lowbush blueberry (V. angustifolium) from Maine, USA, and Nova Scotia, Canada. Populations of E. maculosum from the southeastern USA and from lowbush blueberry in Maine and Nova Scotia are distinct, but do not represent unique species. No difference in genetic structure was detected between different host tissues or among different host species within the southeastern USA; however, differentiation was detected between populations in Georgia and North Carolina. Overall, E. maculosum showed extreme genetic diversity within the conserved loci with 286 segregating sites among the 1,775 sequenced nucleotides and each isolate representing a unique multilocus haplotype. However, 94% of the nucleotide substitutions were silent, so despite the high number of mutations, selective constraints have limited changes to the amino acid sequences of the housekeeping genes. Overall, these results suggest that the emergence of Exobasidium leaf and fruit spot is not due to a recent introduction or host shift, or the recent evolution of aggressive genotypes of E. maculosum, but more likely as a result of an increasing host population or an environmental change.
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Affiliation(s)
- Jane E. Stewart
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Kyle Brooks
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Phillip M. Brannen
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - William O. Cline
- Department of Plant Pathology, North Carolina State University, Horticultural Crops Research Station, Castle Hayne, North Carolina, United States of America
| | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
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123
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De Gracia M, Cascales M, Expert P, Bellanger MN, Le Cam B, Lemaire C. How Did Host Domestication Modify Life History Traits of Its Pathogens? PLoS One 2015; 10:e0122909. [PMID: 26091067 PMCID: PMC4475019 DOI: 10.1371/journal.pone.0122909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 02/16/2015] [Indexed: 01/08/2023] Open
Abstract
Understanding evolutionary dynamics of pathogens during domestication of their hosts and rise of agro-ecosystems is essential for durable disease management. Here, we investigated changes in life-history traits of the fungal pathogen Venturia inaequalis during domestication of the apple. Life traits linked to fungal dispersal were compared between 60 strains that were sampled in domestic and wild habitats in Kazakhstan, the center of origin of both host and pathogen. Our two main findings are that transition from wild to agro-ecosystems was associated with an increase of both spore size and sporulation capacity; and that distribution of quantitative traits of the domestic population mostly overlapped with those of the wild population. Our results suggest that apple domestication had a considerable impact on fungal characters linked to its dispersal through selection from standing phenotypic diversity. We showed that pestification of V. inaequalis in orchards led to an enhanced allocation in colonization ability from standing variation in the wild area. This study emphasizes the potential threat that pathogenic fungal populations living in wild environments represent for durability of resistance in agro-ecosystems.
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Affiliation(s)
- Marie De Gracia
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
| | - Mathilde Cascales
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
| | - Pascale Expert
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
| | - Marie-Noelle Bellanger
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
| | - Bruno Le Cam
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
| | - Christophe Lemaire
- INRA, IRHS, SFR QUASAV, Beaucouzé, 49071, France
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Angers, 49045, France
- Agrocampus Ouest, IRHS, SFR QUASAV, Angers, 49045, France
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124
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Gross A, Hosoya T, Zhao YJ, Baral HO. Hymenoscyphus linearis sp. nov: another close relative of the ash dieback pathogen H. fraxineus. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1041-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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125
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Short DPG, Gurung S, Gladieux P, Inderbitzin P, Atallah ZK, Nigro F, Li G, Benlioglu S, Subbarao KV. Globally invading populations of the fungal plant pathogen Verticillium dahliae are dominated by multiple divergent lineages. Environ Microbiol 2015; 17:2824-40. [PMID: 25630463 DOI: 10.1111/1462-2920.12789] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 11/28/2022]
Abstract
The spread of aggressive fungal pathogens into previously non-endemic regions is a major threat to plant health and food security. Analyses of the spatial and genetic structure of plant pathogens offer valuable insights into their origin, dispersal mechanisms and evolution, and have been useful to develop successful disease management strategies. Here, we elucidated the genetic diversity, population structure and demographic history of worldwide invasion of the ascomycete Verticillium dahliae, a soil-borne pathogen, using a global collection of 1100 isolates from multiple plant hosts and countries. Seven well-differentiated genetic clusters were revealed through discriminant analysis of principal components (DAPC), but no strong associations between these clusters and host/geographic origin of isolates were found. Analyses of clonal evolutionary relationships among multilocus genotypes with the eBURST algorithm and analyses of genetic distances revealed that genetic clusters represented several ancient evolutionary lineages with broad geographic distribution and wide host range. Comparison of different scenarios of demographic history using approximate Bayesian computations revealed the branching order among the different genetic clusters and lineages. The different lineages may represent incipient species, and this raises questions with respect to their evolutionary origin and the factors allowing their maintenance in the same areas and same hosts without evidence of admixture between them. Based on the above findings and the biology of V. dahliae, we conclude that anthropogenic movement has played an important role in spreading V. dahliae lineages. Our findings have implications for the development of management strategies such as quarantine measures and crop resistance breeding.
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Affiliation(s)
- Dylan P G Short
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Suraj Gurung
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Pierre Gladieux
- Ecologie Systematique Evolution, CNRS, Université Paris Sud, Orsay, F-91405, France
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Zahi K Atallah
- Department of Advanced Technology, Hartnell College, Salinas, CA, 93905, USA
| | - Franco Nigro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Bari, 70126, Italy
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
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126
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Pintye A, Ropars J, Harvey N, Shin HD, Leyronas C, Nicot PC, Giraud T, Kiss L. Host phenology and geography as drivers of differentiation in generalist fungal mycoparasites. PLoS One 2015; 10:e0120703. [PMID: 25803832 PMCID: PMC4372539 DOI: 10.1371/journal.pone.0120703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/25/2015] [Indexed: 11/19/2022] Open
Abstract
The question as to why parasites remain generalist or become specialist is a key unresolved question in evolutionary biology. Ampelomyces spp., intracellular mycoparasites of powdery mildew fungi, which are themselves plant pathogens, are a useful model for studies of this issue. Ampelomyces is used for the biological control of mildew. Differences in mycohost phenology promote temporal isolation between sympatric Ampelomyces mycoparasites. Apple powdery mildew (APM) causes spring epidemics, whereas other powdery mildew species on plants other than apple cause epidemics later in the season. This has resulted in genetic differentiation between APM and non-APM strains. It is unclear whether there is genetic differentiation between non-APM Ampelomyces lineages due to their specialization on different mycohosts. We used microsatellites to address this question and found no significant differentiation between non-APM Ampelomyces strains from different mycohosts or host plants, but strong differentiation between APM and non-APM strains. A geographical structure was revealed in both groups, with differences between European countries, demonstrating restricted dispersal at the continent scale and a high resolution for our markers. We found footprints of recombination in both groups, possibly more frequent in the APM cluster. Overall, Ampelomyces thus appears to be one of the rare genuine generalist pathogenic fungi able to parasitize multiple hosts in natural populations. It is therefore an excellent model for studying the evolution of pathogens towards a generalist rather than host-specific strategy, particularly in light of the tritrophic interaction between Ampelomyces mycoparasites, their powdery mildew fungal hosts and the mildew host plants.
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Affiliation(s)
- Alexandra Pintye
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences (MTA), Budapest, Hungary
| | - Jeanne Ropars
- CNRS (Centre National de la Recherche Scientifique), Ecologie, Systematique et Evolution (ESE), Orsay, France
- Univ Paris Sud, Ecology, Systematique et Evolution (ESE), Orsay, France
| | - Nick Harvey
- Genetic Marker Services, 7 Brighton, United Kingdom
| | - Hyeon-Dong Shin
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Christel Leyronas
- Institut National de la Recherche Agronomique (INRA), Unite de Recherche UR407, Unité de Pathologie Végétale, Domaine St. Maurice, Montfavet, France
| | - Philippe C. Nicot
- Institut National de la Recherche Agronomique (INRA), Unite de Recherche UR407, Unité de Pathologie Végétale, Domaine St. Maurice, Montfavet, France
| | - Tatiana Giraud
- CNRS (Centre National de la Recherche Scientifique), Ecologie, Systematique et Evolution (ESE), Orsay, France
- Univ Paris Sud, Ecology, Systematique et Evolution (ESE), Orsay, France
- * E-mail: (TG); (LK)
| | - Levente Kiss
- Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences (MTA), Budapest, Hungary
- * E-mail: (TG); (LK)
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Travadon R, Baumgartner K. Molecular Polymorphism and Phenotypic Diversity in the Eutypa Dieback Pathogen Eutypa lata. PHYTOPATHOLOGY 2015; 105:255-264. [PMID: 25084304 DOI: 10.1094/phyto-04-14-0117-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Pathogen adaptation to different hosts can lead to specialization and, when coupled with reproductive isolation, genome-wide differentiation and ecological speciation. We tested the hypothesis of host specialization among California populations of Eutypa lata (causal fungus of Eutypa dieback of grapevine and apricot), which is reported from >90 species. Genetic analyses of nine microsatellite loci in 182 isolates from three hosts (grapevine, apricot, and willow) at three locations were complemented by cross-inoculations on cultivated hosts grapevine and apricot to reveal patterns of host specialization. The cultivated hosts are likely more important sources of inoculum than the wild host willow, based on our findings of higher pathogen prevalence and allelic richness in grapevine and apricot. High levels of gene flow among all three hosts and locations, and no grouping by clustering analyses, suggest neither host nor geographic differentiation. Cross-inoculations revealed diversified phenotypes harboring various performance levels in grapevine and apricot, with no apparent correlation with their host of origin. Such phenotypic diversity may enable this pathogen to persist and reproduce as a generalist. Regular genetic reshuffling through sexual recombination, frequent immigration among hosts, and the lack of habitat choice in this passively dispersed fungus may prevent fixation of alleles controlling host specialization.
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128
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Stewart JE, Turner AN, Brewer MT. Evolutionary history and variation in host range of three Stagonosporopsis species causing gummy stem blight of cucurbits. Fungal Biol 2015; 119:370-82. [PMID: 25937065 DOI: 10.1016/j.funbio.2014.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 12/03/2014] [Accepted: 12/18/2014] [Indexed: 11/28/2022]
Abstract
Recently diverged species may form complexes of morphologically similar, yet genetically distinct lineages that occur in overlapping geographic ranges and niches. Using a multilocus sequencing approach we discovered that gummy stem blight of cucurbits is caused by three genetically distinct species: Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), Stagonosporopsis citrulli, and Stagonosporopsis caricae, which had previously been considered only a pathogen of papaya. Experiments showed that all three species are pathogenic to cucurbits in the genera Cucurbita, Cucumis, and Citrullus, but only S. caricae is aggressive to papaya. Species tree estimates show that S. citrulli and S. cucurbitacearum are phylogenetically distinct sister species, and that S. caricae is the ancestral lineage. The time estimate for divergence of S. caricae from the ancestor of S. cucurbitacearum and S. citrulli at 72 900 YBP pre-dates domestication of papaya and Cucurbita species in the American tropics. The divergence estimate observed for S. cucurbitacearum and S. citrulli at 10 900 YBP suggests that diversification of Cucurbita species and domestication of gourds and squashes could have driven their divergence. This work highlights the use of molecular systematics and population genetics to elucidate genetic identity among previously unassociated fungi and to understand the patterns of pathogen diversification.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Ashley N Turner
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Marin T Brewer
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA.
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129
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Gladieux P, Feurtey A, Hood ME, Snirc A, Clavel J, Dutech C, Roy M, Giraud T. The population biology of fungal invasions. Mol Ecol 2015; 24:1969-86. [DOI: 10.1111/mec.13028] [Citation(s) in RCA: 142] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- P. Gladieux
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - A. Feurtey
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - M. E. Hood
- Department of Biology; Amherst College; Amherst Massachusetts 01002 USA
| | - A. Snirc
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
| | - J. Clavel
- Conservation des Espèces; Restauration et Suivi des Populations - CRBPO; Muséum National d'Histoire Naturelle-CNRS-Université Pierre et Marie Curie; 55 rue Buffon 75005 Paris France
| | - C. Dutech
- Biodiversité Gènes et Communautés; INRA-Université Bordeaux 1; Site de Pierroton 33610 Cestas France
| | - M. Roy
- Evolution et Diversité Biologique; Université Toulouse Paul Sabatier-Ecole Nationale de Formation Agronomique-CNRS; 118 route de Narbonne 31062 Toulouse France
| | - T. Giraud
- Ecologie; Systématique et Evolution; Université Paris-Sud; Bâtiment 360 F-91405 Orsay France
- CNRS; 91405 Orsay France
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130
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Diao Y, Zhang C, Xu J, Lin D, Liu L, Mtung'e OG, Liu X. Genetic differentiation and recombination among geographic populations of the fungal pathogen Colletotrichum truncatum from chili peppers in China. Evol Appl 2015; 8:108-18. [PMID: 25667606 PMCID: PMC4310585 DOI: 10.1111/eva.12233] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 10/22/2014] [Indexed: 11/28/2022] Open
Abstract
Colletotrichum truncatum is an extremely important fungal pathogen. It can cause diseases both in humans and in over 460 plant species. However, little is known about its genetic diversity within and among populations. One of the major plant hosts of C. truncatum is pepper, and China is one of the main pepper-producing countries in the world. Here, we propose the hypotheses that geography has a major influence on the relationships among populations of C. truncatum in China and that infections in different populations need to be managed differently. To test these hypotheses, we obtained and analyzed 266 C. truncatum isolates from 13 regions representing the main pepper-growing areas throughout China. The analysis based on nine microsatellite markers identified high intrapopulation genetic diversity, evidence of sexual recombination, and geographic differentiation. The genetic differentiation was positively correlated with geographic distance, with the southern and northern China populations grouped in two distinct clusters. Interestingly, isolates collected from the pepper-breeding center harbored the most private alleles. The results suggest that the geographic populations of C. truncatum on peppers in China are genetically differentiated and should be managed accordingly. Our study also provides a solid foundation from which to further explore the global genetic epidemiology of C. truncatum in both plants and humans.
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Affiliation(s)
- Yongzhao Diao
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Can Zhang
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Jianping Xu
- Department of Biology, McMaster UniversityHamilton, ON, Canada
| | - Dong Lin
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Li Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Olivo G Mtung'e
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
| | - Xili Liu
- Department of Plant Pathology, College of Agriculture and Biotechnology, China Agricultural UniversityBeijing, China
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Abstract
The malaria parasites (Apicomplexa: Haemosporida) of birds are believed to have diversified across the avian host phylogeny well after the origin of most major host lineages. Although many symbionts with direct transmission codiversify with their hosts, mechanisms of species formation in vector-borne parasites, including the role of host shifting, are poorly understood. Here, we examine the hosts of sister lineages in a phylogeny of 181 putative species of malaria parasites of New World terrestrial birds to determine the role of shifts between host taxa in the formation of new parasite species. We find that host shifting, often across host genera and families, is the rule. Sympatric speciation by host shifting would require local reproductive isolation as a prerequisite to divergent selection, but this mechanism is not supported by the generalized host-biting behavior of most vectors of avian malaria parasites. Instead, the geographic distribution of individual parasite lineages in diverse hosts suggests that species formation is predominantly allopatric and involves host expansion followed by local host-pathogen coevolution and secondary sympatry, resulting in local shifting of parasite lineages across hosts.
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132
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Zhang T, Victor TR, Rajkumar SS, Li X, Okoniewski JC, Hicks AC, Davis AD, Broussard K, LaDeau SL, Chaturvedi S, Chaturvedi V. Mycobiome of the bat white nose syndrome affected caves and mines reveals diversity of fungi and local adaptation by the fungal pathogen Pseudogymnoascus (Geomyces) destructans. PLoS One 2014; 9:e108714. [PMID: 25264864 PMCID: PMC4181696 DOI: 10.1371/journal.pone.0108714] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 09/02/2014] [Indexed: 12/27/2022] Open
Abstract
Current investigations of bat White Nose Syndrome (WNS) and the causative fungus Pseudogymnoascus (Geomyces) destructans (Pd) are intensely focused on the reasons for the appearance of the disease in the Northeast and its rapid spread in the US and Canada. Urgent steps are still needed for the mitigation or control of Pd to save bats. We hypothesized that a focus on fungal community would advance the understanding of ecology and ecosystem processes that are crucial in the disease transmission cycle. This study was conducted in 2010–2011 in New York and Vermont using 90 samples from four mines and two caves situated within the epicenter of WNS. We used culture-dependent (CD) and culture-independent (CI) methods to catalogue all fungi (‘mycobiome’). CD methods included fungal isolations followed by phenotypic and molecular identifications. CI methods included amplification of DNA extracted from environmental samples with universal fungal primers followed by cloning and sequencing. CD methods yielded 675 fungal isolates and CI method yielded 594 fungal environmental nucleic acid sequences (FENAS). The core mycobiome of WNS comprised of 136 operational taxonomic units (OTUs) recovered in culture and 248 OTUs recovered in clone libraries. The fungal community was diverse across the sites, although a subgroup of dominant cosmopolitan fungi was present. The frequent recovery of Pd (18% of samples positive by culture) even in the presence of dominant, cosmopolitan fungal genera suggests some level of local adaptation in WNS-afflicted habitats, while the extensive distribution of Pd (48% of samples positive by real-time PCR) suggests an active reservoir of the pathogen at these sites. These findings underscore the need for integrated disease control measures that target both bats and Pd in the hibernacula for the control of WNS.
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Affiliation(s)
- Tao Zhang
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Tanya R. Victor
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Sunanda S. Rajkumar
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Xiaojiang Li
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Joseph C. Okoniewski
- Bureau of Wildlife, New York State Department of Environmental Conservation, Albany, New York, United States of America
| | - Alan C. Hicks
- Bureau of Wildlife, New York State Department of Environmental Conservation, Albany, New York, United States of America
| | - April D. Davis
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Kelly Broussard
- Rabies Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Shannon L. LaDeau
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Sudha Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail: (SC); (VC)
| | - Vishnu Chaturvedi
- Mycology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- * E-mail: (SC); (VC)
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133
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Bruns E, Carson ML, May G. The jack of all trades is master of none: a pathogen's ability to infect a greater number of host genotypes comes at a cost of delayed reproduction. Evolution 2014; 68:2453-66. [PMID: 24890322 DOI: 10.1111/evo.12461] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 05/20/2014] [Indexed: 01/16/2023]
Abstract
A trade-off between a pathogen's ability to infect many hosts and its reproductive capacity on each host genotype is predicted to limit the evolution of an expanded host range, yet few empirical results provide evidence for the magnitude of such trade-offs. Here, we test the hypothesis for a trade-off between the number of host genotypes that a fungal pathogen can infect (host genotype range) and its reproductive capacity on susceptible plant hosts. We used strains of the oat crown rust fungus that carried widely varying numbers of virulence (avr) alleles known to determine host genotype range. We quantified total spore production and the expression of four pathogen life-history stages: infection efficiency, time until reproduction, pustule size, and spore production per pustule. In support of the trade-off hypothesis, we found that virulence level, the number of avr alleles per pathogen strain, was correlated with significant delays in the onset of reproduction and with smaller pustule sizes. Modeling from our results, we conclude that trade-offs have the capacity to constrain the evolution of host genotype range in local populations. In contrast, long-term trends in virulence level suggest that the continued deployment of resistant host lines over wide regions of the United States has generated selection for increased host genotype range.
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Affiliation(s)
- Emily Bruns
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, Minnesota, 55108; Department of Biology, University of Virginia, Charlottesville, Virginia, 22904.
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Walker AS, Gladieux P, Decognet V, Fermaud M, Confais J, Roudet J, Bardin M, Bout A, C. Nicot P, Poncet C, Fournier E. Population structure and temporal maintenance of the multihost fungal pathogenBotrytis cinerea: causes and implications for disease management. Environ Microbiol 2014; 17:1261-74. [DOI: 10.1111/1462-2920.12563] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/04/2014] [Indexed: 01/02/2023]
Affiliation(s)
- Anne-Sophie Walker
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Pierre Gladieux
- CNRS, UMR 8079 Ecologie Systématique Evolution; Bâtiment 360 Orsay F-91405 France
- University of Paris-Sud; Orsay F-91405 France
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720 USA
| | - Véronique Decognet
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Marc Fermaud
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Johann Confais
- INRA, UR 1290 BIOGER-CPP; Avenue Lucien Brétignières Thiverval-Grignon F-78850 France
| | - Jean Roudet
- INRA UMR 1065 SAVE; ISVV; 71 Avenue Edouard Bourlaux Villenave d'Ornon F-33882 France
| | - Marc Bardin
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | - Alexandre Bout
- INRA, UMR 1355 ISA, TEAPEA; Sophia-Antipolis F-06903 France
| | - Philippe C. Nicot
- INRA, UR 407 Plant Pathology Unit; Domaine Saint Maurice; Montfavet F-84143 France
| | | | - Elisabeth Fournier
- INRA, UMR BGPI; TA A 54/K; Campus International de Baillarguet Montpellier F-34398 France
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135
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Kemen E. Microbe-microbe interactions determine oomycete and fungal host colonization. CURRENT OPINION IN PLANT BIOLOGY 2014; 20:75-81. [PMID: 24845577 DOI: 10.1016/j.pbi.2014.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Revised: 03/22/2014] [Accepted: 04/24/2014] [Indexed: 05/03/2023]
Abstract
Microbial organisms sharing habitats aim for maximum fitness that they can only reach by collaboration. Developing stable networks within communities are crucial and can be achieved by exchanging common goods and genes that benefit the community. Only recently was it shown that horizontal gene transfer is not only common between prokaryotes but also into eukaryotic organisms such as fungi and oomycetes benefiting communal stability. Eukaryotic plant symbionts and pathogens coevolve with the plant microbiome and can acquire the ability to communicate or even collaborate, facilitating communal host colonization. Understanding communal infection will lead to a mechanistic understanding in how new hosts can be colonized under natural conditions and how we can counteract.
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Affiliation(s)
- Eric Kemen
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, Cologne 50829, Germany.
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136
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Oono R, Lutzoni F, Arnold AE, Kaye L, U'Ren JM, May G, Carbone I. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species. AMERICAN JOURNAL OF BOTANY 2014; 101:1362-1374. [PMID: 25156984 DOI: 10.3732/ajb.1400141] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.• METHODS We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.• KEY RESULTS Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.• CONCLUSIONS We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales.
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Affiliation(s)
- Ryoko Oono
- University of California-Santa Barbara, Santa Barbara, California 93106 USA Duke University, Durham, North Carolina 27708 USA North Carolina State University, Raleigh, North Carolina 27695 USA
| | | | | | - Laurel Kaye
- Duke University, Durham, North Carolina 27708 USA
| | - Jana M U'Ren
- University of Arizona, Tucson, Arizona 85721 USA
| | - Georgiana May
- University of Minnesota, St. Paul, Minnesota 55108 USA
| | - Ignazio Carbone
- North Carolina State University, Raleigh, North Carolina 27695 USA
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137
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Rouxel M, Mestre P, Baudoin A, Carisse O, Delière L, Ellis MA, Gadoury D, Lu J, Nita M, Richard-Cervera S, Schilder A, Wise A, Delmotte F. Geographic distribution of cryptic species of Plasmopara viticola causing downy mildew on wild and cultivated grape in eastern North America. PHYTOPATHOLOGY 2014; 104:692-701. [PMID: 24915427 DOI: 10.1094/phyto-08-13-0225-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The putative center of origin of Plasmopara viticola, the causal agent of grape downy mildew, is eastern North America, where it has been described on several members of the family Vitaceae (e.g., Vitis spp., Parthenocissus spp., and Ampelopsis spp.). We have completed the first large-scale sampling of P. viticola isolates across a range of wild and cultivated host species distributed throughout the above region. Sequencing results of four partial genes indicated the presence of a new P. viticola species on Vitis vulpina in Virginia, adding to the four cryptic species of P. viticola recently recorded. The phylogenetic analysis also indicated that the P. viticola species found on Parthenocissus quinquefolia in North America is identical to Plasmopara muralis in Europe. The geographic distribution and host range of five pathogen species was determined through analysis of the internal transcribed spacer polymorphism of 896 isolates of P. viticola. Among three P. viticola species found on cultivated grape, one was restricted to Vitis interspecific hybrids within the northern part of eastern North America. A second species was recovered from V. vinifera and V. labrusca, and was distributed across most of the sampled region. A third species, although less abundant, was distributed across a larger geographical range, including the southern part of eastern North America. P. viticola clade aestivalis predominated (83% of isolates) in vineyards of the European winegrape V. vinifera within the sampled area, indicating that a single pathogen species may represent the primary threat to the European host species within eastern North America.
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138
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Kellner R, Bhattacharyya A, Poppe S, Hsu TY, Brem RB, Stukenbrock EH. Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs. Genome Biol Evol 2014; 6:1353-65. [PMID: 24920004 PMCID: PMC4079195 DOI: 10.1093/gbe/evu101] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen.
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Affiliation(s)
- Ronny Kellner
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | - Amitava Bhattacharyya
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | - Stephan Poppe
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
| | - Tiffany Y Hsu
- Department of Molecular and Cell Biology, University of California, BerkeleyPresent address: Graduate Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA
| | - Rachel B Brem
- Department of Molecular and Cell Biology, University of California, BerkeleyPresent address: Buck Institute for Research on Aging, Novato, CA
| | - Eva H Stukenbrock
- Max Planck Institute for Terrestrial Microbiology, Max Planck Research Group, Fungal Biodiversity, Marburg, Germany
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139
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Aghighi S, Fontanini L, Yeoh PB, Hardy GESJ, Burgess TI, Scott JK. A Conceptual Model to Describe the Decline of European Blackberry (Rubus anglocandicans), A Weed of National Significance in Australia. PLANT DISEASE 2014; 98:580-589. [PMID: 30708565 DOI: 10.1094/pdis-11-13-1124-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human activities have had an adverse impact on ecosystems on a global scale and have caused an unprecedented redispersal of organisms, with both plants and pathogens moving from their regions of origin to other parts of the world. Invasive plants are a potential threat to ecosystems globally, and their management costs tens of billions of dollars per annum. Rubus anglocandicans (European blackberry) is a serious invasive species in Australia. Herbicide and cultural control methods are generally inefficient or require multiple applications. Therefore, a biological control program using stem and leaf rust strains is the main option in Australia. However, biological control using rusts has been patchy, as host factors, climate, and weather can alter the impact of the rust at different locations. In 2007, Yeoh and Fontanini noticed that blackberry plants on the banks of the Donnelly and Warren rivers in the southwest of Western Australia were dying in areas that were being regularly monitored for the impact of rust as a biological control agent. The symptoms on blackberry became known as the disease "blackberry decline". Continuous and intensive investigations are required to discover the different biotic and abiotic components associated with specific declines in plant populations. The only agent so far introduced to Australia for the biological control of blackberry is the rust Phragmidium violaceum.
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Affiliation(s)
- S Aghighi
- Centre for Phytophthora Science and Management, Murdoch University, WA, Australia
| | - L Fontanini
- Warren Catchments Council, Manjimup, WA, Australia
| | - P B Yeoh
- CSIRO Ecosystem Sciences, Wembley, WA, Australia
| | - G E St J Hardy
- Centre for Phytophthora Science and Management, Murdoch University, WA, Australia
| | - T I Burgess
- Centre for Phytophthora Science and Management, Murdoch University, WA, Australia
| | - J K Scott
- CSIRO Ecosystem Sciences, Wembley, WA, Australia
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140
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Rascalou G, Gourbière S. Competition, virulence, host body mass and the diversification of macro-parasites. J R Soc Interface 2014; 11:20131108. [PMID: 24522783 PMCID: PMC3928941 DOI: 10.1098/rsif.2013.1108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/13/2014] [Indexed: 12/17/2022] Open
Abstract
Adaptive speciation has been much debated in recent years, with a strong emphasis on how competition can lead to the diversification of ecological and sexual traits. Surprisingly, little attention has been paid to this evolutionary process to explain intrahost diversification of parasites. We expanded the theory of competitive speciation to look at the effect of key features of the parasite lifestyle, namely fragmentation, aggregation and virulence, on the conditions and rate of sympatric speciation under the standard 'pleiotropic scenario'. The conditions for competitive speciation were found similar to those for non-parasite species, but not the rate of diversification. Adaptive evolution proceeds faster in highly fragmented parasite populations and for weakly aggregated and virulent parasites. Combining these theoretical results with standard empirical allometric relationships, we showed that parasite diversification can be faster in host species of intermediate body mass. The increase in parasite load with body mass, indeed, fuels evolution by increasing mutants production, but because of the deleterious effect of virulence, it simultaneously weakens selection for resource specialization. Those two antagonistic effects lead to optimal parasite burden and host body mass for diversification. Data on the diversity of fishes' gills parasites were found consistent with the existence of such optimum.
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Affiliation(s)
- Guilhem Rascalou
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), UMR Universités Montpellier 1 and 2, CNRS 5290, IRD 224, Montpellier, France
| | - Sébastien Gourbière
- Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
- Université de Perpignan Via Domitia, EA 4218 Institut de Modélisation et d'Analyse en Géo-Environnements et Santé (IMAGES), Perpignan 66100, France
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141
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Troch V, Audenaert K, Wyand RA, Haesaert G, Höfte M, Brown JKM. Formae speciales of cereal powdery mildew: close or distant relatives? MOLECULAR PLANT PATHOLOGY 2014; 15:304-314. [PMID: 24286122 PMCID: PMC6638862 DOI: 10.1111/mpp.12093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Powdery mildew is an important disease of cereals, affecting both grain yield and end-use quality. The causal agent of powdery mildew on cereals, Blumeria graminis, has been classified into eight formae speciales (ff.spp.), infecting crops and wild grasses. Advances in research on host specificity and resistance, and on pathogen phylogeny and origins, have brought aspects of the subspecific classification system of B. graminis into ff.spp. into question, because it is based on adaptation to certain hosts rather than strict host specialization. Cereals therefore cannot be considered as typical non-hosts to non-adapted ff.spp. We introduce the term 'non-adapted resistance' of cereals to inappropriate ff.spp. of B. graminis, which involves both pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is no clear distinction between the mechanisms of resistance to adapted and non-adapted ff.spp. Molecular evolutionary data suggest that the taxonomic grouping of B. graminis into different ff.spp. is not consistent with the phylogeny of the fungus. Imprecise estimates of mutation rates and the lack of genetic variation in introduced populations may explain the uncertainty with regard to divergence times, in the Miocene or Holocene epochs, of ff.spp. of B. graminis which infect cereal crop species. We propose that most evidence favours divergence in the Holocene, during the course of early agriculture. We also propose that the forma specialis concept should be retained for B. graminis pathogenic on cultivated cereals to include clades of the fungus which are strongly specialized to these hosts, i.e. ff.spp. hordei, secalis and tritici, as well as avenae from cultivated A. sativa, and that the forma specialis concept should no longer be applied to B. graminis from most wild grasses.
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Affiliation(s)
- Veronique Troch
- Associated Faculty of Applied Bioscience Engineering, University College Ghent (Ghent University Association), Valentin Vaerwyckweg 1, BE-9000, Ghent, Belgium; Department of Crop Protection, Laboratory of Phytopathology, Ghent University, Coupure links 653, BE-9000, Ghent, Belgium
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142
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Massoumi Alamouti S, Haridas S, Feau N, Robertson G, Bohlmann J, Breuil C. Comparative Genomics of the Pine Pathogens and Beetle Symbionts in the Genus Grosmannia. Mol Biol Evol 2014; 31:1454-74. [DOI: 10.1093/molbev/msu102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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143
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Grandaubert J, Balesdent MH, Rouxel T. [Transposable elements reshaping genomes and favouring the evolutionary and adaptive potential of fungal phytopathogens]. Biol Aujourdhui 2014; 207:277-290. [PMID: 24594576 DOI: 10.1051/jbio/2013026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Indexed: 06/03/2023]
Abstract
Phytopathogenic fungi are a major threat for global food security and show an extreme plasticity in pathogenicity behaviours. They often have a high adaptive potential allowing them to rapidly counteract the control methods used by men in agrosystems. In this paper, we evaluate the link between genome plasticity and adaptive potential using genomics and comparative genomics approaches. Our model is the evolutionary series Leptosphaeria maculans-Leptosphaeria biglobosa, encompassing five distinct entities, whose conspecificity or heterospecificity status is unclear, and which all are pathogens of cruciferous plants. They however differ by their host range and pathogenicity. Compared to other species of the species complex, the species best adapted to oilseed rape, L. maculans "brassicae", causing important losses in the crop, has a genome that was submitted to a recent and massive burst of transposition by a few families of transposable elements (TEs). Whether the genome invasion contributed to speciation is still unclear to-date but there is a coincidence between this burst of TEs and divergence between two species. This TE burst contributed to diversification of effector proteins and thus to generation of novel pathogenic specificities. In addition, the location of effector genes within genome regions enriched in TEs has direct consequences on adaptation to plant resistance and favours a multiplicity of mutation events allowing "breakdown" of resistance. These data are substantiated by other examples in the literature showing that fungi tend to have a "two-speed" genome, in which a plastic compartment enriched in TE host genes is involved in pathogenicity and adaptation to host.
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García-Guzmán G, Heil M. Life histories of hosts and pathogens predict patterns in tropical fungal plant diseases. THE NEW PHYTOLOGIST 2014; 201:1106-1120. [PMID: 24171899 DOI: 10.1111/nph.12562] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/19/2013] [Indexed: 05/26/2023]
Abstract
Plant pathogens affect the fitness of their hosts and maintain biodiversity. However, we lack theories to predict the type and intensity of infections in wild plants. Here we demonstrate using fungal pathogens of tropical plants that an examination of the life histories of hosts and pathogens can reveal general patterns in their interactions. Fungal infections were more commonly reported for light-demanding than for shade-tolerant species and for evergreen rather than for deciduous hosts. Both patterns are consistent with classical defence theory, which predicts lower resistance in fast-growing species and suggests that the deciduous habit can reduce enemy populations. In our literature survey, necrotrophs were found mainly to infect shade-tolerant woody species whereas biotrophs dominated in light-demanding herbaceous hosts. Far-red signalling and its inhibitory effects on jasmonic acid signalling are likely to explain this phenomenon. Multiple changes between the necrotrophic and the symptomless endophytic lifestyle at the ecological and evolutionary scale indicate that endophytes should be considered when trying to understand large-scale patterns in the fungal infections of plants. Combining knowledge about the molecular mechanisms of pathogen resistance with classical defence theory enables the formulation of testable predictions concerning general patterns in the infections of wild plants by fungal pathogens.
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Affiliation(s)
| | - Martin Heil
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Irapuato, Guanajuato, México
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145
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Neuhauser S, Kirchmair M, Bulman S, Bass D. Cross-kingdom host shifts of phytomyxid parasites. BMC Evol Biol 2014; 14:33. [PMID: 24559266 PMCID: PMC4016497 DOI: 10.1186/1471-2148-14-33] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/13/2014] [Indexed: 11/12/2022] Open
Abstract
Background Phytomyxids (plasmodiophorids and phagomyxids) are cosmopolitan, obligate biotrophic protist parasites of plants, diatoms, oomycetes and brown algae. Plasmodiophorids are best known as pathogens or vectors for viruses of arable crops (e.g. clubroot in brassicas, powdery potato scab, and rhizomania in sugar beet). Some phytomyxid parasites are of considerable economic and ecologic importance globally, and their hosts include important species in marine and terrestrial environments. However most phytomyxid diversity remains uncharacterised and knowledge of their relationships with host taxa is very fragmentary. Results Our molecular and morphological analyses of phytomyxid isolates–including for the first time oomycete and sea-grass parasites–demonstrate two cross-kingdom host shifts between closely related parasite species: between angiosperms and oomycetes, and from diatoms/brown algae to angiosperms. Switching between such phylogenetically distant hosts is generally unknown in host-dependent eukaryote parasites. We reveal novel plasmodiophorid lineages in soils, suggesting a much higher diversity than previously known, and also present the most comprehensive phytomyxid phylogeny to date. Conclusion Such large-scale host shifts between closely related obligate biotrophic eukaryote parasites is to our knowledge unique to phytomyxids. Phytomyxids may readily adapt to a wide diversity of new hosts because they have retained the ability to covertly infect alternative hosts. A high cryptic diversity and ubiquitous distribution in agricultural and natural habitats implies that in a changing environment phytomyxids could threaten the productivity of key species in marine and terrestrial environments alike via host shift speciation.
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Affiliation(s)
- Sigrid Neuhauser
- Institute of Microbiology, Leopold-Franzens University Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria.
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146
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David-Palma M, Libkind D, Sampaio JP. Global distribution, diversity hot spots and niche transitions of an astaxanthin-producing eukaryotic microbe. Mol Ecol 2014; 23:921-32. [DOI: 10.1111/mec.12642] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 12/05/2013] [Accepted: 12/13/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Márcia David-Palma
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología; Instituto de Investigaciones en Biodiversidad y Medioambiente (INIBIOMA); CONICET - UNComahue; Quintral 1250 (8400), Bariloche Argentina
| | - José Paulo Sampaio
- Departamento de Ciências da Vida; Faculdade de Ciências e Tecnologia; Centro de Recursos Microbiológicos (CREM); Universidade Nova de Lisboa; 2829-516 Caparica Portugal
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147
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Gladieux P, Ropars J, Badouin H, Branca A, Aguileta G, Vienne DM, Rodríguez de la Vega RC, Branco S, Giraud T. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Mol Ecol 2014; 23:753-73. [DOI: 10.1111/mec.12631] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 12/04/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Pierre Gladieux
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Jeanne Ropars
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Hélène Badouin
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Antoine Branca
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Gabriela Aguileta
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
| | - Damien M. Vienne
- Center for Genomic Regulation (CRG) Dr, Aiguader 88 Barcelona 08003 Spain
- Universitat Pompeu Fabra (UPF) Barcelona 08003 Spain
- Laboratoire de Biométrie et Biologie Evolutive Université Lyon 1 CNRS UMR5558 Villeurbanne 69622 France
| | - Ricardo C. Rodríguez de la Vega
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
| | - Sara Branco
- Department of Plant and Microbial Biology University of California Berkeley CA 94720‐3102 USA
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution UMR8079 University of Paris‐Sud Orsay 91405 France
- Ecologie, Systématique et Evolution CNRS UMR8079 Orsay 91405 France
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148
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Ali S, Gladieux P, Rahman H, Saqib MS, Fiaz M, Ahmad H, Leconte M, Gautier A, Justesen AF, Hovmøller MS, Enjalbert J, de Vallavieille-Pope C. Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogenPuccinia striiformisf.sp.tritici. Mol Ecol 2014; 23:603-17. [DOI: 10.1111/mec.12629] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 11/30/2013] [Accepted: 12/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Sajid Ali
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; The University of Agriculture; Peshawar 25000 Pakistan
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Pierre Gladieux
- Department of Plant and Microbial Biology; University of California; Berkeley CA 94720-3102 USA
- Ecologie, Systématique et Evolution; UMR8079; Univ Paris-Sud; 91405 Orsay France
- Ecologie, Systématique et Evolution; UMR8079; CNRS; 91405 Orsay France
| | - Hidayatur Rahman
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | - Muhammad S. Saqib
- Department of Plant Breeding and Genetics; The University of Agriculture; Peshawar 25000 Pakistan
| | | | | | - Marc Leconte
- INRA UR 1290 BIOGER-CPP; BP01 78850 Thiverval-Grignon France
| | | | | | - Mogens S. Hovmøller
- Department of Agroecology; Aarhus University; Flakkebjerg; DK-4200 Slagelse Denmark
| | - Jérôme Enjalbert
- INRA UMR 320 Génétique Végétale; Ferme du Moulon; 91190 Gif sur Yvette France
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149
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Leroy T, Le Cam B, Lemaire C. When virulence originates from non-agricultural hosts: new insights into plant breeding. INFECTION GENETICS AND EVOLUTION 2014; 27:521-9. [PMID: 24412509 DOI: 10.1016/j.meegid.2013.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 12/27/2022]
Abstract
Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence - the allele that allows pathogens to overcome resistance - is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance.
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Affiliation(s)
- Thibault Leroy
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Bruno Le Cam
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Christophe Lemaire
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France.
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150
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Restrepo S, Tabima JF, Mideros MF, Grünwald NJ, Matute DR. Speciation in fungal and oomycete plant pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:289-316. [PMID: 24906125 DOI: 10.1146/annurev-phyto-102313-050056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The process of speciation, by definition, involves evolution of one or more reproductive isolating mechanisms that split a single species into two that can no longer interbreed. Determination of which processes are responsible for speciation is important yet challenging. Several studies have proposed that speciation in pathogens is heavily influenced by host-pathogen dynamics and that traits that mediate such interactions (e.g., host mobility, reproductive mode of the pathogen, complexity of the life cycle, and host specificity) must lead to reproductive isolation and ultimately affect speciation rates. In this review, we summarize the main evolutionary processes that lead to speciation of fungal and oomycete plant pathogens and provide an outline of how speciation can be studied rigorously, including novel genetic/genomic developments.
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Affiliation(s)
- Silvia Restrepo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
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