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Albornoz MV, Lolas M, Verdugo JA, Ramírez CC. Identification of Virulences of the Rust Fungus Melampsora larici-populina Occurring in Chile. Plant Dis 2018; 102:2201-2204. [PMID: 30216126 DOI: 10.1094/pdis-01-18-0033-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Melampsora larici-populina Kleb. is a Eurasian species that causes leaf rust of many species of Populus from sections Tacamahaca and Aigeiros. This rust has been inadvertently introduced to many parts around the world affecting poplar species that grow naturally, which may be susceptible to this fungus. In Chile, early European settlers introduced poplars; rust, attributed to M. larici-populina, has been reported in these trees since 1918. However, a modern confirmation has been lacking, and pathogenic variation of the Chilean population of M. larici-populina has not been investigated. Using a morphological analysis of urediniospores and sequencing of internal transcribed spacer (ITS) regions, we confirmed the presence of M. larici-populina in Chile. ITS regions exhibited 100% homology with M. larici-populina. Scanning electron microscopy showed that spores were 26 to 47 µm in length, 13 to 16 µm in width, and echinulate except for apices, which are smooth, characteristics described for this species of rust. The variability of M. larici-populina is characterized by the presence of pathotypes, which allows the fungus to infect despite the resistance of certain poplar hybrids. We concluded that the identified spores belong to M. larici-populina, with virulences 1, 2, 3, 4, 5, and 6. These results describe variation in virulence of M. larici-populina, which suggests the presence of a sexual stage in Chile.
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Affiliation(s)
- Marta V Albornoz
- Centro Regional de Innovación Hortofrutícola de Valparaíso Ceres, Pontificia Universidad Católica de Valparaíso, Quillota, Chile
| | - Mauricio Lolas
- Laboratorio de Fitopatología, Facultad de Ciencias Agrarias, Universidad de Talca, Chile
| | - Jaime A Verdugo
- Centre for Molecular and Functional Ecology, Instituto de Ciencias Biológicas, Universidad de Talca, Chile
| | - Claudio C Ramírez
- Centre for Molecular and Functional Ecology, Instituto de Ciencias Biológicas, Universidad de Talca, Chile
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Persoons A, Hayden KJ, Fabre B, Frey P, De Mita S, Tellier A, Halkett F. The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust. Mol Ecol 2017; 26:1902-1918. [PMID: 28012228 DOI: 10.1111/mec.13980] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/15/2016] [Indexed: 01/14/2023]
Abstract
Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25-year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) - above all - the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics.
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Affiliation(s)
| | | | | | - Pascal Frey
- UMR IAM, INRA, Université de Lorraine, 54000, Nancy, France
| | | | - Aurélien Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354, Freising, Germany
| | - Fabien Halkett
- UMR IAM, INRA, Université de Lorraine, 54000, Nancy, France
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Pernaci M, De Mita S, Andrieux A, Pétrowski J, Halkett F, Duplessis S, Frey P. Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina. Front Plant Sci 2014; 5:454. [PMID: 25309554 PMCID: PMC4159982 DOI: 10.3389/fpls.2014.00454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 08/21/2014] [Indexed: 05/16/2023]
Abstract
The poplar rust fungus Melampsora larici-populina causes significant yield reduction and severe economic losses in commercial poplar plantations. After several decades of breeding for qualitative resistance and subsequent breakdown of the released resistance genes, breeders now focus on quantitative resistance, perceived to be more durable. But quantitative resistance also can be challenged by an increase of aggressiveness in the pathogen. Thus, it is of primary importance to better understand the genetic architecture of aggressiveness traits. To this aim, our goal is to build a genetic linkage map for M. larici-populina in order to map quantitative trait loci related to aggressiveness. First, a large progeny of M. larici-populina was generated through selfing of the reference strain 98AG31 (which genome sequence is available) on larch plants, the alternate host of the poplar rust fungus. The progeny's meiotic origin was validated through a segregation analysis of 115 offspring with 14 polymorphic microsatellite markers, of which 12 segregated in the expected 1:2:1 Mendelian ratio. A microsatellite-based linkage disequilibrium analysis allowed us to identify one potential linkage group comprising two scaffolds. The whole genome of a subset of 47 offspring was resequenced using the Illumina HiSeq 2000 technology at a mean sequencing depth of 6X. The reads were mapped onto the reference genome of the parental strain and 144,566 SNPs were identified across the genome. Analysis of distribution and polymorphism of the SNPs along the genome led to the identification of 2580 recombination blocks. A second linkage disequilibrium analysis, using the recombination blocks as markers, allowed us to group 81 scaffolds into 23 potential linkage groups. These preliminary results showed that a high-density linkage map could be constructed by using high-quality SNPs based on low-coverage resequencing of a larger number of M. larici-populina offspring.
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Affiliation(s)
- Michaël Pernaci
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Stéphane De Mita
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Axelle Andrieux
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Jérémy Pétrowski
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Fabien Halkett
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Sébastien Duplessis
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
| | - Pascal Frey
- Interactions Arbres - Micro organismes, Institut national de la recherche agronomique, UMR1136Champenoux, France
- Interactions Arbres - Micro organismes, Université de Lorraine, UMR1136Vandoeuvre-lès-Nancy, France
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XHAARD CONSTANCE, BARRÈS BENOÎT, ANDRIEUX AXELLE, BOUSSET LYDIA, HALKETT FABIEN, FREY PASCAL. Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach. Mol Ecol 2012; 21:2383-98. [DOI: 10.1111/j.1365-294x.2012.05556.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Feau N, Decourcelle T, Husson C, Desprez-Loustau ML, Dutech C. Finding single copy genes out of sequenced genomes for multilocus phylogenetics in non-model fungi. PLoS One 2011; 6:e18803. [PMID: 21533204 PMCID: PMC3076447 DOI: 10.1371/journal.pone.0018803] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/18/2011] [Indexed: 11/17/2022] Open
Abstract
Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species.
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Affiliation(s)
- Nicolas Feau
- INRA, UMR1202, BIOGECO (Biodiversité Gènes et Communautés), Cestas, France.
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