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Ramírez Martínez J, Guillou S, Le Prieur S, Di Vittorio P, Bonal F, Taliadoros D, Gueret E, Fournier E, Stukenbrock EH, Valade R, Gladieux P. Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen. Microb Genom 2024; 10:001241. [PMID: 38713188 PMCID: PMC11170133 DOI: 10.1099/mgen.0.001241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/09/2024] [Indexed: 05/08/2024] Open
Abstract
Invasive fungal pathogens pose a substantial threat to widely cultivated crop species, owing to their capacity to adapt to new hosts and new environmental conditions. Gaining insights into the demographic history of these pathogens and unravelling the mechanisms driving coevolutionary processes are crucial for developing durably effective disease management programmes. Pyrenophora teres is a significant fungal pathogen of barley, consisting of two lineages, Ptt and Ptm, with global distributions and demographic histories reflecting barley domestication and spread. However, the factors influencing the population structure of P. teres remain poorly understood, despite the varietal and environmental heterogeneity of barley agrosystems. Here, we report on the population genomic structure of P. teres in France and globally. We used genotyping-by-sequencing to show that Ptt and Ptm can coexist in the same area in France, with Ptt predominating. Furthermore, we showed that differences in the vernalization requirement of barley varieties were associated with population differentiation within Ptt in France and at a global scale, with one population cluster found on spring barley and another population cluster found on winter barley. Our results demonstrate how cultivation conditions, possibly associated with genetic differences between host populations, can be associated with the maintenance of divergent invasive pathogen populations coexisting over large geographic areas. This study not only advances our understanding of the coevolutionary dynamics of the Pt-barley pathosystem but also prompts further research on the relative contributions of adaptation to the host versus adaptation to abiotic conditions in shaping Ptt populations.
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Affiliation(s)
- Julie Ramírez Martínez
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia Guillou
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | | | - Pauline Di Vittorio
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Florelle Bonal
- UMR AGAP (Amélioration génétique et adaptation des plantes), Montpellier, France
| | - Demetris Taliadoros
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | - Elise Gueret
- MGX-Montpellier GenomiX, University of Montpellier, CNRS, INSERM, Montpellier, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Eva H. Stukenbrock
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 9-11, 24118, Kiel, Germany
| | | | - Pierre Gladieux
- PHIM Plant Health Institute, Univ. Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
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Cissé OH, Ma L, Kovacs JA. Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii. Microbiol Mol Biol Rev 2024:e0020222. [PMID: 38587383 DOI: 10.1128/mmbr.00202-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
SUMMARYEvery human being is presumed to be infected by the fungus Pneumocystis jirovecii at least once in his or her lifetime. This fungus belongs to a large group of species that appear to exclusively infect mammals, with P. jirovecii being the only one known to cause disease in humans. The mystery of P. jirovecii origin and speciation is just beginning to unravel. Here, we provide a review of the major steps of P. jirovecii evolution. The Pneumocystis genus likely originated from soil or plant-associated organisms during the period of Cretaceous ~165 million years ago and successfully shifted to mammals. The transition coincided with a substantial loss of genes, many of which are related to the synthesis of nutrients that can be scavenged from hosts or cell wall components that could be targeted by the mammalian immune system. Following the transition, the Pneumocystis genus cospeciated with mammals. Each species specialized at infecting its own host. Host specialization is presumably built at least partially upon surface glycoproteins, whose protogene was acquired prior to the genus formation. P. jirovecii appeared at ~65 million years ago, overlapping with the emergence of the first primates. P. jirovecii and its sister species P. macacae, which infects macaques nowadays, may have had overlapping host ranges in the distant past. Clues from molecular clocks suggest that P. jirovecii did not cospeciate with humans. Molecular evidence suggests that Pneumocystis speciation involved chromosomal rearrangements and the mounting of genetic barriers that inhibit gene flow among species.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
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Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
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Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation. IMA Fungus 2021; 12:16. [PMID: 34193315 PMCID: PMC8246709 DOI: 10.1186/s43008-021-00068-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/23/2021] [Indexed: 02/06/2023] Open
Abstract
The genus Phytophthora comprises many economically and ecologically important plant pathogens. Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. Phytophthora hybrids therefore pose a serious threat to agriculture as well as to natural ecosystems. Early and correct identification of hybrids is therefore essential for adequate plant protection but this is hampered by the limitations of morphological and traditional molecular methods. Identification of hybrids is also important in evolutionary studies as the positioning of hybrids in a phylogenetic tree can lead to suboptimal topologies. To improve the identification of hybrids we have combined genotyping-by-sequencing (GBS) and genome size estimation on a genus-wide collection of 614 Phytophthora isolates. Analyses based on locus- and allele counts and especially on the combination of species-specific loci and genome size estimations allowed us to confirm and characterize 27 previously described hybrid species and discover 16 new hybrid species. Our method was also valuable for species identification at an unprecedented resolution and further allowed correct naming of misidentified isolates. We used both a concatenation- and a coalescent-based phylogenomic method to construct a reliable phylogeny using the GBS data of 140 non-hybrid Phytophthora isolates. Hybrid species were subsequently connected to their progenitors in this phylogenetic tree. In this study we demonstrate the application of two validated techniques (GBS and flow cytometry) for relatively low cost but high resolution identification of hybrids and their phylogenetic relations.
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St. Leger RJ, Wang JB. Metarhizium: jack of all trades, master of many. Open Biol 2020; 10:200307. [PMID: 33292103 PMCID: PMC7776561 DOI: 10.1098/rsob.200307] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The genus Metarhizium and Pochonia chlamydosporia comprise a monophyletic clade of highly abundant globally distributed fungi that can transition between long-term beneficial associations with plants to transitory pathogenic associations with frequently encountered protozoans, nematodes or insects. Some very common 'specialist generalist' species are adapted to particular soil and plant ecologies, but can overpower a wide spectrum of insects with numerous enzymes and toxins that result from extensive gene duplications made possible by loss of meiosis and associated genome defence mechanisms. These species use parasexuality instead of sex to combine beneficial mutations from separate clonal individuals into one genome (Vicar of Bray dynamics). More weakly endophytic species which kill a narrow range of insects retain sexuality to facilitate host-pathogen coevolution (Red Queen dynamics). Metarhizium species can fit into numerous environments because they are very flexible at the genetic, physiological and ecological levels, providing tractable models to address how new mechanisms for econutritional heterogeneity, host switching and virulence are acquired and relate to diverse sexual life histories and speciation. Many new molecules and functions have been discovered that underpin Metarhizium associations, and have furthered our understanding of the crucial ecology of these fungi in multiple habitats.
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Hartmann FE, Rodríguez de la Vega RC, Gladieux P, Ma WJ, Hood ME, Giraud T. Higher Gene Flow in Sex-Related Chromosomes than in Autosomes during Fungal Divergence. Mol Biol Evol 2020; 37:668-682. [PMID: 31651949 PMCID: PMC7038665 DOI: 10.1093/molbev/msz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonrecombining sex chromosomes are widely found to be more differentiated than autosomes among closely related species, due to smaller effective population size and/or to a disproportionally large-X effect in reproductive isolation. Although fungal mating-type chromosomes can also display large nonrecombining regions, their levels of differentiation compared with autosomes have been little studied. Anther-smut fungi from the Microbotryum genus are castrating pathogens of Caryophyllaceae plants with largely nonrecombining mating-type chromosomes. Using whole genome sequences of 40 fungal strains, we quantified genetic differentiation among strains isolated from the geographically overlapping North American species and subspecies of Silene virginica and S. caroliniana. We inferred that gene flow likely occurred at the early stages of divergence and then completely stopped. We identified large autosomal genomic regions with chromosomal inversions, with higher genetic divergence than the rest of the genomes and highly enriched in selective sweeps, supporting a role of rearrangements in preventing gene flow in genomic regions involved in ecological divergence. Unexpectedly, the nonrecombining mating-type chromosomes showed lower divergence than autosomes due to higher gene flow, which may be promoted by adaptive introgressions of less degenerated mating-type chromosomes. The fact that both mating-type chromosomes are always heterozygous and nonrecombining may explain such patterns that oppose to those found for XY or ZW sex chromosomes. The specific features of mating-type chromosomes may also apply to the UV sex chromosomes determining sexes at the haploid stage in algae and bryophytes and may help test general hypotheses on the evolutionary specificities of sex-related chromosomes.
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Affiliation(s)
- Fanny E Hartmann
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Wen-Juan Ma
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Michael E Hood
- Biology Department, Science Centre, Amherst College, Amherst, MA
| | - Tatiana Giraud
- Ecologie Systematique Evolution, Batiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
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Abstract
Global change is pressing forest pathologists to solve increasingly complex problems. We argue that understanding interactive effects between forest pathogens and global warming, globalization, and land-use changes may benefit from a functional ecology mindset. Traits can be more informative about ecological functions than species inventories and may deliver a more mechanistic description of forest disease. Myriad microbes with pathogenic potential interact with forest ecosystems at different organizational levels. Elucidation of functional traits may enable the microbial complexity to be reduced into manageable categories with predictive power. In this review, we propose guidelines that allow the research community to develop a functional forest pathology approach. We suggest new angles by which functional questions can be used to resolve burning issues on tree disease. Building up functional databases for pathogenicity is key to implementing these approaches.
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Affiliation(s)
- Jonàs Oliva
- Department of Crop and Forest Sciences, University of Lleida, 25198 Lleida, Spain
- Joint Research Unit CTFC-Agrotecnio, 25198 Lleida, Spain
| | - Miguel Ángel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden;
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden;
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8
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Fungal Evolution in Anthropogenic Environments: Botrytis cinerea Populations Infecting Small Fruit Hosts in the Pacific Northwest Rapidly Adapt to Human-Induced Selection Pressures. Appl Environ Microbiol 2020; 86:AEM.02908-19. [PMID: 32086310 DOI: 10.1128/aem.02908-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022] Open
Abstract
Many fungal pathogens have short generation times, large population sizes, and mixed reproductive systems, providing high potential to adapt to heterogeneous environments of agroecosystems. Such adaptation complicates disease management and threatens food production. A better understanding of pathogen population biology in such environments is important to reveal key aspects of adaptive divergence processes to allow improved disease management. Here, we studied how evolutionary forces shape population structure of Botrytis cinerea, the causal agent of gray mold, in the Pacific Northwest agroecosystems. Populations of B. cinerea from adjacent fields of small fruit hosts were characterized by combining neutral markers (microsatellites) with markers that directly respond to human-induced selection pressures (fungicide resistance). Populations were diverse, without evidence for recombination and association of pathogen genotype with host. Populations were highly localized with limited migration even among adjacent fields within a farm. A fungicide resistance marker revealed strong selection on population structure due to fungicide use. We found no association of resistance allele with genetic background, suggesting de novo development of fungicide resistance and frequent extinction/recolonization events by different genotypes rather than the spread of resistance alleles among fields via migration of a dominant genotype. Overall our results showed that in agroecosystems, B. cinerea populations respond strongly to selection by fungicide use with greater effect on population structure compared to adaptation to host plant species. This knowledge will be used to improve disease management by developing strategies that limit pathogen local adaptation to fungicides and other human-induced selection pressures present in Pacific Northwest agroecosystems and elsewhere.IMPORTANCE Agroecosystems represent an efficient model for studying fungal adaptation and evolution in anthropogenic environments. In this work, we studied what evolutionary forces shape populations of one of the most important fungal plant pathogens, B. cinerea, in small fruit agroecosystems of the Pacific Northwest. We hypothesized that host, geographic, and anthropogenic factors of agroecosystems structure B. cinerea populations. By combining neutral markers with markers that directly respond to human-induced selection pressures, we show that pathogen populations are highly localized and that selection pressure caused by fungicide use can have a greater effect on population structure than adaptation to host. Our results give a better understanding of population biology and evolution of this important plant pathogen in heterogeneous environments but also provide a practical framework for the development of efficient management strategies by limiting pathogen adaptation to fungicides and other human-induced selection pressures present in agroecosystems of the Pacific Northwest and elsewhere.
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9
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Mercier A, Carpentier F, Duplaix C, Auger A, Pradier JM, Viaud M, Gladieux P, Walker AS. The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations. Environ Microbiol 2019; 21:4808-4821. [PMID: 31608584 DOI: 10.1111/1462-2920.14829] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mould management, while suggesting spatial optimization of crop organization within agricultural landscapes.
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Affiliation(s)
- Alex Mercier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Florence Carpentier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,UR MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémentine Duplaix
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Jean-Marc Pradier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier Supagro, Université de Montpellier, Montpellier, France
| | - Anne-Sophie Walker
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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10
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Feurtey A, Stukenbrock EH. Interspecific Gene Exchange as a Driver of Adaptive Evolution in Fungi. Annu Rev Microbiol 2018; 72:377-398. [DOI: 10.1146/annurev-micro-090817-062753] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Throughout evolutionary history in the kingdom Fungi, taxa have exchanged genetic information among species, as revealed in particular by analyses of genome sequences. In fungi, hybridization can occur by sexual mating or by fusion of vegetative structures giving rise to new species or leaving traces of introgression in the genome. Furthermore, gene exchange can occur by horizontal gene transfer between species and can even include organisms outside the kingdom Fungi. In several cases, interspecific gene exchange has been instrumental in rapid adaptive evolution of fungal species and has notably played a role in the emergence of new pathogens. Here we summarize mechanisms and examples of gene exchange in fungi with a particular focus on the genomic context. We emphasize the need for and potential of applying population genetic approaches to better understand the processes and the impact of interspecific gene exchange in rapid adaptive evolution and species diversification. The broad occurrence of gene exchange among fungal species challenges our species concepts in the kingdom Fungi.
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Affiliation(s)
- Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
| | - Eva H. Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany;,
- Environmental Genomics, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
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11
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Lawrence DP, Holland LA, Nouri MT, Travadon R, Abramians A, Michailides TJ, Trouillas FP. Molecular phylogeny of Cytospora species associated with canker diseases of fruit and nut crops in California, with the descriptions of ten new species and one new combination. IMA Fungus 2018; 9:333-370. [PMID: 30622886 PMCID: PMC6317586 DOI: 10.5598/imafungus.2018.09.02.07] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/12/2018] [Indexed: 11/29/2022] Open
Abstract
Cytospora species are destructive canker and dieback pathogens of woody hosts in natural and agroecosystems around the world. In this genus, molecular identification has been limited due to the paucity of multi-locus sequence typing studies and the lack of sequence data from type specimens in public repositories, stalling robust phylogenetic reconstructions. In most cases a morphological species concept could not be applied due to the plasticity of characters and significant overlap of morphological features such as spore dimensions and fruiting body characters. In this study, we employed a molecular phylogenetic framework with the inclusion of four nuclear loci (ITS, translation elongation factor 1-alpha, actin, and beta-tubulin) to unveil the biodiversity and taxonomy of this understudied important genus of plant pathogens. Phylogenetic inferences based on 150 Californian isolates revealed 15 Cytospora species associated with branch and twig cankers and dieback of almond, apricot, cherry, cottonwood, olive, peach, pistachio, plum, pomegranate, and walnut trees in California. Of the 15 species recovered in this study, 10 are newly described and typified, in addition to one new combination. The pathogenic status of the newly described Cytospora species requires further investigation as most species were associated with severe dieback and decline of diverse and economically important fruit and nut crops in California.
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Affiliation(s)
- Daniel P Lawrence
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Leslie A Holland
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mohamed T Nouri
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ara Abramians
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Themis J Michailides
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
| | - Florent P Trouillas
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
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12
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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13
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018. [PMID: 29487238 DOI: 10.01210.01128/mbio] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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14
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018; 9:e01219-17. [PMID: 29487238 PMCID: PMC5829825 DOI: 10.1128/mbio.01219-17] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/20/2017] [Indexed: 11/25/2022] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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15
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Michalecka M, Masny S, Leroy T, Puławska J. Population structure of Venturia inaequalis, a causal agent of apple scab, in response to heterogeneous apple tree cultivation. BMC Evol Biol 2018; 18:5. [PMID: 29351730 PMCID: PMC5775622 DOI: 10.1186/s12862-018-1122-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tracking newly emergent virulent populations in agroecosystems provides an opportunity to increase our understanding of the co-evolution dynamics of pathogens and their hosts. On the one hand host plants exert selective pressure on pathogen populations, thus dividing them into subpopulations of different virulence, while on the other hand they create an opportunity for secondary contact between the two divergent populations on one tree. The main objectives of the study were to explore whether the previously reported structure between two Venturia inaequalis population types, virulent or avirulent towards Malus x domestica cultivars carrying Rvi6 gene, is maintained or broken several years after the first emergence of new virulent strains in Poland, and to investigate the relationship between 'new' and 'native' populations derived from the same commercial orchards. For this purpose, we investigated the genetic structure of populations of the apple scab fungus, occurring on apple tree cultivars containing Rvi6, Rvi1 or Rvi17 resistance gene or no resistance at all, based on microsatellite data obtained from 606 strains sampled in 10 orchards composed of various host cultivars. RESULTS Application of genetic distance inferring and clustering methods allowed us to observe clear genetic distinctness of the populations virulent towards cultivars carrying Rvi6 gene from the Rvi6-avirulent populations and substructures within the Rvi6-group as a consequence of independent immigration events followed by rare, long-distance dispersals. We did not observe such a structuring effect of other genes determining apple scab resistance on any other populations, which in turn were genetically homogenous. However, in two orchards the co-occurrence of strains of different virulence pattern on the same trees was detected, blurring the genetic boundaries between populations. CONCLUSIONS Among several resistance genes studied, only Rvi6 exerted selective pressure on pathogens populations: those virulent toward Rvi6 hosts show unique and clear genetic and virulence pattern. For the first time in commercial Malus x domestica orchards, we reported secondary contacts between populations virulent and avirulent toward Rvi6 hosts. These two populations, first diverged in allopatry, second came into contact and subsequently began interbreeding, in such way that they show unambiguous footprints of gene flow today.
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Affiliation(s)
- Monika Michalecka
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Sylwester Masny
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | | | - Joanna Puławska
- Department of Phytopathology, Research Institute of Horticulture, Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
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16
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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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17
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Fournier E, Giraud T, Albertini C, Brygoo Y. Partition of theBotrytis cinereacomplex in France using multiple gene genealogies. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832734] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Elisabeth Fournier
- PMDV, INRA Centre de Versailles, Route de Saint-Cyr, F-78026 Versailles cedex, France
| | - Tatiana Giraud
- ESE, Bât. 360, UMR 8079 Université Paris Sud-CNRS, F-91405 Orsay cedex, France
| | - Catherine Albertini
- Phytopharmacie et Médiateurs Chimiques, INRA Centre de Versailles, Route de Saint-Cyr, F-78026 Versailles cedex, France
| | - Yves Brygoo
- PMDV, INRA Centre de Versailles, Route de Saint-Cyr, F-78026 Versailles cedex, France
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18
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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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19
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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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20
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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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21
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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: 10] [Impact Index Per Article: 1.1] [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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22
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Muehlenbein MP, Pacheco MA, Taylor JE, Prall SP, Ambu L, Nathan S, Alsisto S, Ramirez D, Escalante AA. Accelerated diversification of nonhuman primate malarias in Southeast Asia: adaptive radiation or geographic speciation? Mol Biol Evol 2015; 32:422-39. [PMID: 25389206 PMCID: PMC4298170 DOI: 10.1093/molbev/msu310] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Although parasitic organisms are found worldwide, the relative importance of host specificity and geographic isolation for parasite speciation has been explored in only a few systems. Here, we study Plasmodium parasites known to infect Asian nonhuman primates, a monophyletic group that includes the lineage leading to the human parasite Plasmodium vivax and several species used as laboratory models in malaria research. We analyze the available data together with new samples from three sympatric primate species from Borneo: The Bornean orangutan and the long-tailed and the pig-tailed macaques. We find several species of malaria parasites, including three putatively new species in this biodiversity hotspot. Among those newly discovered lineages, we report two sympatric parasites in orangutans. We find no differences in the sets of malaria species infecting each macaque species indicating that these species show no host specificity. Finally, phylogenetic analysis of these data suggests that the malaria parasites infecting Southeast Asian macaques and their relatives are speciating three to four times more rapidly than those with other mammalian hosts such as lemurs and African apes. We estimate that these events took place in approximately a 3-4-Ma period. Based on the genetic and phenotypic diversity of the macaque malarias, we hypothesize that the diversification of this group of parasites has been facilitated by the diversity, geographic distributions, and demographic histories of their primate hosts.
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Affiliation(s)
| | - M Andreína Pacheco
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe
| | - Jesse E Taylor
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe
| | - Sean P Prall
- Department of Anthropology, Indiana University, Bloomington
| | | | | | - Sylvia Alsisto
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Diana Ramirez
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Ananias A Escalante
- Center for Evolutionary Medicine and Informatics, The Biodesign Institute, Arizona State University, Tempe School of Life Sciences, Arizona State University, Tempe
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Ramírez-López I, Villegas-Ríos M, Salas-Lizana R, Garibay-Orijel R, Alvarez-Manjarrez J. Thelephora versatilis and Thelephora pseudoversatilis: two new cryptic species with polymorphic basidiomes inhabiting tropical deciduous and sub-perennial forests of the Mexican Pacific coast. Mycologia 2014; 107:346-58. [PMID: 25550304 DOI: 10.3852/14-151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thelephora is a genus of ectomycorrhizal basidiomycetes with basidiomes of varied shape which has been poorly studied in tropical ecosystems. In this paper, we present Thelephora versatilis and Thelephora pseudoversatilis, two new species collected in the same localities of deciduous and sub-perennial tropical forests of Jalisco, Mexico. Basidiomes of both species are brownish gray to violet brown with clavarioid-mesopodal, sub-resupinate or completely resupinate growth forms. In turn, phylogenetic analyses using nrDNA ITS sequences showed that these species are not closed related, nevertheless they are part of a well-supported clade conformed by several species of Thelephora, Tomentella and some undescribed Thelephorales. Morphological segregation of these species was attained by analyzing spore and hyphae characters using a wide sample. Significant statistical differences between the new species were observed regarding spore size, spine size and context hyphae width. This work exemplifies the relevance of integrating both morphological and molecular data, as well of the use of an appropriate sample size in order to discriminate among morphological cryptic species.
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Affiliation(s)
- Itzel Ramírez-López
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Margarita Villegas-Ríos
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F.
| | - Rodolfo Salas-Lizana
- Laboratorios de Micología, Depto. de Biología Comparada, Facultad de Ciencias, Universidad Nacional Autónoma de México. Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
| | - Julieta Alvarez-Manjarrez
- Instituto de Biología, Universidad Nacional Autónoma de México, Tercer Circuito s/n, Ciudad Universitaria, Coyoacán, 04510, México D.F
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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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25
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Zervakis GI, Ntougias S, Gargano ML, Besi MI, Polemis E, Typas MA, Venturella G. A reappraisal of the Pleurotus eryngii complex - new species and taxonomic combinations based on the application of a polyphasic approach, and an identification key to Pleurotus taxa associated with Apiaceae plants. Fungal Biol 2014; 118:814-34. [PMID: 25209640 DOI: 10.1016/j.funbio.2014.07.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2014] [Revised: 06/24/2014] [Accepted: 07/01/2014] [Indexed: 11/30/2022]
Abstract
The Pleurotus eryngii species-complex comprises choice edible mushrooms growing on roots and lower stem residues of Apiaceae (umbellifers) plants. Material deriving from extensive sampling was studied by mating compatibility, morphological and ecological criteria, and through analysis of ITS1-5.8S-ITS2 and IGS1 rRNA sequences. Results revealed that P. eryngii sensu stricto forms a diverse and widely distributed aggregate composed of varieties elaeoselini, eryngii, ferulae, thapsiae, and tingitanus. Pleurotuseryngii subsp. tuoliensis comb. nov. is a phylogenetically sister group to the former growing only on various Ferula species in Asia. The existence of Pleurotusnebrodensis outside of Sicily (i.e., in Greece) is reported for the first time on the basis of molecular data, while P. nebrodensis subsp. fossulatus comb. nov. is a related Asiatic taxon associated with the same plant (Prangos ferulacea). Last, Pleurotusferulaginis sp. nov. grows on Ferulago campestris in northeast Italy, Slovenia and Hungary; it occupies a distinct phylogenetic position accompanied with significant differences in spore size and mating incompatibility versus other Pleurotus populations. Coevolution with umbellifers and host/substrate specificity seem to play key roles in speciation processes within this fungal group. An identification key to the nine Pleurotus taxa growing in association with Apiaceae plants is provided.
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Affiliation(s)
- Georgios I Zervakis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece.
| | - Spyridon Ntougias
- Democritus University of Thrace, Department of Environmental Engineering, Laboratory of Wastewater Management and Treatment Technologies, Vas. Sofias 12, 67100 Xanthi, Greece
| | - Maria Letizia Gargano
- Università di Palermo, Department of Agricultural and Forest Sciences, Viale delle Scienze, 11, 90128 Palermo, Italy
| | - Maria I Besi
- John Innes Centre, Department of Disease and Stress Biology, Colney Lane, Norwich NR4 7UH, UK
| | - Elias Polemis
- Agricultural University of Athens, Laboratory of General and Agricultural Microbiology, Iera Odos 75, 11855 Athens, Greece
| | - Milton A Typas
- National and Kapodistrian University of Athens, Department of Genetics and Biotechnology, Faculty of Biology, Panepistemiopolis, Athens 15701, Greece
| | - Giuseppe Venturella
- Università di Palermo, Department of Agricultural and Forest Sciences, Viale delle Scienze, 11, 90128 Palermo, Italy
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Tuovila H, Davey ML, Yan L, Huhtinen S, Rikkinen J. New resinicolous Chaenothecopsis species from China. Mycologia 2014; 106:989-1003. [PMID: 24891410 DOI: 10.3852/13-178] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Four new resinicolous species of Chaenothecopsis are described from China: Chaenothecopsis perforata from exudate of Rhus chinensis (Anacardiaceae), C. pallida from exudate of Ailanthus altissima (Simaroubaceae), C. resinophila from exudate of Kalopanax septemlobus (Araliaceae) and C. hunanensis from resin of Pinus massoniana (Pinaceae). All the new species are compared with previously described resinicolous mycocalicioid taxa, and several new features in these species are presented. The newly described species cannot always be distinguished by any single character, but they all possess unique combinations of morphological, chemical and ecological features. Several aspects in the ecology and evolution of boreal and tropical resinicolous species are briefly discussed.
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Affiliation(s)
- Hanna Tuovila
- Department of Biosciences, P.O. Box 65, FIN-00014 University of Helsinki, Finland
| | - Marie L Davey
- Arctic Biology Department, University Centre in Svalbard, P.O. Box 156, N-9171 Longyearbyen, Norway
| | - Lihong Yan
- Hunan Province Forest Botanical Garden, Botanical Garden Road 111, Dongjingpu, Yuhua District, Changsha, Hunan, P.R. China (P.C. 410116)
| | - Seppo Huhtinen
- Herbarium, University of Turku, FIN-20014 Turku, Finland
| | - Jouko Rikkinen
- Department of Biosciences, P.O. Box 65, FIN-00014 University of Helsinki, Finland
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27
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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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28
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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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29
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Walker DM, Castlebury LA, Rossman AY, Struwe L. Host conservatism or host specialization? Patterns of fungal diversification are influenced by host plant specificity inOphiognomonia(Gnomoniaceae: Diaporthales). Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Donald M. Walker
- Department of Natural Sciences; The University of Findlay; 1000 North Main Street Findlay OH 45840 USA
- Department of Plant Biology and Pathology; Rutgers University; 59 Dudley Road New Brunswick NJ 08901 USA
| | - Lisa A. Castlebury
- Systematic Mycology & Microbiology Laboratory; USDA Agricultural Research Service; 10300 Baltimore Avenue Beltsville MD 20705 USA
| | - Amy Y. Rossman
- Systematic Mycology & Microbiology Laboratory; USDA Agricultural Research Service; 10300 Baltimore Avenue Beltsville MD 20705 USA
| | - Lena Struwe
- Department of Plant Biology and Pathology; Rutgers University; 59 Dudley Road New Brunswick NJ 08901 USA
- Department of Ecology, Evolution and Natural Resources; Rutgers University; 14 College Farm Road New Brunswick NJ 08901 USA
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30
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de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. THE NEW PHYTOLOGIST 2013; 198:347-385. [PMID: 23437795 DOI: 10.1111/nph.12150] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/19/2012] [Indexed: 05/26/2023]
Abstract
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host-symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host-parasite and host-mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host-symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.
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Affiliation(s)
- D M de Vienne
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - G Refrégier
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91405, Orsay, France
- CNRS, UMR8621, 91405, Orsay, France
| | - M López-Villavicencio
- Muséum National d'Histoire Naturelle, 57 rue Cuvier, F-75231, Paris Cedex 05, France
| | - A Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85354, Freising, Germany
| | - M E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - T Giraud
- Université Paris-Sud, Ecologie, Systématique et Evolution, UMR 8079, 91405, Orsay, France
- CNRS, UMR8079, 91405, Orsay, France
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Baysal Ö, Karaaslan Ç, Siragusa M, Alessandro R, Carimi F, De Pasquale F, Teixeira da Silva JA. Molecular markers reflect differentiation of Fusarium oxysporum forma speciales on tomato and forma on eggplant. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Leroy T, Lemaire C, Dunemann F, Le Cam B. The genetic structure of a Venturia inaequalis population in a heterogeneous host population composed of different Malus species. BMC Evol Biol 2013; 13:64. [PMID: 23497223 PMCID: PMC3626921 DOI: 10.1186/1471-2148-13-64] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 02/26/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Adaptation, which induces differentiation between populations in relation to environmental conditions, can initiate divergence. The balance between gene flow and selection determines the maintenance of such a structure in sympatry. Studying these two antagonistic forces in plant pathogens is made possible because of the high ability of pathogens to disperse and of the strong selective pressures exerted by their hosts. In this article, we analysed the genetic structure of the population of the apple scab fungus, Venturia inaequalis, in a heterogeneous environment composed of various Malus species. Inferences were drawn from microsatellite and AFLP data obtained from 114 strains sampled in a single orchard on nine different Malus species to determine the forces that shape the genetic structure of the pathogen. RESULTS Using clustering methods, we first identified two specialist subpopulations: (i) a virulent subpopulation sampled on Malus trees carrying the Rvi6 resistance gene; and (ii) a subpopulation infecting only Malus trees that did not carry this resistance gene. A genome scan of loci on these two subpopulations did not detect any locus under selection. Additionally, we did not detect any other particular substructure linked to different hosts. However, an isolation-by-distance (IBD) pattern at the orchard scale revealed free gene flow within each subpopulation. CONCLUSIONS Our work shows a rare example of a very strong effect of a resistance gene on pathogen populations. Despite the high diversity of Malus hosts, the presence of Rvi6 seems sufficient to explain the observed genetic structure. Moreover, detection of an IBD pattern at the orchard scale revealed a very low average dispersal distance that is particularly significant for epidemiologists and landscape managers for the design of scab control strategies.
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Affiliation(s)
- Thibault Leroy
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Boulevard Lavoisier, Angers, 49045 France
- INRA, IRHS, PRES UNAM, SFR QUASAV, Rue Georges Morel, Beaucouzé, 49071 France
- Agrocampus Ouest, IRHS, PRES UNAM, SFR QUASAV, Rue Le Nôtre, F-49045 Angers, France
| | - Christophe Lemaire
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Boulevard Lavoisier, Angers, 49045 France
- INRA, IRHS, PRES UNAM, SFR QUASAV, Rue Georges Morel, Beaucouzé, 49071 France
- Agrocampus Ouest, IRHS, PRES UNAM, SFR QUASAV, Rue Le Nôtre, F-49045 Angers, France
| | - Frank Dunemann
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Horticultural and Fruit Crops, Erwin-Baur-Strasse 27, 06484, Quedlinburg, Germany
| | - Bruno Le Cam
- Université d’Angers, IRHS, PRES UNAM, SFR QUASAV, Boulevard Lavoisier, Angers, 49045 France
- INRA, IRHS, PRES UNAM, SFR QUASAV, Rue Georges Morel, Beaucouzé, 49071 France
- Agrocampus Ouest, IRHS, PRES UNAM, SFR QUASAV, Rue Le Nôtre, F-49045 Angers, France
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Asadollahi M, Fekete E, Karaffa L, Flipphi M, Árnyasi M, Esmaeili M, Váczy KZ, Sándor E. Comparison of Botrytis cinerea populations isolated from two open-field cultivated host plants. Microbiol Res 2013; 168:379-388. [PMID: 23353014 DOI: 10.1016/j.micres.2012.12.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/04/2012] [Accepted: 12/20/2012] [Indexed: 11/17/2022]
Abstract
The necrotrophic fungus Botrytis cinerea is reported to infect more than 220 host plants worldwide. In phylogenetical-taxonomical terms, the pathogen is considered a complex of two cryptic species, group I and group II. We sampled populations of B. cinerea on sympatric strawberry and raspberry cultivars in the North-East of Hungary for three years during flowering and the harvest period. Four hundred and ninety group II B. cinerea isolates were analyzed for the current study. Three different data sets were generated: (i) PCR-RFLP patterns of the ADP-ATP translocase and nitrate reductase genes, (ii) MSB1 minisatellite sequence data, and (iii) the fragment sizes of five microsatellite loci. The structures of the different populations were similar as indicated by Nei's gene diversity and haplotype diversity. The F statistics (Fst, Gst), and the gene flow indicated ongoing differentiation within sympatric populations. The population genetic parameters were influenced by polymorphisms within the three data sets as assessed using Bayesian algorithms. Data Mining analysis pointed towards the five microsatellite loci as the most defining markers to study differentiation in the 490 isolates. The results suggest the occurrence of host-specific, sympatric divergence of generalist phytoparasites in perennial hosts.
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Affiliation(s)
- Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary; Institute of Food Processing, Quality Assurance and Microbiology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Mariann Árnyasi
- Sámuel Diószegi Institute of Agricultural Innovation, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary
| | - Mahdi Esmaeili
- Department of Computer Science, Islamic Azad University, Kashan Branch, Kashan, Iran
| | - Kálmán Zoltán Váczy
- KRC Research Institute for Viticulture and Enology, Kőlyuktető, PO Box 83, 3301 Eger, Hungary
| | - Erzsébet Sándor
- Institute of Food Processing, Quality Assurance and Microbiology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary.
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Zhan J, McDonald BA. Experimental measures of pathogen competition and relative fitness. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:131-53. [PMID: 23767846 DOI: 10.1146/annurev-phyto-082712-102302] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Competition among pathogen strains for limited host resources can have a profound effect on pathogen evolution. A better understanding of the principles and consequences of competition can be useful in designing more sustainable disease management strategies. The competitive ability and relative fitness of a pathogen strain are determined by its intrinsic biological properties, the resistance and heterogeneity of the corresponding host population, the population density and genetic relatedness of the competing strains, and the physical environment. Competitive ability can be inferred indirectly from fitness components, such as basic reproduction rate or transmission rate. However, pathogen strains that exhibit higher fitness components when they infect a host alone may not exhibit a competitive advantage when they co-infect the same host. The most comprehensive measures of competitive ability and relative fitness come from calculating selection coefficients in a mixed infection in a field setting. Mark-release-recapture experiments can be used to estimate fitness costs associated with unnecessary virulence and fungicide resistance.
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Affiliation(s)
- Jiasui Zhan
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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35
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Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species. Proc Natl Acad Sci U S A 2012; 109:10954-9. [PMID: 22711811 DOI: 10.1073/pnas.1201403109] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a genome alignment of five individuals of the ascomycete fungus Zymoseptoria pseudotritici, a close relative of the wheat pathogen Z. tritici (synonym Mycosphaerella graminicola), we observed peculiar diversity patterns. Long regions up to 100 kb without variation alternate with similarly long regions of high variability. The variable segments in the genome alignment are organized into two main haplotype groups that have diverged ∼3% from each other. The genome patterns in Z. pseudotritici are consistent with a hybrid speciation event resulting from a cross between two divergent haploid individuals. The resulting hybrids formed the new species without backcrossing to the parents. We observe no variation in 54% of the genome in the five individuals and estimate a complete loss of variation for at least 30% of the genome in the entire species. A strong population bottleneck following the hybridization event caused this loss of variation. Variable segments in the Z. pseudotritici genome exhibit the two haplotypes contributed by the parental individuals. From our previously estimated recombination map of Z. tritici and the size distribution of variable chromosome blocks untouched by recombination we estimate that the hybridization occurred ∼380 sexual generations ago. We show that the amount of lost variation is explained by genetic drift during the bottleneck and by natural selection, as evidenced by the correlation of presence/absence of variation with gene density and recombination rate. The successful spread of this unique reproductively isolated pathogen highlights the strong potential of hybridization in the emergence of pathogen species with sexual reproduction.
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Abstract
Reproductive isolation is an essential ingredient of speciation, and much has been learned in recent years about the evolution of reproductive isolation and the genetics of reproductive barriers in animals and plants. Fungi have been neglected on these aspects, despite being tractable model eukaryotes. Here, we used a model fitting approach to look at the importance of different barriers to gene flow to explain the decrease of reproductive compatibility with genetic distance in fungi. We found support for the occurrence of reinforcement in the presyngamy compatibility among basidiomycetes. In contrast, no evidence for reinforcement was detected in ascomycetes, concurring with the idea that host/habitat adaptation in this group can pleiotropically cause reproductive isolation. We found no evidence of a snowballing accumulation of postsyngamic reproductive incompatibilities in either ascomycetes or the complex of anther smut fungi. Together with previous studies, our results suggest that ecologically based barriers to gene flow and karyotypic differences may have an important role in hybrid inviability and sterility in fungi. Interestingly, hybrid sterility appeared to evolve faster than hybrid inviability in fungi.
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Fekete É, Fekete E, Irinyi L, Karaffa L, Árnyasi M, Asadollahi M, Sándor E. Genetic diversity of a Botrytis cinerea cryptic species complex in Hungary. Microbiol Res 2012; 167:283-91. [DOI: 10.1016/j.micres.2011.10.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 10/16/2011] [Accepted: 10/26/2011] [Indexed: 11/26/2022]
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KOBMOO N, MONGKOLSAMRIT S, TASANATHAI K, THANAKITPIPATTANA D, LUANGSA-ARD JJ. Molecular phylogenies reveal host-specific divergence ofOphiocordyceps unilateralis sensu latofollowing its host ants. Mol Ecol 2012; 21:3022-31. [DOI: 10.1111/j.1365-294x.2012.05574.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Judova J, Dubikova K, Gaperova S, Gaper J, Pristas P. The occurrence and rapid discrimination of Fomes fomentarius genotypes by ITS-RFLP analysis. Fungal Biol 2012; 116:155-60. [DOI: 10.1016/j.funbio.2011.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 10/17/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
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40
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Walker AS, Gautier AL, Confais J, Martinho D, Viaud M, Le P Cheur P, Dupont J, Fournier E. Botrytis pseudocinerea, a new cryptic species causing gray mold in French vineyards in sympatry with Botrytis cinerea. PHYTOPATHOLOGY 2011; 101:1433-45. [PMID: 21830954 DOI: 10.1094/phyto-04-11-0104] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Botrytis cinerea is a major crop pathogen infesting >220 hosts worldwide. A cryptic species has been identified in some French populations but the new species, B. pseudocinerea, has not been fully delimited and established. The aim of this study was to distinguish between the two species, using phylogenetic, biological, morphological, and ecological criteria. Multiple gene genealogies confirmed that the two species belonged to different, well-supported phylogenetic clades. None of the morphological criteria tested (spore size, germination rate, or mycelial growth) was able to discriminate between these two species. Sexual crosses between individuals from the same species and different species were carried out. Only crosses between individuals from the same species were successful. Moreover, population genetics analysis revealed a high level of diversity within each species and a lack of gene flow between them. Finally, a population survey over time showed that B. cinerea was the predominant species but that B. pseudocinerea was more abundant in spring, on floral debris. This observation could not be explained by temperature adaptation in tests carried out in vitro or by aggressiveness on tomato or bean leaves. This study clearly establishes that B. cinerea and B. pseudocinerea constitute a complex of two cryptic species living in sympatry on several hosts, including grapevine and blackberry. We propose several biological or molecular tools for unambiguous differentiation between the two species. B. pseudocinerea probably makes a negligible contribution to gray mold epidemics on grapevine. This new species has been deposited in the MycoBank international database.
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GLADIEUX PIERRE, GUÉRIN FABIEN, GIRAUD TATIANA, CAFFIER VALÉRIE, LEMAIRE CHRISTOPHE, PARISI LUCIANA, DIDELOT FRÉDÉRIQUE, LE CAM BRUNO. Emergence of novel fungal pathogens by ecological speciation: importance of the reduced viability of immigrants. Mol Ecol 2011; 20:4521-32. [DOI: 10.1111/j.1365-294x.2011.05288.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Henk DA, Eagle CE, Brown K, Van Den Berg MA, Dyer PS, Peterson SW, Fisher MC. Speciation despite globally overlapping distributions in Penicillium chrysogenum: the population genetics of Alexander Fleming's lucky fungus. Mol Ecol 2011; 20:4288-301. [PMID: 21951491 DOI: 10.1111/j.1365-294x.2011.05244.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Eighty years ago, Alexander Fleming described the antibiotic effects of a fungus that had contaminated his bacterial culture, kick starting the antimicrobial revolution. The fungus was later ascribed to a putatively globally distributed asexual species, Penicillium chrysogenum. Recently, the species has been shown to be genetically diverse, and possess mating-type genes. Here, phylogenetic and population genetic analyses show that this apparently ubiquitous fungus is actually composed of at least two genetically distinct species with only slight differences detected in physiology. We found each species in air and dust samples collected in and around St Mary's Hospital where Fleming worked. Genotyping of 30 markers across the genome showed that preserved fungal material from Fleming's laboratory was nearly identical to derived strains currently in culture collections and in the same distinct species as a wild progenitor strain of current penicillin producing industrial strains rather than the type species P. chrysogenum. Global samples of the two most common species were found to possess mating-type genes in a near 1:1 ratio, and show evidence of recombination with little geographic population subdivision evident. However, no hybridization was detected between the species despite an estimated time of divergence of less than 1MYA. Growth studies showed significant interspecific inhibition by P. chrysogenum of the other common species, suggesting that competition may facilitate species maintenance despite globally overlapping distributions. Results highlight under-recognized diversity even among the best-known fungal groups and the potential for speciation despite overlapping distribution.
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Affiliation(s)
- D A Henk
- Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
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Cai L, Giraud T, Zhang N, Begerow D, Cai G, Shivas RG. The evolution of species concepts and species recognition criteria in plant pathogenic fungi. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0127-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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44
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XHAARD C, FABRE B, ANDRIEUX A, GLADIEUX P, BARRÈS B, FREY P, HALKETT F. The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication. Mol Ecol 2011; 20:2739-55. [DOI: 10.1111/j.1365-294x.2011.05138.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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45
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ALAMOUTI SEPIDEHM, WANG VINCENT, DiGUISTINI SCOTT, SIX DIANAL, BOHLMANN JÖRG, HAMELIN RICHARDC, FEAU NICOLAS, BREUIL COLETTE. Gene genealogies reveal cryptic species and host preferences for the pine fungal pathogen Grosmannia clavigera. Mol Ecol 2011; 20:2581-602. [DOI: 10.1111/j.1365-294x.2011.05109.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Kiss L, Pintye A, Kovács GM, Jankovics T, Fontaine MC, Harvey N, Xu X, Nicot PC, Bardin M, Shykoff JA, Giraud T. Temporal isolation explains host-related genetic differentiation in a group of widespread mycoparasitic fungi. Mol Ecol 2011; 20:1492-507. [PMID: 21261766 DOI: 10.1111/j.1365-294x.2011.05007.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Understanding the mechanisms responsible for divergence and specialization of pathogens on different hosts is of fundamental importance, especially in the context of the emergence of new diseases via host shifts. Temporal isolation has been reported in a few plants and parasites, but is probably one of the least studied speciation processes. We studied whether temporal isolation could be responsible for the maintenance of genetic differentiation among sympatric populations of Ampelomyces, widespread intracellular mycoparasites of powdery mildew fungi, themselves plant pathogens. The timing of transmission of Ampelomyces depends on the life cycles of the powdery mildew species they parasitize. Internal transcribed spacer sequences and microsatellite markers showed that Ampelomyces populations found in apple powdery mildew (Podosphaera leucotricha) were genetically highly differentiated from other Ampelomyces populations sampled from several other powdery mildew species across Europe, infecting plant hosts other than apple. While P. leucotricha starts its life cycle early in spring, and the main apple powdery mildew epidemics occur before summer, the fungal hosts of the other Ampelomyces cause epidemics mainly in summer and autumn. When two powdery mildew species were experimentally exposed to Ampelomyces strains naturally occurring in P. leucotricha in spring, and to strains naturally present in other mycohost species in autumn, cross-infections always occurred. Thus, the host-related genetic differentiation in Ampelomyces cannot be explained by narrow physiological specialization, because Ampelomyces were able to infect powdery mildew species they were unlikely to have encountered in nature, but instead appears to result from temporal isolation.
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Affiliation(s)
- Levente Kiss
- Plant Protection Institute of the Hungarian Academy of Sciences, Budapest, Hungary.
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47
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Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A, Giraud T. Maintenance of fungal pathogen species that are specialized to different hosts: allopatric divergence and introgression through secondary contact. Mol Biol Evol 2010; 28:459-71. [PMID: 20837605 DOI: 10.1093/molbev/msq235] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Sympatry of species that lack complete prezygotic isolation is ideal for the study of how species can be maintained in the face of potential gene flow. This is particularly important in the context of emerging diseases on new hosts because pathogen adaptation is facilitated by reduced gene flow from ancestral populations. Here, we investigated divergence and gene flow between two closely related fungal species, Microbotryum lychnidis-dioicae and M. silenes-dioicae, causing anther-smut disease on the wide-spread plant species Silene latifolia and S. dioica, respectively. Using model-based clustering algorithms on microsatellite data from samples across Europe, we identified rare disease transmission between the host species and rare pathogen hybrids. Using a coalescent-based approach and an isolation-with-migration model, the age of divergence between the two fungal species was estimated at approximately 4.2 × 10(5) years. Levels of gene flow were low and concentrated in very recent times. In addition, gene flow appeared unidirectional from M. silenes-dioicae to M. lychnidis-dioicae. Altogether, our findings are consistent with a scenario of recurrent introgressive hybridization but at a very low level and through secondary contact following initial divergence in allopatry. Asymmetry in the direction of gene flow mirrors previous findings on introgression between the two host plants. Our study highlights the consequences of bringing closely related pathogens into contact, which is increasing through modern global changes and favors cross-species disease transmission, hybridization, and introgression by pathogens.
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Affiliation(s)
- Pierre Gladieux
- Laboratoire Ecologie, Systématique et Evolution, Univ Paris Sud, UMR8079, Orsay, France.
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Giraud T, Gladieux P, Gavrilets S. Linking the emergence of fungal plant diseases with ecological speciation. Trends Ecol Evol 2010; 25:387-95. [PMID: 20434790 DOI: 10.1016/j.tree.2010.03.006] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 03/27/2010] [Accepted: 03/30/2010] [Indexed: 11/18/2022]
Abstract
Emerging diseases represent a growing worldwide problem accompanying global environmental changes. There is tremendous interest in identifying the factors controlling the appearance and spread of these diseases. Here, we discuss emerging fungal plant diseases, and argue that they often result from host shift speciation (a particular case of ecological speciation). We consider the factors controlling local adaptation and ecological speciation, and show that certain life-history traits of many fungal plant pathogens are conducive for rapid ecological speciation, thus favoring the emergence of novel pathogen species adapted to new hosts. We argue that placing the problem of emerging fungal diseases of plants within the context of ecological speciation can significantly improve our understanding of the biological mechanisms governing the emergence of such diseases.
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Affiliation(s)
- Tatiana Giraud
- Ecologie, Systematique et Evolution, Universite Paris-Sud, 92120 Orsay, France
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49
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Gladieux P, Caffier V, Devaux M, Le Cam B. Host-specific differentiation among populations of Venturia inaequalis causing scab on apple, pyracantha and loquat. Fungal Genet Biol 2010; 47:511-21. [PMID: 20060485 DOI: 10.1016/j.fgb.2009.12.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 12/14/2009] [Accepted: 12/16/2009] [Indexed: 10/20/2022]
Abstract
Patterns of multilocus DNA sequence variation within and between closely related taxa can provide insights into the history of divergence. Here, we report on DNA polymorphism and divergence at six nuclear loci in globally distributed samples of the ascomycete Venturia inaequalis, responsible for scab on apple, loquat, and pyracantha. Isolates from different hosts were differentiated but did not form diagnosable distinct phylogenetic species. Parameters of an Isolation-with-Migration model estimated from the data suggested that the large amount of variation shared among groups more likely resulted from recent splitting than from extensive genetic exchanges. Inferred levels of gene flow among groups were low and more concentrated toward recent times, and we identified two potentially recent one-off shifters from apple and pyracantha to loquat. These findings support a scenario of recent divergence in allopatry followed by introgression through secondary contact, with groups from loquat and pyracantha being the most recently differentiated.
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Affiliation(s)
- P Gladieux
- INRA, UMR 077, 42 rue George Morel, Beaucouzé, France.
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50
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Frenkel O, Peever TL, Chilvers MI, Özkilinc H, Can C, Abbo S, Shtienberg D, Sherman A. Ecological genetic divergence of the fungal pathogen Didymella rabiei on sympatric wild and domesticated Cicer spp. (Chickpea). Appl Environ Microbiol 2010; 76:30-9. [PMID: 19897759 PMCID: PMC2798644 DOI: 10.1128/aem.01181-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 10/31/2009] [Indexed: 11/20/2022] Open
Abstract
For millennia, chickpea (Cicer arietinum) has been grown in the Levant sympatrically with wild Cicer species. Chickpea is traditionally spring-sown, while its wild relatives germinate in the autumn and develop in the winter. It has been hypothesized that the human-directed shift of domesticated chickpea to summer production was an attempt to escape the devastating Ascochyta disease caused by Didymella rabiei. We estimated genetic divergence between D. rabiei isolates sampled from wild Cicer judaicum and domesticated C. arietinum and the potential role of temperature adaptation in this divergence. Neutral genetic markers showed strong differentiation between pathogen samples from the two hosts. Isolates from domesticated chickpea demonstrated increased adaptation to higher temperatures when grown in vitro compared with isolates from the wild host. The distribution of temperature responses among progeny from crosses of isolates from C. judaicum with isolates from C. arietinum was continuous, suggesting polygenic control of this trait. In vivo inoculations of host plants indicated that pathogenic fitness of the native isolates was higher than that of their hybrid progeny. The results indicate that there is a potential for adaptation to higher temperatures; however, the chances for formation of hybrids which are capable of parasitizing both hosts over a broad temperature range are low. We hypothesize that this pathogenic fitness cost is due to breakdown of coadapted gene complexes controlling pathogenic fitness on each host and may be responsible for maintenance of genetic differentiation between the pathogen demes.
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Affiliation(s)
- Omer Frenkel
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Tobin L. Peever
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Martin I. Chilvers
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Hilal Özkilinc
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Canan Can
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Shahal Abbo
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Dani Shtienberg
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
| | - Amir Sherman
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel, Department of Genomics, ARO, The Volcani Center, Bet-Dagan 50250, Israel, Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430, Department of Biology, University of Gaziantep, Gaziantep 27310, Turkey, Department of Plant Pathology and Weed Research, ARO, The Volcani Center, Bet-Dagan 50250, Israel
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