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Runno-Paurson E, Agho CA, Nassar H, Hansen M, Leitaru K, Hallikma T, Cooke DEL, Niinemets Ü. The Variability of Phytophthora infestans Isolates Collected from Estonian Islands in the Baltic Sea. PLANT DISEASE 2024; 108:1645-1658. [PMID: 38127634 DOI: 10.1094/pdis-07-23-1399-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Knowledge of a pathogen's genetic variability and population structure is of great importance to effective disease management. In this study, 193 isolates of Phytophthora infestans collected from three Estonian islands were characterized over 3 years using simple sequence repeat (SSR) marker data complemented by information on their mating type and resistance to metalaxyl. In combination with SSR marker data from samples in the neighboring Pskov region of Northwest Russia, the impact of regional and landscape structure on the level of genetic exchange was also examined. Among the 111 P. infestans isolates from Estonian islands, 49 alleles were detected among 12 SSR loci, and 59 SSR multilocus genotypes were found, of which 64% were unique. The genetic variation was higher among years than that among islands, as revealed by the analysis of molecular variance. The frequency of metalaxyl-resistant isolates increased from 9% in 2012 to 30% in 2014, and metalaxyl resistance was most frequent among A1 isolates. The test for isolation by distance among the studied regions was not significant, and coupled with the absence of genetic differentiation, the result revealed gene flow and the absence of local adaptation. The data are consistent with a sexual population in which diversity is driven by an annual germination of soilborne oospores. The absence of shared genotypes over the years has important implications when it comes to the management of diseases. Such population diversity can make it difficult to predict the nature of the outbreak in the coming year as the genetic makeup is different for each year.
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Affiliation(s)
- Eve Runno-Paurson
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Collins A Agho
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Helina Nassar
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Merili Hansen
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Kätlin Leitaru
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Tiit Hallikma
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | | | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
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2
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Shaw CL, Bilich R, Duffy MA. A common multi-host parasite shows genetic structuring at the host species and population levels. Parasitology 2024; 151:557-566. [PMID: 38616414 DOI: 10.1017/s0031182024000428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Although individual parasite species commonly infect many populations across physical space as well as multiple host species, the extent to which parasites traverse physical and phylogenetic distances is unclear. Population genetic analyses of parasite populations can reveal how parasites move across space or between host species, including helping assess whether a parasite is more likely to infect a different host species in the same location or the same host species in a different location. Identifying these transmission barriers could be exploited for effective disease control. Here, we analysed population genetic structuring of the parasite Pasteuria ramosa in daphniid host species from different lakes. Outbreaks occurred most often in the common host species Daphnia dentifera and Daphnia retrocurva. The genetic distance between parasite samples tended to be smaller when samples were collected from the same lake, the same host species and closer in time. Within lakes, the parasite showed structure by host species and sampling date; within a host species, the parasite showed structure by lake and sampling date. However, despite this structuring, we found the same parasite genotype infecting closely related host species, and we sometimes found the same genotype in nearby lakes. Thus, P. ramosa experiences challenges infecting different host species and moving between populations, but doing so is possible. In addition, the structuring by sampling date indicates potential adaptation to or coevolution with host populations and supports prior findings that parasite population structure is dynamic during outbreaks.
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Affiliation(s)
- Clara L Shaw
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Rebecca Bilich
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Meghan A Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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3
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Sulaiman HY, Runno-Paurson E, Niinemets Ü. The same boat, different storm: stress volatile emissions in response to biotrophic fungal infections in primary and alternate hosts. PLANT SIGNALING & BEHAVIOR 2023; 18:2217030. [PMID: 37232366 PMCID: PMC10730184 DOI: 10.1080/15592324.2023.2217030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Rust infection results in stress volatile emissions, but due to the complexity of host-pathogen interaction and variations in innate defense and capacity to induce defense, biochemical responses can vary among host species. Fungal-dependent modifications in volatile emissions have been well documented in numerous host species, but how emission responses vary among host species is poorly understood. Our recent experiments demonstrated that the obligate biotrophic crown rust fungus (P. coronata) differently activated primary and secondary metabolic pathways in its primary host Avena sativa and alternate host Rhamnus frangula. In A. sativa, emissions of methyl jasmonate, short-chained lipoxygenase products, long-chained saturated fatty acid derivatives, mono- and sesquiterpenes, carotenoid breakdown products, and benzenoids were initially elicited in an infection severity-dependent manner, but the emissions decreased under severe infection and photosynthesis was almost completely inhibited. In R. frangula, infection resulted in low-level induction of stress volatile emissions, but surprisingly, in enhanced constitutive isoprene emissions, and even severely-infected leaves maintained a certain photosynthesis rate. Thus, the same pathogen elicited a much stronger response in the primary than in the alternate host. We argue that future work should focus on resolving mechanisms of different fungal tolerance and resilience among primary and secondary hosts.
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Affiliation(s)
- Hassan Yusuf Sulaiman
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Eve Runno-Paurson
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, Estonia
- Estonian Academy of Sciences, Tallinn, Estonia
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Boixel AL, Goyeau H, Berder J, Moinard J, Suffert F, Soubeyrand S, Sache I, Vidal T. A landscape-scale field survey demonstrates the role of wheat volunteers as a local and diversified source of leaf rust inoculum. Sci Rep 2023; 13:20411. [PMID: 37990120 PMCID: PMC10663564 DOI: 10.1038/s41598-023-47499-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/14/2023] [Indexed: 11/23/2023] Open
Abstract
Deploying disease-resistant cultivars is one of the most effective control strategies to manage crop diseases such as wheat leaf rust, caused by Puccinia triticina. After harvest, this biotrophic fungal pathogen can survive on wheat volunteers present at landscape scale and constitute a local source of primary inoculum for the next cropping season. In this study, we characterised the diversity of P. triticina populations surveyed on wheat volunteer seedlings for six consecutive years (2007-2012) at the landscape scale. A total of 642 leaf rust samples classified in 52 virulence profiles (pathotypes) were collected within a fixed 5-km radius. The pathotype composition (identity and abundance) of field-collected populations was analyzed according to the distance between the surveyed wheat plots and to the cultivars of origin of isolates. Our study emphasised the high diversity of P. triticina populations on wheat volunteers at the landscape scale. We observed an impact of cultivar of origin on pathogen population composition. Levels of population diversity differed between cultivars and their deployment in the study area. Our results suggest that wheat volunteers could provide a significant though highly variable contribution to the composition of primary inoculum and subsequent initiation of leaf rust epidemics.
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Affiliation(s)
- A-L Boixel
- Université Paris-Saclay, INRAE, UR BIOGER, 91123, Palaiseau, France
| | - H Goyeau
- Université Paris-Saclay, INRAE, UR BIOGER, 91123, Palaiseau, France
| | - J Berder
- Université Paris-Saclay, INRAE, UR BIOGER, 91123, Palaiseau, France
| | - J Moinard
- DRAAF Midi-Pyrénées, 31074, Toulouse, France
| | - F Suffert
- Université Paris-Saclay, INRAE, UR BIOGER, 91123, Palaiseau, France
| | | | - I Sache
- AgroParisTech, 91123, Palaiseau, France
| | - T Vidal
- Université Paris-Saclay, INRAE, UR BIOGER, 91123, Palaiseau, France.
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Susi H, Burdon JJ, Thrall PH, Nemri A, Barrett LG. Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini. PLoS Pathog 2020; 16:e1008731. [PMID: 32810177 PMCID: PMC7454959 DOI: 10.1371/journal.ppat.1008731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic. Melampsora lini is a rust fungus that infects native flax, Linum marginale in south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure of M. lini has been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region, M. lini lacks the capacity to reproduce sexually–we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation within M. lini populations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.
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Affiliation(s)
- Hanna Susi
- CSIRO Agriculture & Food, Canberra, Australia
- * E-mail:
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Sharma-Poudyal D, Bai Q, Wan A, Wang M, See D, Chen X. Molecular Characterization of International Collections of the Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici Reveals High Diversity and Intercontinental Migration. PHYTOPATHOLOGY 2020; 110:933-942. [PMID: 31895005 DOI: 10.1094/phyto-09-19-0355-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust), one of the most important wheat diseases worldwide. To understand the genetic variation of the pathogen in a global scale, 283 P. striiformis f. sp. tritici isolates collected from 16 countries in eight geographic regions were genotyped using 24 codominant simple sequence repeat markers. The overall collection had a high level of genetic diversity, and the diversity levels in the Asian populations were generally higher than those of the other regions. Heterozygosity of isolates ranged from 0 to 75%, with an average of 46%. Mean heterozygosity in individual countries ranged from 34 to 59%. A total of 265 multilocus genotypes (MLGs) were detected, which were classified into eight molecular groups. Some of the molecular groups were present in all geographic regions. Moreover, many isolates from different regions were found to be identical or very closely related MLGs. Analysis of molecular variance revealed high variation within countries and intermediate variation between countries, but it revealed low and insignificant variation among geographic regions. Pairwise comparisons of regional populations detected considerable effective migrants and only low to moderate levels of differentiation. The molecular genotypes had a moderate level of correlation with the virulence phenotypes, and some of the molecular/virulence groups contained isolates from different continents. The results indicate tremendous migrations of P. striiformis f. sp. tritici and warrant the development of management strategies considering the global pathogen population.
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Affiliation(s)
- Dipak Sharma-Poudyal
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Qing Bai
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Anmin Wan
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
| | - Deven See
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Pullman, WA 99164-6430
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Pullman, WA 99164-6430
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7
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Burdon JJ. Lessons from a Life in Time and Space. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:1-13. [PMID: 31082308 DOI: 10.1146/annurev-phyto-082718-095938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A research career investigating epidemiological and evolutionary patterns in both natural and crop host-pathogen systems emphasizes the need for flexibility in thinking and a willingness to adopt ideas from a wide diversity of subdisciplines. Here, I reflect on the pivotal issues, research areas, and interactions, including the role of science management, that shaped my career in the hope of demonstrating that career paths and collaborations in science can be as diverse and unpredictable as the natural world in which we study our organisms of choice.
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Laine AL, Barrès B, Numminen E, Siren JP. Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation. eLife 2019; 8:47091. [PMID: 31210640 PMCID: PMC6667214 DOI: 10.7554/elife.47091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/18/2019] [Indexed: 11/17/2022] Open
Abstract
Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens. The existence of sex – broadly defined as the coming together of genes from different individuals – is one of the big evolutionary puzzles. Reproduction allows an organism to pass on its genes to future generations. However, while asexual and self-fertilizing individuals transmit all of their genes to their offspring, individuals that reproduce through sex transmit only half of their genome. This is considered the cost of sex. Many pathogens reproduce through sex, despite often also being able to reproduce asexually or by self-fertilization. Typically a pre-requisite of sex in pathogens is for at least two different strains to infect the same host. Aside from this limitation, little is known about when, where and why pathogens have sex. It has been tricky to study due to the microscopic size of pathogens and the difficulties of identifying different sexes. Moreover, sexual reproduction may be triggered by environmental cues that are difficult to mimic under controlled experimental conditions. Are there any benefits associated with pathogen sex? To find out, Laine et al. analyzed data collected over the course of four years from thousands of populations of a powdery mildew fungus that infected plants across the Åland islands. This revealed that the opportunities for pathogen sex vary in different locations. Areas where multiple strains of the fungus commonly infect the same plants result in hotspots of new genetic diversity. These mixed populations are also more likely to survive winter. This demonstrates the potential for pathogen sexual reproduction to provide an ecological benefit. Identifying areas and populations where pathogens have sex can help to identify when and where new strains are most likely to emerge. In the future, studies that use similar methods to Laine et al. could help to predict where infections and diseases are highly likely to arise.
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Affiliation(s)
- Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Switzerland
| | - Benoit Barrès
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Elina Numminen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Jukka P Siren
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology, Department of Computer Science, Aalto University, Espoo, Finland
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Anderson C, Khan MA, Catanzariti AM, Jack CA, Nemri A, Lawrence GJ, Upadhyaya NM, Hardham AR, Ellis JG, Dodds PN, Jones DA. Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini. BMC Genomics 2016; 17:667. [PMID: 27550217 PMCID: PMC4994203 DOI: 10.1186/s12864-016-3011-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/11/2016] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field. RESULTS To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein. CONCLUSIONS The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.
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Affiliation(s)
- Claire Anderson
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Muhammad Adil Khan
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
- Current address: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 Australia
| | - Ann-Maree Catanzariti
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | - Cameron A. Jack
- ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT 2601 Australia
| | - Adnane Nemri
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
- Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574 Germany
| | | | | | - Adrienne R. Hardham
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
| | | | - Peter N. Dodds
- CSIRO Agriculture, GPO Box 1600, Canberra, ACT 2601 Australia
| | - David A. Jones
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT 2601 Australia
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Thrall PH, Barrett LG, Dodds PN, Burdon JJ. Epidemiological and Evolutionary Outcomes in Gene-for-Gene and Matching Allele Models. FRONTIERS IN PLANT SCIENCE 2016; 6:1084. [PMID: 26779200 PMCID: PMC4703789 DOI: 10.3389/fpls.2015.01084] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 11/19/2015] [Indexed: 05/30/2023]
Abstract
Gene-for-gene (GFG) and matching-allele (MA) models are qualitatively different paradigms for describing the outcome of genetic interactions between hosts and pathogens. The GFG paradigm was largely built on the foundations of Flor's early work on the flax-flax rust interaction and is based on the concept of genetic recognition leading to incompatible disease outcomes, typical of host immune recognition. In contrast, the MA model is based on the assumption that genetic recognition leads to compatible interactions, which can result when pathogens require specific host factors to cause infection. Results from classical MA and GFG models have led to important predictions regarding various coevolutionary phenomena, including the role of fitness costs associated with resistance and infectivity, the distribution of resistance genes in wild populations, patterns of local adaptation and the evolution and maintenance of sexual reproduction. Empirical evidence (which we review briefly here), particularly from recent molecular advances in understanding of the mechanisms that determine the outcome of host-pathogen encounters, suggests considerable variation in specific details of the functioning of interactions between hosts and pathogens, which may contain elements of both models. In this regard, GFG and MA scenarios likely represent endpoints of a continuum of potentially more complex interactions that occur in nature. Increasingly, this has been recognized in theoretical studies of coevolutionary processes in plant host-pathogen and animal host-parasite associations (e.g., departures from strict GFG/MA assumptions, diploid genetics, multi-step infection processes). However, few studies have explored how different genetic assumptions about host resistance and pathogen infectivity might impact on disease epidemiology or pathogen persistence within and among populations. Here, we use spatially explicit simulations of the basic MA and GFG scenarios to highlight qualitative differences between these scenarios with regard to patterns of disease and impacts on host demography. Given that such impacts drive evolutionary trajectories, future theoretical advances that aim to capture more complex genetic scenarios should explicitly address the interaction between epidemiology and different models of host-pathogen interaction genetics.
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11
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Gill US, Lee S, Mysore KS. Host versus nonhost resistance: distinct wars with similar arsenals. PHYTOPATHOLOGY 2015; 105:580-7. [PMID: 25626072 DOI: 10.1094/phyto-11-14-0298-rvw] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Plants face several challenges by bacterial, fungal, oomycete, and viral pathogens during their life cycle. In order to defend against these biotic stresses, plants possess a dynamic, innate, natural immune system that efficiently detects potential pathogens and initiates a resistance response in the form of basal resistance and/or resistance (R)-gene-mediated defense, which is often associated with a hypersensitive response. Depending upon the nature of plant-pathogen interactions, plants generally have two main defense mechanisms, host resistance and nonhost resistance. Host resistance is generally controlled by single R genes and less durable compared with nonhost resistance. In contrast, nonhost resistance is believed to be a multi-gene trait and more durable. In this review, we describe the mechanisms of host and nonhost resistance against fungal and bacterial plant pathogens. In addition, we also attempt to compare host and nonhost resistance responses to identify similarities and differences, and their practical applications in crop improvement.
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Affiliation(s)
- Upinder S Gill
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Seonghee Lee
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Kirankumar S Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401
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12
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Laine AL, Burdon JJ, Nemri A, Thrall PH. Host ecotype generates evolutionary and epidemiological divergence across a pathogen metapopulation. Proc Biol Sci 2015; 281:rspb.2014.0522. [PMID: 24870042 DOI: 10.1098/rspb.2014.0522] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The extent and speed at which pathogens adapt to host resistance varies considerably. This presents a challenge for predicting when--and where--pathogen evolution may occur. While gene flow and spatially heterogeneous environments are recognized to be critical for the evolutionary potential of pathogen populations, we lack an understanding of how the two jointly shape coevolutionary trajectories between hosts and pathogens. The rust pathogen Melampsora lini infects two ecotypes of its host plant Linum marginale that occur in close proximity yet in distinct populations and habitats. In this study, we found that within-population epidemics were different between the two habitats. We then tested for pathogen local adaptation at host population and ecotype level in a reciprocal inoculation study. Even after controlling for the effect of spatial structure on infection outcome, we found strong evidence of pathogen adaptation at the host ecotype level. Moreover, sequence analysis of two pathogen infectivity loci revealed strong genetic differentiation by host ecotype but not by distance. Hence, environmental variation can be a key determinant of pathogen population genetic structure and coevolutionary dynamics and can generate strong asymmetry in infection risks through space.
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Affiliation(s)
- Anna-Liisa Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, PO Box 65, Helsinki 00014, Finland
| | - Jeremy J Burdon
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Adnane Nemri
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - Peter H Thrall
- CSIRO Plant Industry, GPO Box 1600, Canberra, Australian Capital Territory 2601, Australia
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Barrett LG, Encinas-Viso F, Burdon JJ, Thrall PH. Specialization for resistance in wild host-pathogen interaction networks. FRONTIERS IN PLANT SCIENCE 2015; 6:761. [PMID: 26442074 PMCID: PMC4585140 DOI: 10.3389/fpls.2015.00761] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 09/04/2015] [Indexed: 05/05/2023]
Abstract
Properties encompassed by host-pathogen interaction networks have potential to give valuable insight into the evolution of specialization and coevolutionary dynamics in host-pathogen interactions. However, network approaches have been rarely utilized in previous studies of host and pathogen phenotypic variation. Here we applied quantitative analyses to eight networks derived from spatially and temporally segregated host (Linum marginale) and pathogen (Melampsora lini) populations. First, we found that resistance strategies are highly variable within and among networks, corresponding to a spectrum of specialist and generalist resistance types being maintained within all networks. At the individual level, specialization was strongly linked to partial resistance, such that partial resistance was effective against a greater number of pathogens compared to full resistance. Second, we found that all networks were significantly nested. There was little support for the hypothesis that temporal evolutionary dynamics may lead to the development of nestedness in host-pathogen infection networks. Rather, the common patterns observed in terms of nestedness suggests a universal driver (or multiple drivers) that may be independent of spatial and temporal structure. Third, we found that resistance networks were significantly modular in two spatial networks, clearly reflecting spatial and ecological structure within one of the networks. We conclude that (1) overall patterns of specialization in the networks we studied mirror evolutionary trade-offs with the strength of resistance; (2) that specific network architecture can emerge under different evolutionary scenarios; and (3) network approaches offer great utility as a tool for probing the evolutionary and ecological genetics of host-pathogen interactions.
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Affiliation(s)
- Luke G. Barrett
- Commonwealth Scientific and Industrial Research Organization Agriculture FlagshipCanberra, ACT, Australia
- *Correspondence: Luke G. Barrett, Commonwealth Scientific and Industrial Research Organization Agriculture Flagship, GPO Box 1600, Canberra ACT 2601, Australia
| | - Francisco Encinas-Viso
- Centre for Australian National Biodiversity Research, Commonwealth Scientific and Industrial Research OrganizationCanberra, ACT, Australia
| | - Jeremy J. Burdon
- Commonwealth Scientific and Industrial Research Organization Agriculture FlagshipCanberra, ACT, Australia
| | - Peter H. Thrall
- Commonwealth Scientific and Industrial Research Organization Agriculture FlagshipCanberra, ACT, Australia
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Stefansson TS, McDonald BA, Willi Y. The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus. PLoS One 2014; 9:e112523. [PMID: 25383967 PMCID: PMC4226542 DOI: 10.1371/journal.pone.0112523] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/06/2014] [Indexed: 11/26/2022] Open
Abstract
Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by conducting a QST/FST analysis using agricultural populations of the barley pathogen Rhynchosporium commune. Population divergence for eight quantitative traits (QST) was compared with divergence at eight neutral microsatellite loci (FST) for 126 pathogen strains originating from nine globally distributed field populations to infer the effects of genetic drift and types of selection acting on each trait. Our analyses indicated that five of the eight traits had QST values significantly lower than FST, consistent with stabilizing selection, whereas one trait, growth under heat stress (22°C), showed evidence of diversifying selection and local adaptation (QST>FST). Estimates of heritability were high for all traits (means ranging between 0.55–0.84), and average heritability across traits was negatively correlated with microsatellite gene diversity. Some trait pairs were genetically correlated and there was significant evidence for a trade-off between spore size and spore number, and between melanization and growth under benign temperature. Our findings indicate that many ecologically and agriculturally important traits are under stabilizing selection in R. commune and that high within-population genetic variation is maintained for these traits.
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Affiliation(s)
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Yvonne Willi
- Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
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15
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Tack AJM, Thrall PH, Barrett LG, Burdon JJ, Laine AL. Variation in infectivity and aggressiveness in space and time in wild host-pathogen systems: causes and consequences. J Evol Biol 2012; 25:1918-1936. [PMID: 22905782 DOI: 10.1111/j.1420-9101.2012.02588.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 07/02/2012] [Accepted: 07/05/2012] [Indexed: 12/18/2022]
Abstract
Variation in host resistance and in the ability of pathogens to infect and grow (i.e. pathogenicity) is important as it provides the raw material for antagonistic (co)evolution and therefore underlies risks of disease spread, disease evolution and host shifts. Moreover, the distribution of this variation in space and time may inform us about the mode of coevolutionary selection (arms race vs. fluctuating selection dynamics) and the relative roles of G × G interactions, gene flow, selection and genetic drift in shaping coevolutionary processes. Although variation in host resistance has recently been reviewed, little is known about overall patterns in the frequency and scale of variation in pathogenicity, particularly in natural systems. Using 48 studies from 30 distinct host-pathogen systems, this review demonstrates that variation in pathogenicity is ubiquitous across multiple spatial and temporal scales. Quantitative analysis of a subset of extensively studied plant-pathogen systems shows that the magnitude of within-population variation in pathogenicity is large relative to among-population variation and that the distribution of pathogenicity partly mirrors the distribution of host resistance. At least part of the variation in pathogenicity found at a given spatial scale is adaptive, as evidenced by studies that have examined local adaptation at scales ranging from single hosts through metapopulations to entire continents and - to a lesser extent - by comparisons of pathogenicity with neutral genetic variation. Together, these results support coevolutionary selection through fluctuating selection dynamics. We end by outlining several promising directions for future research.
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Affiliation(s)
- A J M Tack
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - P H Thrall
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - L G Barrett
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - J J Burdon
- CSIRO-Plant Industry, Canberra, ACT, Australia
| | - A-L Laine
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
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Nemri A, Barrett LG, Laine AL, Burdon JJ, Thrall PH. Population processes at multiple spatial scales maintain diversity and adaptation in the Linum marginale--Melampsora lini association. PLoS One 2012; 7:e41366. [PMID: 22859978 PMCID: PMC3409196 DOI: 10.1371/journal.pone.0041366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 06/20/2012] [Indexed: 11/24/2022] Open
Abstract
Host-pathogen coevolution is a major driver of species diversity, with an essential role in the generation and maintenance of genetic variation in host resistance and pathogen infectivity. Little is known about how resistance and infectivity are structured across multiple geographic scales and what eco-evolutionary processes drive these patterns. Across southern Australia, the wild flax Linum marginale is frequently attacked by its rust fungus Melampsora lini. Here, we compare the genetic and phenotypic structure of resistance and infectivity among population pairs from two regions where environmental differences associate with specific life histories and mating systems. We find that both host and pathogen populations are genetically distinct between these regions. The region with outcrossing hosts and pathogens that go through asexual cycles followed by sexual reproduction showed greater diversity of resistance and infectivity phenotypes, higher levels of resistance and less clumped within-population spatial distribution of resistance. However, in the region where asexual pathogens infect selfing hosts, pathogens were more infective and better adapted to sympatric hosts. Our findings largely agree with expectations based on the distinctly different host mating systems in the two regions, with a likely advantage for hosts undergoing recombination. For the pathogen in this system, sexual reproduction may primarily be a survival mechanism in the region where it is observed. While it appears to potentially have adverse effects on local adaptation in the short term, it may be necessary for longer-term coevolution with outcrossing hosts.
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Affiliation(s)
- Adnane Nemri
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Luke G. Barrett
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Anna-Liisa Laine
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
- Metapopulation Research Group, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jeremy J. Burdon
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
| | - Peter H. Thrall
- CSIRO Plant Industry, Canberra, Australian Capital Territory, Australia
- * E-mail:
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Thrall PH, Laine AL, Ravensdale M, Nemri A, Dodds PN, Barrett LG, Burdon JJ. Rapid genetic change underpins antagonistic coevolution in a natural host-pathogen metapopulation. Ecol Lett 2012; 15:425-35. [PMID: 22372578 PMCID: PMC3319837 DOI: 10.1111/j.1461-0248.2012.01749.x] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antagonistic coevolution is a critical force driving the evolution of diversity, yet the selective processes underpinning reciprocal adaptive changes in nature are not well understood. Local adaptation studies demonstrate partner impacts on fitness and adaptive change, but do not directly expose genetic processes predicted by theory. Specifically, we have little knowledge of the relative importance of fluctuating selection vs. arms-race dynamics in maintaining polymorphism in natural systems where metapopulation processes predominate. We conducted cross-year epidemiological, infection and genetic studies of multiple wild host and pathogen populations in the Linum-Melampsora association. We observed asynchronous phenotypic fluctuations in resistance and infectivity among demes. Importantly, changes in allelic frequencies at pathogen infectivity loci, and in host recognition of these genetic variants, correlated with disease prevalence during natural epidemics. These data strongly support reciprocal coevolution maintaining balanced resistance and infectivity polymorphisms, and highlight the importance of characterising spatial and temporal dynamics in antagonistic interactions.
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Affiliation(s)
- Peter H. Thrall
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Anna-Liisa Laine
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
- Metapopulation Research Group, Department of Biosciences, PO Box 65, FI-00014, University of Helsinki, Finland
| | - Michael Ravensdale
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Adnane Nemri
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Peter N. Dodds
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Luke G. Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
| | - Jeremy J. Burdon
- CSIRO Plant Industry, GPO Box 1600, Canberra ACT 2601, Australia
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Abstract
Rust fungi are cosmopolitan in distribution and parasitize a wide range of plants, including economically important crop species such as wheat. Detailed regional, national, and continental surveys of pathogenic variability in wheat-attacking rust pathogens over periods of up to 90 years have shown that in the absence of sexual recombination, genetic diversity is generated by periodic introduction of exotic isolates, single-step mutation, and somatic hybridization. Laboratory studies have provided evidence for somatic hybridization between many rust species and formae speciales, and there is evidence for the process in nature within and between rust species on Linum, poplar, Senecio, wheat, and several grass species. Although the mechanisms involved in somatic hybridization are not well understood, they are thought to involve the fusion of dikaryotic vegetative hyphae, nuclear exchange, and possibly exchange of whole chromosomes between nuclei or parasexuality via the fusion of the two haploid nuclei, followed by mitotic crossing over and vegetative haploidization. In three cases, hybrid isolates rendered resistant plant genotypes susceptible because of new combinations of virulence. Implications for resistance breeding and future prospects in understanding the process are discussed.
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Affiliation(s)
- Robert F Park
- Plant Breeding Institute, The University of Sydney, Sydney, New South Wales 2570, Australia.
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Sandrock C, Schirrmeister BE, Vorburger C. Evolution of reproductive mode variation and host associations in a sexual-asexual complex of aphid parasitoids. BMC Evol Biol 2011; 11:348. [PMID: 22132834 PMCID: PMC3259107 DOI: 10.1186/1471-2148-11-348] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022] Open
Abstract
Background The Lysiphlebus fabarum group is a taxonomically poorly resolved complex of aphid parasitoids, presently split into three described species that comprise sexual (arrhenotokous) and asexual (thelytokous) lineages of unknown relationship. Specifically, it is unclear how asexuals evolved from sexuals in this system, to what extent reproductive modes are still connected by genetic exchange, how much the complex is structured by geography or by host-associated differentiation, and whether species designations are valid. Using a combination of population genetic and phylogenetic approaches, we addressed these issues in a comprehensive sample of parasitoid wasps from across Europe. Results Asexual reproduction predominated in parasitoids of the L. fabarum group, with asexual populations exhibiting high genotypic diversity. Sexual populations were only common in southern France; elsewhere sexual reproduction was restricted to specific aphid hosts. Although reproductive modes were aggregated on the mitochondrial genealogy and significantly differentiated at nuclear microsatellite loci, there was clear evidence for genetic exchange, especially on hosts attacked by sexual and asexual parasitoids. The microsatellite data further revealed that parasitoids collected from certain host aphids were significantly differentiated, yet the mitochondrial sequence variation across the entire L. fabarum group did not exceed 1.32% and exhibited a very shallow topology. Morphological characters used for delineation of described species were found to be phylogenetically non-conservative. Conclusions Our results suggest that the sexual-asexual L. fabarum group represents a young complex of lineages with incomplete isolation between reproductive modes. We propose three mechanisms of genetic exchange that may jointly explain the high genotypic diversity observed in asexual parasitoids: (i) the formation of new asexual lineages via 'contagious parthenogenesis', (ii) introgression from sexual lineages through matings between sexual males and thelytokous females, and (iii) 'cryptic sex' within asexuals, mediated by rare males that thelytokous lines are known to produce spontaneously. The partially strong differentiation among wasps collected from different aphids suggests that host specialization can evolve readily in these parasitoids. Finally, we conclude that in the light of our data, the current taxonomic division of the L. fabarum group into three species cannot be upheld.
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Affiliation(s)
- Christoph Sandrock
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
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20
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Arthofer W, Schlick-Steiner BC, Steiner FM. optiFLP: software for automated optimization of amplified fragment length polymorphism scoring parameters. Mol Ecol Resour 2011; 11:1113-8. [PMID: 21707959 DOI: 10.1111/j.1755-0998.2011.03043.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amplified fragment length polymorphism (AFLP), a widely used method for DNA fingerprinting, has shifted from polyacrylamide gel to capillary electrophoresis over the last years. Currently, most AFLP data are generated in a computer-readable format, and several programs are available that automatically score raw data into binary profiles. Good scoring parameters are the key to good AFLP profiles. optiFLP is the first open source program for automatic optimization of AFLP scoring parameters. It searches parameter space to maximize the contrast among groups of AFLP profiles, with the allocation of profiles to groups in either a supervised or an unsupervised mode. The software produces output files ready for use in a range of downstream applications.
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Affiliation(s)
- W Arthofer
- Molecular Ecology Group, Institute of Ecology, University of Innsbruck, Technikerstrasse 25, 6020 Innsbruck, Austria.
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21
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Ravensdale M, Nemri A, Thrall PH, Ellis JG, Dodds PN. Co-evolutionary interactions between host resistance and pathogen effector genes in flax rust disease. MOLECULAR PLANT PATHOLOGY 2011; 12:93-102. [PMID: 21118351 PMCID: PMC2999005 DOI: 10.1111/j.1364-3703.2010.00657.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Plant-pathogen co-evolutionary selection processes are continuous, complex and occur across many spatial and temporal scales. Comprehensive studies of the flax-flax rust pathosystem have led to the postulation of the gene-for-gene model, a genetic paradigm describing recognition events between host disease resistance proteins and pathogen effector proteins. The identification of directly interacting fungal effector proteins and plant disease resistance proteins in this pathosystem has facilitated the study of both the physical nature of these interactions and the evolutionary forces that have resulted in a molecular arms race between these organisms. The flax-flax rust pathosystem has also been detailed on the scale of interacting populations, and the integration of molecular- and population-scale datasets represents a unique opportunity to further our understanding of many poorly understood facets of host-pathogen dynamics. In this article, we discuss recent developments and insights in the flax-flax rust pathosystem and their implications for both long-term co-evolutionary dynamics in natural settings, as well as short-term co-evolutionary dynamics in agro-ecosystems.
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22
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Anderson JP, Gleason CA, Foley RC, Thrall PH, Burdon JB, Singh KB. Plants versus pathogens: an evolutionary arms race. FUNCTIONAL PLANT BIOLOGY : FPB 2010; 37:499-512. [PMID: 21743794 PMCID: PMC3131095 DOI: 10.1071/fp09304] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The analysis of plant-pathogen interactions is a rapidly moving research field and one that is very important for productive agricultural systems. The focus of this review is on the evolution of plant defence responses and the coevolution of their pathogens, primarily from a molecular-genetic perspective. It explores the evolution of the major types of plant defence responses including pathogen associated molecular patterns and effector triggered immunity as well as the forces driving pathogen evolution, such as the mechanisms by which pathogen lineages and species evolve. Advances in our understanding of plant defence signalling, stomatal regulation, R gene-effector interactions and host specific toxins are used to highlight recent insights into the coevolutionary arms race between pathogens and plants. Finally, the review considers the intriguing question of how plants have evolved the ability to distinguish friends such as rhizobia and mycorrhiza from their many foes.
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Affiliation(s)
- Jonathan P. Anderson
- CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag #5, Wembley, WA 6913, Australia
| | - Cynthia A. Gleason
- CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag #5, Wembley, WA 6913, Australia
| | - Rhonda C. Foley
- CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag #5, Wembley, WA 6913, Australia
| | - Peter H. Thrall
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Jeremy B. Burdon
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Karam B. Singh
- CSIRO Plant Industry, Centre for Environment and Life Sciences, Private Bag #5, Wembley, WA 6913, Australia
- The Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia
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Barrett LG, Kniskern JM, Bodenhausen N, Zhang W, Bergelson J. Continua of specificity and virulence in plant host-pathogen interactions: causes and consequences. THE NEW PHYTOLOGIST 2009; 183:513-529. [PMID: 19563451 DOI: 10.1111/j.1469-8137.2009.02927.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Ecological, evolutionary and molecular models of interactions between plant hosts and microbial pathogens are largely based around a concept of tightly coupled interactions between species pairs. However, highly pathogenic and obligate associations between host and pathogen species represent only a fraction of the diversity encountered in natural and managed systems. Instead, many pathogens can infect a wide range of hosts, and most hosts are exposed to more than one pathogen species, often simultaneously. Furthermore, outcomes of pathogen infection vary widely because host plants vary in resistance and tolerance to infection, while pathogens are also variable in their ability to grow on or within hosts. Environmental heterogeneity further increases the potential for variation in plant host-pathogen interactions by influencing the degree and fitness consequences of infection. Here, we describe these continua of specificity and virulence inherent within plant host-pathogen interactions. Using this framework, we describe and contrast the genetic and environmental mechanisms that underlie this variation, outline consequences for epidemiology and community structure, explore likely ecological and evolutionary drivers, and highlight several key areas for future research.
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Affiliation(s)
- Luke G Barrett
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joel M Kniskern
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Natacha Bodenhausen
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA
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Barrett LG, Thrall PH, Dodds PN, van der Merwe M, Linde CC, Lawrence GJ, Burdon JJ. Diversity and evolution of effector loci in natural populations of the plant pathogen Melampsora lini. Mol Biol Evol 2009; 26:2499-513. [PMID: 19633228 DOI: 10.1093/molbev/msp166] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genetic variation for pathogen infectivity is an important driver of disease incidence and prevalence in both natural and managed systems. Here, we use the interaction between the rust pathogen, Melampsora lini, and two host plants, Linum marginale and Linum usitatissimum, to examine how host-pathogen interactions influence the maintenance of polymorphism in genes underlying pathogen virulence. Extensive sequence variation at two effector loci (AvrP123, AvrP4) was found in M. lini isolates collected from across the native range of L. marginale in Australia, as well as in isolates collected from a second host, the cultivated species L. usitatissimum. A highly significant excess of nonsynonymous compared with synonymous polymorphism was found at both loci, suggesting that diversifying selection is important for the maintenance of the observed sequence diversity. Agrobacterium-mediated transient transformation assays were used to demonstrate that variants of both the AvrP123 and AvrP4 genes are differentially recognized by resistance genes in L. marginale. We further characterized patterns of nucleotide variation at AvrP123 and AvrP4 in 10 local populations of M. lini infecting the wild host L. marginale. Populations were significantly differentiated with respect to allelic representation at the Avr loci, suggesting the possibility of local selection maintaining distinct genetic structures between pathogen populations, whereas limited diversity may be explained via selective sweeps and demographic bottlenecks. Together, these results imply that interacting selective and nonselective factors, acting across a broad range of scales, are important for the generation and maintenance of adaptively significant variation in populations of M. lini.
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Affiliation(s)
- Luke G Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT Australia.
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25
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Dodds P, Thrall P. Recognition events and host-pathogen co-evolution in gene-for-gene resistance to flax rust. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:395-408. [PMID: 21760756 PMCID: PMC3134234 DOI: 10.1071/fp08320] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The outcome of infection of individual plants by pathogenic organisms is governed by complex interactions between the host and pathogen. These interactions are the result of long-term co-evolutionary processes involving selection and counterselection between plants and their pathogens. These processes are ongoing, and occur at many spatio-temporal scales, including genes and gene products, cellular interactions within host individuals, and the dynamics of host and pathogen populations. However, there are few systems in which host-pathogen interactions have been studied across these broad scales. In this review, we focus on research to elucidate the structure and function of plant resistance and pathogen virulence genes in the flax-flax rust interaction, and also highlight complementary co-evolutionary studies of a related wild plant-pathogen interaction. The confluence of these approaches is beginning to shed new light on host-pathogen molecular co-evolution in natural environments.
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Affiliation(s)
- Peter Dodds
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Peter Thrall
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia
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26
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Barrett LG, Thrall PH, Burdon JJ, Linde CC. Life history determines genetic structure and evolutionary potential of host-parasite interactions. Trends Ecol Evol 2008; 23:678-85. [PMID: 18947899 DOI: 10.1016/j.tree.2008.06.017] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Revised: 06/25/2008] [Accepted: 06/26/2008] [Indexed: 02/04/2023]
Abstract
Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.
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Affiliation(s)
- Luke G Barrett
- CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia.
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