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Zhang Z, Chen W, Liang J, Zhang L, Han Y, Huang J, Liang Z. Revealing the non-overlapping characteristics between original centers and genetic diversity of Purpureocillium lilacinum. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Castillo AI, Tsai CW, Su CC, Weng LW, Lin YC, Cho ST, Almeida RPP, Kuo CH. Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microb Genom 2021; 7. [PMID: 34898423 PMCID: PMC8767338 DOI: 10.1099/mgen.0.000727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chiou-Chu Su
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Taichung 413, Taiwan, ROC
| | - Ling-Wei Weng
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
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Chong P, Essoh JN, Arango Isaza RE, Keizer P, Stergiopoulos I, Seidl MF, Guzman M, Sandoval J, Verweij PE, Scalliet G, Sierotzski H, de Lapeyre de Bellaire L, Crous PW, Carlier J, Cros S, Meijer HJG, Peralta EL, Kema GHJ. A world-wide analysis of reduced sensitivity to DMI fungicides in the banana pathogen Pseudocercospora fijiensis. PEST MANAGEMENT SCIENCE 2021; 77:3273-3288. [PMID: 33764651 PMCID: PMC8252799 DOI: 10.1002/ps.6372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/19/2021] [Accepted: 03/25/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pseudocercospora fijiensis is the causal agent of the black leaf streak disease (BLSD) of banana. Bananas are important global export commodities and a major staple food. Their susceptibility to BLSD pushes disease management towards excessive fungicide use, largely relying on multisite inhibitors and sterol demethylation inhibitors (DMIs). These fungicides are ubiquitous in plant disease control, targeting the CYP51 enzyme. We examined sensitivity to DMIs in P. fijiensis field isolates collected from various major banana production zones in Colombia, Costa Rica, Dominican Republic, Ecuador, the Philippines, Guadalupe, Martinique and Cameroon and determined the underlying genetic reasons for the observed phenotypes. RESULTS We observed a continuous range of sensitivity towards the DMI fungicides difenoconazole, epoxiconazole and propiconazole with clear cross-sensitivity. Sequence analyses of PfCYP51 in 266 isolates showed 28 independent amino acid substitutions, nine of which correlated with reduced sensitivity to DMIs. In addition to the mutations, we observed up to six insertions in the Pfcyp51 promoter. Such promoter insertions contain repeated elements with a palindromic core and correlate with the enhanced expression of Pfcyp51 and hence with reduced DMI sensitivity. Wild-type isolates from unsprayed bananas fields did not contain any promoter insertions. CONCLUSION The presented data significantly contribute to understanding of the evolution and global distribution of DMI resistance mechanisms in P. fijiensis field populations and facilitate the prediction of different DMI efficacy. The overall reduced DMI sensitivity calls for the deployment of a wider range of solutions for sustainable control of this major banana disease. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Pablo Chong
- Centro de Investigaciones Biotecnológicas del Ecuador, CIBELaboratorio de FitopatologíaEscuela Superior Politécnica del Litoral, ESPOL.km 30.5 via perimetralGuayaquil090112Ecuador
- Wageningen ResearchWageningen University and ResearchWageningenThe Netherlands
| | - Josué Ngando Essoh
- Unité de Recherches sur les Systèmes de Production Durables (SYSPROD)Laboratoire de PhytopathologieCentre Africain de Recherches sur Bananiers et Plantain, CARBAPDoualaCameroun
- UPR GECOCIRADMontpellierFrance
| | - Rafael E Arango Isaza
- Escuela de BiocienciasUniversidad Nacional de Colombia, Sede Medellín (UNALMED)MedellínColombia
- Corporación para Investigaciones BiológicasUnidad de biotecnología Vegetal (CIB)MedellínColombia
| | - Paul Keizer
- BiometrisWageningen University and ResearchWageningenThe Netherlands
| | | | | | - Mauricio Guzman
- Departamento de FitoprotecciónCorporación Bananera Nacional (CORBANA S.A.)LimónCosta Rica
| | - Jorge Sandoval
- Departamento de FitoprotecciónCorporación Bananera Nacional (CORBANA S.A.)LimónCosta Rica
| | - Paul E Verweij
- Department of Medical MicrobiologyRadboud University Nijmegen Medical CenterNijmegenThe Netherlands
| | - Gabriel Scalliet
- Disease control groupSyngenta Crop Protection AGSteinSwitzerland
| | - Helge Sierotzski
- Disease control groupSyngenta Crop Protection AGSteinSwitzerland
| | | | - Pedro W Crous
- Hugo R. KruytgebouwUtrecht UniversityUtrechtThe Netherlands
- Lab of Evolutionary PhytopahtologyCBS‐KNAW Fungal Biodiversity CenterUtrechtThe Netherlands
| | - Jean Carlier
- UMR BGPICIRADMontpellierFrance
- BGPIMontpellier University, Cirad, Inrae, Montpellier SupAgroMontpellierFrance
| | - Sandrine Cros
- BGPIMontpellier University, Cirad, Inrae, Montpellier SupAgroMontpellierFrance
| | - Harold J G Meijer
- Wageningen ResearchWageningen University and ResearchWageningenThe Netherlands
| | - Esther Lilia Peralta
- Centro de Investigaciones Biotecnológicas del Ecuador, CIBELaboratorio de FitopatologíaEscuela Superior Politécnica del Litoral, ESPOL.km 30.5 via perimetralGuayaquil090112Ecuador
| | - Gert H J Kema
- Wageningen ResearchWageningen University and ResearchWageningenThe Netherlands
- Laboratory of PhytopathologyWageningen University and ResearchWageningenThe Netherlands
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Kimunye JN, Muzhinji N, Mostert D, Viljoen A, Bester-van der Merwe AE, Mahuku G. Genetic Diversity and Mating Type Distribution of Pseudocercospora fijiensis on Banana in Uganda and Tanzania. PHYTOPATHOLOGY 2021; 111:741-750. [PMID: 32931393 DOI: 10.1094/phyto-04-20-0138-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Black Sigatoka, caused by Pseudocercospora fijiensis, is a major foliar disease of banana and plantain worldwide. There are few available data regarding the genetic diversity and population structure of the pathogen in East Africa, which are needed to design effective and durable disease management strategies. We genotyped 319 single-spore isolates of P. fijiensis collected from seven regions in Uganda and Tanzania and five isolates from Nigeria using 16 simple sequence repeat markers and mating type-specific primers. Isolates from each country and region within the country were treated as populations and subpopulations, respectively. A total of 296 multilocus genotypes (MLGs) were recovered, representing a clonal fraction of 7%. Subpopulations had a moderate level of genetic diversity (Hexp = 0.12 to 0.31; mean, 0.29). Mating type distribution did not deviate from equilibrium (MAT1-1: MAT1-2, 1:1 ratio) in Uganda; however, in Tanzania the mating types were not in equilibrium (4:1 ratio). The index of association tests (IA and r̄d) showed that all populations were at linkage equilibrium (P > 0.05), thus supporting the hypothesis of random association of alleles. These findings are consistent with a pathogen that reproduces both clonally and sexually. Low and insignificant levels of population differentiation were detected, with 90% of the variation occurring among isolates within subpopulations. The high intrapopulation variation has implications in breeding for resistance to P. fijiensis because isolates differing in aggressiveness and virulence are likely to exist over small spatial scales. Diverse isolates will be required for resistance screening to ensure selection of banana cultivars with durable resistance to Sigatoka in East Africa.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Janet N Kimunye
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Norman Muzhinji
- Department of Applied and Natural Sciences, Namibia University of Science and Technology, Private Bag 13388, Windhoek, Namibia
| | - Diane Mostert
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | - Altus Viljoen
- Department of Plant Pathology, Private Bag X1, Stellenbosch University, Matieland 7602, South Africa
| | | | - George Mahuku
- International Institute of Tropical Agriculture, P.O. Box 7878, Kampala, Uganda
- International Institute of Tropical Agriculture, P.O. Box, 34441, Dar es Salaam, Tanzania
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Emerging infectious diseases threatening food security and economies in Africa. GLOBAL FOOD SECURITY 2021. [DOI: 10.1016/j.gfs.2020.100479] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was to reveal the genomic basis of adaptation to such a resistance in populations of the fungus Pseudocercospora fijiensis, a major devastating pathogen of banana, by studying convergent adaptation on different cultivars. Samples from P. fijiensis populations showing a local adaptation pattern on new banana hybrids with quantitative resistance were compared, based on a genome scan approach, with samples from traditional and more susceptible cultivars in Cuba and the Dominican Republic. Whole-genome sequencing of pools of P. fijiensis isolates (pool-seq) sampled from three locations per country was conducted according to a paired population design. The findings of different combined analyses highly supported the existence of convergent adaptation on the study cultivars between locations within but not between countries. Five to six genomic regions involved in this adaptation were detected in each country. An annotation analysis and available biological data supported the hypothesis that some genes within the detected genomic regions may play a role in quantitative pathogenicity, including gene regulation. The results suggested that the genetic basis of fungal adaptation to quantitative plant resistance is at least oligogenic, while highlighting the existence of specific host-pathogen interactions for this kind of resistance.IMPORTANCE Understanding the genetic basis of pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment. In this context, a population genomic approach was developed for a major plant pathogen (the fungus Pseudocercospora fijiensis causing black leaf streak disease of banana) whereby samples from new resistant banana hybrids were compared with samples from more susceptible conventional cultivars in two countries. A total of 11 genomic regions for which there was strong evidence of selection by quantitative resistance were detected. An annotation analysis and available biological data supported the hypothesis that some of the genes within these regions may play a role in quantitative pathogenicity. These results suggested a polygenic basis of quantitative pathogenicity in this fungal pathogen and complex molecular plant-pathogen interactions in quantitative disease development involving several genes on both sides.
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Carlier J, Robert S, Roussel V, Chilin-Charles Y, Lubin-Adjanoh N, Gilabert A, Abadie C. Central American and Caribbean population history of the Pseudocercospora fijiensis fungus responsible for the latest worldwide pandemics on banana. Fungal Genet Biol 2021; 148:103528. [PMID: 33515682 DOI: 10.1016/j.fgb.2021.103528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/18/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
Among the emerging fungal diseases threatening food security, the Pseudocercospora fijiensis fungus causing black leaf streak disease of banana is one of the most marked examples of a recent worldwide pandemic on a major crop. We assessed how this pathogen spread throughout the latest invaded region, i.e. Central America and the Caribbean. We retraced its population history combining detailed monitoring information on disease outbreaks and population genetic analyses based on large-scale sampling of P. fijiensis isolates from 121 locations throughout the region. The results first suggested that sexual reproduction was not lost during the P. fijiensis expansion, even in the insular Caribbean context, and a high level of genotypic diversity was maintained in all the populations studied. The population genetic structure of P. fijiensis and historical data showed that two disease waves swept northward and southward in all banana-producing countries in the study area from an initial entry point in Honduras, probably mainly through gradual stepwise spore dispersal. Serial founder events accompanying the northern and southern waves led to the establishment of two different genetic groups. A different population structure was detected on the latest invaded islands (Martinique, Dominica and Guadeloupe), revealing multiple introductions and admixture events that may have been partly due to human activities. The results of this study highlight the need to step up surveillance to limit the spread of other known emerging diseases of banana spread mainly by humans, but also to curb gene flow between established pathogen populations which could increase their evolutionary potential.
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Affiliation(s)
- Jean Carlier
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
| | - Stéphanie Robert
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Véronique Roussel
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Yolande Chilin-Charles
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nadia Lubin-Adjanoh
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Aude Gilabert
- CIRAD, UMR PHIM, F-34398 Montpellier, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Catherine Abadie
- CIRAD, UMR PHIM, F-97130 Capesterre-Belle-Eau, Guadeloupe, France; PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Georges-Filteau J, Hamelin RC, Blanchette M. Mycorrhiza: genotype assignment using phylogenetic networks. Bioinformatics 2020; 36:212-220. [PMID: 31197316 DOI: 10.1093/bioinformatics/btz476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 05/03/2019] [Accepted: 06/06/2019] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. RESULTS In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy. AVAILABILITY AND IMPLEMENTATION Mycorrhiza is released as an easy to use open-source python package at github.com/jgeofil/mycorrhiza. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, The University of British Columbia, Vancouver, BC, Canada.,Département des sciences du bois et de la forêt, Université Laval, Québec, Canada
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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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Dumartinet T, Abadie C, Bonnot F, Carreel F, Roussel V, Habas R, Martinez RT, Perez‐Vicente L, Carlier J. Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop. Evol Appl 2020; 13:824-836. [PMID: 32211070 PMCID: PMC7086059 DOI: 10.1111/eva.12904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.
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Affiliation(s)
- Thomas Dumartinet
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Catherine Abadie
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
- CIRADUMR BGPICapesterre‐Belle‐EauFrance
| | - François Bonnot
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Françoise Carreel
- UMR AGAPUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Véronique Roussel
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Rémy Habas
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | | | | | - Jean Carlier
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
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Yonow T, Ramirez-Villegas J, Abadie C, Darnell RE, Ota N, Kriticos DJ. Black Sigatoka in bananas: Ecoclimatic suitability and disease pressure assessments. PLoS One 2019; 14:e0220601. [PMID: 31412052 PMCID: PMC6693783 DOI: 10.1371/journal.pone.0220601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/21/2019] [Indexed: 12/04/2022] Open
Abstract
Black leaf streak disease, or black Sigatoka, is caused by the fungus Pseudocercospora fijiensis, and has been identified as a major constraint to global production of banana and plantain. We fitted a climatic niche model (CLIMEX) for P. fijiensis to gain an understanding of the patterns of climate suitability, and hence hazard from this disease. We then calibrated the climate suitability patterns against the results of an expert elicitation of disease pressure patterns. We found a moderately strong non-linear relationship between modelled climate suitability for P.°fijiensis and the expert ratings for disease pressure. The strength of the relationship provides a cross-validation between the CLIMEX model and the expert elicitation process. The bulk of global banana production experiences high potential threat from P. fijiensis, and the higher yielding areas for banana and plantain production are at greatest threat. By explicitly considering the role of irrigation we have been able to identify how strategic irrigation could be used to support banana production in areas that are at low risk from P. fijiensis.
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Affiliation(s)
- Tania Yonow
- HarvestChoice, InSTePP, University of Minnesota, St. Paul, MN, United States of America
- CSIRO, Canberra ACT, Australia
| | - Julian Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Cali, Colombia
- Visiting Research Fellow, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Catherine Abadie
- BGPI, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-97130 Capesterre Belle-Eau, Guadeloupe, France
| | | | | | - Darren J. Kriticos
- HarvestChoice, InSTePP, University of Minnesota, St. Paul, MN, United States of America
- CSIRO, Canberra ACT, Australia
- The University of Queensland, School of Biological Sciences, St. Lucia, QLD, Australia
- * E-mail:
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Invasion of the assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae) to Japan: Source estimation inferred from mitochondrial and nuclear gene sequences. Int J Biol Macromol 2018; 118:1565-1573. [PMID: 29981333 DOI: 10.1016/j.ijbiomac.2018.06.191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/21/2018] [Accepted: 06/30/2018] [Indexed: 11/21/2022]
Abstract
A large-sized assassin bug Agriosphodrus dohrni (Signoret), has been recorded from India, Vietnam, China and Japan. It is one of the potential biological control agents against some important agricultural and forest pests. This species is speculated to have invaded Japan from its native range in China about 60 years ago. We used three mitochondrial gene fragments (COI, Cytb, and ND5) and one nuclear gene fragment (EF-1α) to clarify the invasion history of A. dohrni and assess the effects of geographic events and associated ecological adaptation on the distribution pattern. The native populations of A. dohrni in China are divided into three distinct groups, which might be molded by the Early Pleistocene glaciation event and diverged during the Calabrian Stage. However, consistent with the hypothesis of a recent invasion, extremely low level of genetic variation was detected in the Japanese populations, with only two haplotypes for the combined mitochondrial genes. Both the splits network and the ML/BI phylogenetic trees revealed that haplotypes of Japan were more closely-related to those from eastern China. Therefore, we postulate that there has been only one introduction event, probably from somewhere around the Nanjing (NJ) and Lin'an (LA) populations of eastern China.
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Manawasinghe IS, Zhang W, Li X, Zhao W, Chethana K, Xu J, Chen Z, Dissanayaka AJ, Mugnai L, Úrbez-Torres JR, Savocchia S, Hyde KD, Yan J. Novel microsatellite markers reveal multiple origins of Botryosphaeria dothidea causing the Chinese grapevine trunk disease. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Lombaert E, Guillemaud T, Deleury E. Biases of STRUCTURE software when exploring introduction routes of invasive species. Heredity (Edinb) 2018; 120:485-499. [PMID: 29339802 DOI: 10.1038/s41437-017-0042-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 10/06/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Abstract
Population genetic methods are widely used to retrace the introduction routes of invasive species. The unsupervised Bayesian clustering algorithm implemented in STRUCTURE is amongst the most frequently used of these methods, but its ability to provide reliable information about introduction routes has never been assessed. We simulated microsatellite datasets to evaluate the extent to which the results provided by STRUCTURE were misleading for the inference of introduction routes. We focused on an invasion scenario involving one native and two independently introduced populations, because it is the sole scenario that can be rejected when obtaining a particular clustering with a STRUCTURE analysis at K = 2 (two clusters). Results were classified as "misleading" or "non-misleading". We investigated the influence of effective size, bottleneck severity and number of loci on the type and frequency of misleading results. We showed that misleading STRUCTURE results were obtained for 10% of all simulated datasets. Our results highlighted two categories of misleading output. The first occurs when the native population has a low level of diversity. In this case, the two introduced populations may be very similar, despite their independent introduction histories. The second category results from convergence issues in STRUCTURE for K = 2, with strong bottleneck severity and/or large numbers of loci resulting in high levels of differentiation between the three populations. Overall, the risk of being misled by STRUCTURE in the context of introduction routes inferences is moderate, but it is important to remain cautious when low genetic diversity or genuine multimodality between runs are involved.
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Affiliation(s)
- Eric Lombaert
- INRA, CNRS, Université Côte d'Azur, ISA, Paris, France.
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15
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Pino-Bodas R, Laakso I, Stenroos S. Genetic variation and factors affecting the genetic structure of the lichenicolous fungus Heterocephalacria bachmannii (Filobasidiales, Basidiomycota). PLoS One 2017; 12:e0189603. [PMID: 29253026 PMCID: PMC5734755 DOI: 10.1371/journal.pone.0189603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/29/2017] [Indexed: 11/26/2022] Open
Abstract
Heterocephalacria bachmannii is a lichenicolous fungus that takes as hosts numerous lichen species of the genus Cladonia. In the present study we analyze whether the geographical distance, the host species or the host secondary metabolites determine the genetic structure of this parasite. To address the question, populations mainly from the Southern Europe, Southern Finland and the Azores were sampled. The specimens were collected from 20 different host species representing ten chemotypes. Three loci, ITS rDNA, LSU rDNA and mtSSU, were sequenced. The genetic structure was assessed by AMOVA, redundance analyses and Bayesian clustering methods. The results indicated that the host species and the host secondary metabolites are the most influential factors over the genetic structure of this lichenicolous fungus. In addition, the genetic structure of H. bachmannii was compared with that of one of its hosts, Cladonia rangiformis. The population structure of parasite and host were discordant. The contents in phenolic compounds and fatty acids of C. rangiformis were quantified in order to test whether it had some influence on the genetic structure of the species. But no correlation was found with the genetic clusters of H. bachmannii.
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Affiliation(s)
| | - Into Laakso
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
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16
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Zhang W, Manawasinghe IS, Zhao W, Xu J, Brooks S, Zhao X, Hyde KD, Chethana KWT, Liu J, Li X, Yan J. Multiple gene genealogy reveals high genetic diversity and evidence for multiple origins of Chinese Plasmopara viticola population. Sci Rep 2017; 7:17304. [PMID: 29230063 PMCID: PMC5725484 DOI: 10.1038/s41598-017-17569-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/28/2017] [Indexed: 11/14/2022] Open
Abstract
Downy mildew caused by Plasmopara viticola is one of the most devastating diseases of grapevines worldwide. So far, the genetic diversity and origin of the Chinese P. viticola population are unclear. In the present study, 103 P. viticola isolates were sequenced at four gene regions: internal transcribed spacer one (ITS), large subunit of ribosomal RNA (LSU), actin gene (ACT) and beta-tubulin (TUB). The sequences were analyzed to obtain polymorphism and diversity information of the Chinese population as well as to infer the relationships between Chinese and American isolates. High genetic diversity was observed for the Chinese population, with evidence of sub-structuring based on climate. Phylogenetic analysis and haplotype networks showed evidence of close relationships between some American and Chinese isolates, consistent with recent introduction from America to China via planting materials. However, there is also evidence for endemic Chinese P. viticola isolates. Our results suggest that the current Chinese Plasmopara viticola population is an admixture of endemic and introduced isolates.
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Affiliation(s)
- Wei Zhang
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Ishara S Manawasinghe
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Wensheng Zhao
- College of Plant Protection, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Jianping Xu
- Department of Biology, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Siraprapa Brooks
- School of Science, Mae Fah Luang University, Chiang, Rai, 57100, Thailand
| | - Xueyan Zhao
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - K W Thilini Chethana
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Jianhua Liu
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China
| | - Xinghong Li
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
| | - Jiye Yan
- Beijing Municipal Key Laboratory for Environmental Friendly Management on Pests of North China Fruits, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People's Republic of China.
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Saville A, Charles M, Chavan S, Muñoz M, Gómez-Alpizar L, Ristaino JB. Population Structure of Pseudocercospora fijiensis in Costa Rica Reveals Shared Haplotype Diversity with Southeast Asian Populations. PHYTOPATHOLOGY 2017; 107:1541-1548. [PMID: 28820343 DOI: 10.1094/phyto-02-17-0045-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Pseudocercospora fijiensis is the causal pathogen of black Sigatoka, a devastating disease of banana that can cause 20 to 80% yield loss in the absence of fungicides in banana crops. The genetic structure of populations of P. fijiensis in Costa Rica was examined and compared with Honduran and global populations to better understand migration patterns and inform management strategies. In total, 118 isolates of P. fijiensis collected from Costa Rica and Honduras from 2010 to 2014 were analyzed using multilocus genotyping of six loci and compared with a previously published global dataset of populations of P. fijiensis. The Costa Rican and Honduran populations shared haplotype diversity with haplotypes from Southeast Asia, Oceania, and the Americas but not Africa for all but one of the six loci studied. Gene flow and shared haplotype diversity was found in Honduran and Costa Rican populations of the pathogen. The data indicate that the haplotypic diversity observed in Costa Rican populations of P. fijiensis is derived from dispersal from initial outbreak sources in Honduras and admixtures between genetically differentiated sources from Southeast Asia, Oceania, and the Americas.
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Affiliation(s)
- Amanda Saville
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
| | - Melodi Charles
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
| | - Suchitra Chavan
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
| | - Miguel Muñoz
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
| | - Luis Gómez-Alpizar
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
| | - Jean Beagle Ristaino
- First, second, third, and sixth authors: Department of Plant Pathology, North Carolina State University, Raleigh 27695; third author: Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29631; fourth author: Dole Standard Fruits, SA, Tropical Research Department, Rio Frio, Costa Rica; and fifth author: Agronomic Research Center, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
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18
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Genetic signatures of variation in population size in a native fungal pathogen after the recent massive plantation of its host tree. Heredity (Edinb) 2017; 119:402-410. [PMID: 28930289 DOI: 10.1038/hdy.2017.58] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 08/05/2017] [Indexed: 12/23/2022] Open
Abstract
Historical fluctuations in forests' distribution driven by past climate changes and anthropogenic activities can have large impacts on the demographic history of pathogens that have a long co-evolution history with these host trees. Using a population genetic approach, we investigated that hypothesis by reconstructing the demographic history of Armillaria ostoyae, one of the major pathogens of the maritime pine (Pinus pinaster), in the largest monospecific pine planted forest in Europe (south-western France). Genetic structure analyses and approximate Bayesian computation approaches revealed that a single pathogen population underwent a severe reduction in effective size (12 times lower) 1080-2080 generations ago, followed by an expansion (4 times higher) during the last 4 generations. These results are consistent with the history of the maritime pine forest in the region characterized by a strong recession during the last glaciation (~19 000 years ago) and massive plantations during the second half of the nineteenth century. Results suggest that recent and intensive plantations of a host tree population have offered the opportunity for a rapid spread and adaptation of their pathogens.
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19
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Mullett M, Brown A, Fraser S, Baden R, Tubby K. Insights into the pathways of spread and potential origins of Dothistroma septosporum in Britain. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Ravigné V, Lemesle V, Walter A, Mailleret L, Hamelin FM. Mate Limitation in Fungal Plant Parasites Can Lead to Cyclic Epidemics in Perennial Host Populations. Bull Math Biol 2017; 79:430-447. [PMID: 28091971 DOI: 10.1007/s11538-016-0240-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
Fungal plant parasites represent a growing concern for biodiversity and food security. Most ascomycete species are capable of producing different types of infectious spores both asexually and sexually. Yet the contributions of both types of spores to epidemiological dynamics have still to been fully researched. Here we studied the effect of mate limitation in parasites which perform both sexual and asexual reproduction in the same host. Since mate limitation implies positive density dependence at low population density, we modeled the dynamics of such species with both density-dependent (sexual) and density-independent (asexual) transmission rates. A first simple SIR model incorporating these two types of transmission from the infected compartment, suggested that combining sexual and asexual spore production can generate persistently cyclic epidemics in a significant part of the parameter space. It was then confirmed that cyclic persistence could occur in realistic situations by parameterizing a more detailed model fitting the biology of the Black Sigatoka disease of banana, for which literature data are available. We discuss the implications of these results for research on and management of Sigatoka diseases of banana.
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Affiliation(s)
- Virginie Ravigné
- UMR BGPI, CIRAD, 34398, Montpellier, France. .,UMR PVBMT, CIRAD, 97410, Saint Pierre, Réunion, France.
| | | | - Alicia Walter
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, 35000, Rennes, France
| | - Ludovic Mailleret
- INRA, CNRS, ISA, Université Côte d'Azur, 06903, Sophia Antipolis, France.,Inria, INRA, CNRS, UPMC Univ. Paris 06, Université Côte d'Azur, 06902, Sophia Antipolis, France
| | - Frédéric M Hamelin
- IGEPP, Agrocampus Ouest, INRA, Université de Rennes 1, Université Bretagne-Loire, 35000, Rennes, France
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21
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Abstract
The tropics produce a range of fruit from tree crops that cannot be grown in colder climates. Bananas, mangos, several nuts, spices, coffee, and cacao are widely traded and much sought after around the world. However, the sustainable production of these tropical tree fruit crops faces significant challenges. Among these, losses due to pests and diseases play a large part in reducing yields, quality, and profitability. Using bananas and cacao as key examples, we outline some of the reasons fungal and oomycete diseases cause such significant losses to tropical tree crops. Cultivation of monocultures derived from limited genetic diversity, environmental conditions conducive for disease development, high levels of disease incidence and severity, a lack of disease resistance in planting materials, shortages of labor, and inadequate infrastructure and investment pose significant challenges, especially for smallholder producers. The expansion of travel and trade has given rise to emerging infectious plant diseases that add further insecurity and pressure. We conclude that holistic actions are needed on multiple fronts to address the growing problem of disease in tropical fruit tree crops.
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Affiliation(s)
- André Drenth
- Centre for Plant Science, University of Queensland, Brisbane, QLD 4072, Australia;
| | - David I Guest
- Faculty of Agriculture and Environment, University of Sydney, Sydney, NSW 2006, Australia;
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22
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23
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Taole M, Bihon W, Wingfield BD, Wingfield MJ, Burgess TI. Multiple introductions from multiple sources: invasion patterns for an important Eucalyptus leaf pathogen. Ecol Evol 2015; 5:4210-20. [PMID: 26445668 PMCID: PMC4588637 DOI: 10.1002/ece3.1693] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 11/06/2022] Open
Abstract
Many population studies on invasive plant pathogens are undertaken without knowing the center of origin of the pathogen. Most leaf pathogens of Eucalyptus originate in Australia and consequently with indigenous populations available, and it is possible to study the pathways of invasion. Teratosphaeria suttonii is a commonly occurring leaf pathogen of Eucalyptus species, naturally distributed in tropical and subtropical regions of eastern Australia where it is regarded as a minor pathogen infecting older leaves; however, repeated infections, especially in exotic plantations, can result in severe defoliation and tree deaths. Nine polymorphic microsatellite markers were used to assess the genetic structure of 11 populations of T. suttonii of which four where from within its native range in eastern Australia and the remaining seven from exotic Eucalyptus plantations. Indigenous populations exhibited high allele and haplotype diversity, predominantly clonal reproduction, high population differentiation, and low gene flow. The diversity of the invasive populations varied widely, but in general, the younger the plantation industry in a country or region, the lower the diversity of T. suttonii. Historical gene flow was from Australia, and while self-recruitment was dominant in all populations, there was evidence for contemporary gene flow, with South Africa being the most common source and Uruguay the most common sink population. This points distinctly to human activities underlying long-distance spread of this pathogen, and it highlights lessons to be learned regarding quarantine.
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Affiliation(s)
- Matsepo Taole
- Department of Biology National University of Lesotho P. O. 180 Roma Lesotho ; Department of Genetics Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa
| | - Wubetu Bihon
- Department of Genetics Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa ; Agricultural Research Council Vegetable & Ornamental Plant Institute Pretoria South Africa
| | - Brenda D Wingfield
- Department of Genetics Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa ; School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
| | - Treena I Burgess
- Department of Genetics Forestry and Agriculture Biotechnology Institute (FABI) University of Pretoria Pretoria 0002 South Africa ; School of Veterinary and Life Sciences Murdoch University Murdoch WA 6150 Australia
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24
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Leduc A, Traoré YN, Boyer K, Magne M, Grygiel P, Juhasz CC, Boyer C, Guerin F, Wonni I, Ouedraogo L, Vernière C, Ravigné V, Pruvost O. Bridgehead invasion of a monomorphic plant pathogenic bacterium:Xanthomonas citripv. citri, an emerging citrus pathogen in Mali and Burkina Faso. Environ Microbiol 2015; 17:4429-42. [DOI: 10.1111/1462-2920.12876] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Affiliation(s)
- A. Leduc
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | | | - K. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - M. Magne
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - P. Grygiel
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. C. Juhasz
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - C. Boyer
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - F. Guerin
- UMR PVBMT; Université de la Réunion; 97410 Saint Pierre La Réunion France
| | - I. Wonni
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - L. Ouedraogo
- Institut de l'Environnement et de Recherches agricoles; 01 BP910 Bobo Dioulasso Burkina Faso
| | - C. Vernière
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
| | - V. Ravigné
- UMR BGPI; CIRAD; 34398 Montpellier France
| | - O. Pruvost
- UMR PVBMT; CIRAD; 97410 Saint Pierre La Réunion France
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25
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Short DPG, Gurung S, Gladieux P, Inderbitzin P, Atallah ZK, Nigro F, Li G, Benlioglu S, Subbarao KV. Globally invading populations of the fungal plant pathogen Verticillium dahliae are dominated by multiple divergent lineages. Environ Microbiol 2015; 17:2824-40. [PMID: 25630463 DOI: 10.1111/1462-2920.12789] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 11/28/2022]
Abstract
The spread of aggressive fungal pathogens into previously non-endemic regions is a major threat to plant health and food security. Analyses of the spatial and genetic structure of plant pathogens offer valuable insights into their origin, dispersal mechanisms and evolution, and have been useful to develop successful disease management strategies. Here, we elucidated the genetic diversity, population structure and demographic history of worldwide invasion of the ascomycete Verticillium dahliae, a soil-borne pathogen, using a global collection of 1100 isolates from multiple plant hosts and countries. Seven well-differentiated genetic clusters were revealed through discriminant analysis of principal components (DAPC), but no strong associations between these clusters and host/geographic origin of isolates were found. Analyses of clonal evolutionary relationships among multilocus genotypes with the eBURST algorithm and analyses of genetic distances revealed that genetic clusters represented several ancient evolutionary lineages with broad geographic distribution and wide host range. Comparison of different scenarios of demographic history using approximate Bayesian computations revealed the branching order among the different genetic clusters and lineages. The different lineages may represent incipient species, and this raises questions with respect to their evolutionary origin and the factors allowing their maintenance in the same areas and same hosts without evidence of admixture between them. Based on the above findings and the biology of V. dahliae, we conclude that anthropogenic movement has played an important role in spreading V. dahliae lineages. Our findings have implications for the development of management strategies such as quarantine measures and crop resistance breeding.
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Affiliation(s)
- Dylan P G Short
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Suraj Gurung
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Pierre Gladieux
- Ecologie Systematique Evolution, CNRS, Université Paris Sud, Orsay, F-91405, France
| | - Patrik Inderbitzin
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Zahi K Atallah
- Department of Advanced Technology, Hartnell College, Salinas, CA, 93905, USA
| | - Franco Nigro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Bari, 70126, Italy
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
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26
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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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27
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Stergiopoulos I, Cordovez V, Okmen B, Beenen HG, Kema GHJ, de Wit PJGM. Positive selection and intragenic recombination contribute to high allelic diversity in effector genes of Mycosphaerella fijiensis, causal agent of the black leaf streak disease of banana. MOLECULAR PLANT PATHOLOGY 2014; 15:447-60. [PMID: 24245940 PMCID: PMC6638713 DOI: 10.1111/mpp.12104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Previously, we have determined the nonhost-mediated recognition of the MfAvr4 and MfEcp2 effector proteins from the banana pathogen Mycosphaerella fijiensis in tomato, by the cognate Cf-4 and Cf-Ecp2 resistance proteins, respectively. These two resistance proteins could thus mediate resistance against M. fijiensis if genetically transformed into banana (Musa spp.). However, disease resistance controlled by single dominant genes can be overcome by mutated effector alleles, whose products are not recognized by the cognate resistance proteins. Here, we surveyed the allelic variation within the MfAvr4, MfEcp2, MfEcp2-2 and MfEcp2-3 effector genes of M. fijiensis in a global population of the pathogen, and assayed its impact on recognition by the tomato Cf-4 and Cf-Ecp2 resistance proteins, respectively. We identified a large number of polymorphisms that could reflect a co-evolutionary arms race between host and pathogen. The analysis of nucleotide substitution patterns suggests that both positive selection and intragenic recombination have shaped the evolution of M. fijiensis effectors. Clear differences in allelic diversity were observed between strains originating from South-East Asia relative to strains from other banana-producing continents, consistent with the hypothesis that M. fijiensis originated in the Asian-Pacific region. Furthermore, transient co-expression of the MfAvr4 effector alleles and the tomato Cf-4 resistance gene, as well as of MfEcp2, MfEcp2-2 and MfEcp2-3 and the putative Cf-Ecp2 resistance gene, indicated that effector alleles able to overcome these resistance genes are already present in natural populations of the pathogen, thus questioning the durability of resistance that can be provided by these genes in the field.
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Affiliation(s)
- Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, One Shields Avenue, Davis, CA, 95616-8751, USA; Laboratory of Phytopathology, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen, 6708PB, the Netherlands; Centre for BioSystems Genomics, PO Box 98, Wageningen, 6700 AB, the Netherlands
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Saleh D, Milazzo J, Adreit H, Fournier E, Tharreau D. South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus, Magnaporthe oryzae. THE NEW PHYTOLOGIST 2014; 201:1440-1456. [PMID: 24320224 PMCID: PMC4265293 DOI: 10.1111/nph.12627] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/23/2013] [Indexed: 05/11/2023]
Abstract
• Inferring invasion routes and identifying reservoirs of diversity of plant pathogens are essential in proposing new strategies for their control. Magnaporthe oryzae, the fungus responsible for rice blast disease, has invaded all rice growing areas. Virulent genotypes regularly (re)emerge, causing rapid resistance breakdowns. However, the world-wide genetic subdivision of M. oryzae populations on rice and its past history of invasion have never been elucidated. • In order to investigate the centers of diversity, origin and migration of M. oryzae on rice, we analyzed the genetic diversity of 55 populations from 15 countries. • Three genetic clusters were identified world-wide. Asia was the center of diversity and the origin of most migrations to other continents. In Asia, two centers of diversity were revealed in the Himalayan foothills: South China-Laos-North Thailand, and western Nepal. Sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all M. oryzae populations on rice. • Our results suggest a scenario of early evolution of M. oryzae on rice that matches the past history of rice domestication. This study confirms that crop domestication may have considerable influence on the pestification process of natural enemies.
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Affiliation(s)
- Dounia Saleh
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
- INRA, UMR BGPITA A54/K, F 34398, Montpellier, France
| | | | - Henri Adreit
- CIRAD, UMR BGPITA A54/K, F 34398, Montpellier, France
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Vernière C, Bui Thi Ngoc L, Jarne P, Ravigné V, Guérin F, Gagnevin L, Le Mai N, Chau NM, Pruvost O. Highly polymorphic markers reveal the establishment of an invasive lineage of the citrus bacterial pathogen Xanthomonas citri pv. citri in its area of origin. Environ Microbiol 2014; 16:2226-37. [PMID: 24373118 DOI: 10.1111/1462-2920.12369] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/13/2013] [Indexed: 11/28/2022]
Abstract
Investigating the population biology of plant pathogens in their native areas is essential to understand the factors that shape their population structure and favour their spread. Monomorphic pathogens dispatch extremely low genetic diversity in invaded areas, and native areas constitute a major reservoir for future emerging strains. One of these, the gammaproteobacterium Xanthomonas citri pv. citri, causes Asiatic canker and is a considerable threat to citrus worldwide. We studied its population genetic structure by genotyping 555 strains from 12 Vietnam provinces at 14 tandem repeat loci and insertion sequences. Discriminant analysis of principal components identified six clusters. Five of them were composed of endemic strains distributed heterogeneously across sampled provinces. A sixth cluster, VN6, displayed a much lower diversity and a clonal expansion structure, suggesting recent epidemic spread. No differences in aggressiveness on citrus or resistance to bactericides were detected between VN6 and other strains. VN6 likely represents a case of bioinvasion following introduction in a native area likely through contaminated plant propagative material. Highly polymorphic markers are useful for revealing migration patterns of recently introduced populations of a monomorphic bacterial plant pathogen.
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de Queiroz CB, Santana MF, da Silva GF, Mizubuti ESG, de Araújo EF, de Queiroz MV. Use of the IRAP marker to study genetic variability in Pseudocercospora fijiensis populations. Curr Microbiol 2013; 68:358-64. [PMID: 24190756 DOI: 10.1007/s00284-013-0454-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 08/05/2013] [Indexed: 11/25/2022]
Abstract
Pseudocercospora fijiensis is the etiological agent of black Sigatoka, which is currently considered as one of the most destructive banana diseases in all locations where it occurs. It is estimated that a large portion of the P. fijiensis genome consists of transposable elements, which allows researchers to use transposon-based molecular markers in the analysis of genetic variability in populations of this pathogen. In this context, the inter-retrotransposon-amplified polymorphism (IRAP) was used to study the genetic variability in P. fijiensis populations from different hosts and different geographical origins in Brazil. A total of 22 loci were amplified and 77.3 % showed a polymorphism. Cluster analysis revealed two major groups in Brazil. The observed genetic diversity (H E) was 0.22, and through molecular analysis of variance, it was determined that the greatest genetic variability occurs within populations. The discriminant analysis of principal components revealed no structuring related to the geographical origin of culture of the host. The IRAP-based marker system is a suitable tool for the study of genetic variability in P. fijiensis.
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31
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The effect of mating system on invasiveness: some genetic load may be advantageous when invading new environments. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0544-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Gaskin JF, Schwarzländer M, Kinter CL, Smith JF, Novak SJ. Propagule pressure, genetic structure, and geographic origins of Chondrilla juncea (Asteraceae): an apomictic invader on three continents. AMERICAN JOURNAL OF BOTANY 2013; 100:1871-82. [PMID: 24018855 DOI: 10.3732/ajb.1200621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
PREMISE OF THE STUDY Assessing propagule pressure and geographic origins of invasive species provides insight into the invasion process. Rush skeletonweed (Chondrilla juncea; Asteraceae) is an apomictic, perennial plant that is invasive in Australia, South America (Argentina), and North America (Canada and the United States). This study comprehensively compares propagule pressure and geographic structure of genotypes to improve our understanding of a clonal invasion and enhance management strategies. • METHODS We analyzed 1056 native range plants from Eurasia and 1156 plants from three invaded continents using amplified fragment length polymorphism (AFLP) techniques. We used measures of diversity (Simpson's D) and evenness (E), analysis of molecular variance, and Mantel tests to compare invasions, and genotype similarity to determine origins of invasive genotypes. • KEY RESULTS We found 682 unique genotypes in the native range, but only 13 in the invaded regions. Each invaded region contained distinct AFLP genotypes, suggesting independent introduction events, probably with different geographic origins. Relatively low propagule pressure was associated with each introduction around the globe, but levels of among-population variation differed. We found exact AFLP genotype matches between the native and invaded ranges for five of the 13 invasive genotypes. • CONCLUSIONS Invasion dynamics can vary across invaded ranges within a species. Intensive sampling for molecular analyses can provide insight for understanding intraspecific invasion dynamics, which can hold significance for the management of plant species, especially by finding origins and distributions of invasive genotypes for classical biological control efforts.
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Affiliation(s)
- John F Gaskin
- USDA Agricultural Research Service, Northern Plains Agricultural Research Laboratory, 1500 N. Central Ave., Sidney, Montana 59270, USA
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Fontaine MC, Austerlitz F, Giraud T, Labbé F, Papura D, Richard-Cervera S, Delmotte F. Genetic signature of a range expansion and leap-frog event after the recent invasion of Europe by the grapevine downy mildew pathogenPlasmopara viticola. Mol Ecol 2013; 22:2771-86. [DOI: 10.1111/mec.12293] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 02/11/2013] [Accepted: 02/14/2013] [Indexed: 01/26/2023]
Affiliation(s)
- Michael C. Fontaine
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Univ Paris Diderot; Sorbonne Paris Cité F-75231 Paris Cedex 5 France
| | - Fréderic Austerlitz
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
- Eco-Anthropologie et Ethnobiologie; UMR 7206 CNRS; MNHN; Univ Paris Diderot; Sorbonne Paris Cité F-75231 Paris Cedex 5 France
| | - Tatiana Giraud
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
| | - Frédéric Labbé
- Ecologie, Systématique et Evolution; UMR 8079 Université Paris Sud Laboratoire Ecologie; Systematique et Evolution; UMR8079 Orsay Cedex F-91405 France
| | - Daciana Papura
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
| | - Sylvie Richard-Cervera
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
| | - François Delmotte
- INRA; UMR1065 Santé et Agroécologie du Vignoble; ISVV; F-33883 Villenave d'Ornon Cedex France
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Morin L, Gomez DR, Evans KJ, Neill TM, Mahaffee WF, Linde CC. Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance. Biol Invasions 2013. [DOI: 10.1007/s10530-013-0413-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Rieux A, De Lapeyre De Bellaire L, Zapater MF, Ravigne V, Carlier J. Recent range expansion and agricultural landscape heterogeneity have only minimal effect on the spatial genetic structure of the plant pathogenic fungus Mycosphaerella fijiensis. Heredity (Edinb) 2012; 110:29-38. [PMID: 22990310 DOI: 10.1038/hdy.2012.55] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Understanding how geographical and environmental features affect genetic variation at both the population and individual levels is crucial in biology, especially in the case of pathogens. However, distinguishing between these factors and the effects of historical range expansion on spatial genetic structure remains challenging. In the present study, we investigated the case of Mycosphaerella fijiensis-a plant pathogenic fungus that has recently colonized an agricultural landscape characterized by the presence of potential barriers to gene flow, including several commercial plantations in which disease control practises such as the use of fungicides are applied frequently, and low host density areas. We first genotyped 300 isolates sampled at a global scale on untreated plants in two dimensions over a 50 × 80-km area. Using two different clustering algorithms, no genetic structure was detected in the studied area, suggesting expansion of large populations and/or no influence of potential barriers. Second, we investigated the potential effect of disease control practises on M. fijiensis diversity by comparing populations sampled in commercial vs food-crop plantations. At this local scale, we detected significantly higher allelic richness inside commercial plantations compared with the surrounding food-crop plantation populations. Analysis of molecular variance indicated that 99% of the total genetic variance occurred within populations. We discuss the suggestion that high population size and/or high migration rate between populations might be responsible for the absence of any effect of disease control practises on genetic diversity and differentiation.
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Affiliation(s)
- A Rieux
- CIRAD, UMR BGPI, TA A-54K, Campus International de Baillarguet, Montpellier Cedex 5, France
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