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Moroz N, Colvin B, Jayasinghe S, Gleason C, Tanaka K. Phytocytokine StPep1-Secreting Bacteria Suppress Potato Powdery Scab Disease. PHYTOPATHOLOGY 2024:PHYTO01240019R. [PMID: 38970808 DOI: 10.1094/phyto-01-24-0019-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2024]
Abstract
Powdery scab is an important potato disease caused by the soilborne pathogen Spongospora subterranea f. sp. subterranea. Currently, reliable chemical control and resistant cultivars for powdery scab are unavailable. As an alternative control strategy, we propose a novel approach involving the effective delivery of a phytocytokine to plant roots by the rhizobacterium Bacillus subtilis. The modified strain is designed to secrete the plant elicitor peptide StPep1. In our experiments employing a hairy root system, we observed a significant reduction in powdery scab pathogen infection when we directly applied the StPep1 peptide. Furthermore, our pot assay, which involved pretreating potato roots with StPep1-secreting B. subtilis, demonstrated a substantial decrease in disease symptoms, including reduced root galling and fewer tuber lesions. These findings underscore the potential of engineered bacteria as a promising strategy for safeguarding plants against powdery scab.
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Affiliation(s)
- Natalia Moroz
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Benjamin Colvin
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Samodya Jayasinghe
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Cynthia Gleason
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
| | - Kiwamu Tanaka
- Department of Plant Pathology, Washington State University, Pullman, WA 99164
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2
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Ozturk IK, Buchholz E, Bentley A, Halterman D, Rioux R. Spongospora subterranea f. sp. subterranea Affects Plant Susceptibility to Subsequent Pathogen Infections Under Controlled-Environment Conditions. PLANT DISEASE 2024; 108:2148-2153. [PMID: 38468137 DOI: 10.1094/pdis-02-24-0276-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: 03/13/2024]
Abstract
Spongospora subterranea f. sp. subterranea (Sss) is a soilborne potato pathogen responsible for causing powdery scab on tubers and galls on roots, reducing root water uptake through colonizing root hairs, and vectoring of Potato mop-top virus (PMTV). However, effects of Sss on overall plant susceptibilities against subsequent infections of potato pathogens above ground have not been previously reported. This study aimed to investigate the effects of Sss on root and tuber disease expression, yield, and susceptibilities to subsequent late blight and white mold infections across six potato varieties. Sss-infected Silverton plants had 28.3% less total tuber yield and 29% fewer tubers compared to noninfected Silverton plants. We did not find a correlation across the varieties between root colonization and root gall formation. Sss-infected Silverton plants were more susceptible to hemibiotrophic late blight and less susceptible to necrotrophic white mold. Sss infection also increased susceptibilities of Goldrush and Atlantic plants to white mold. We also evaluated prevalence of asymptomatic Sss infections across the six varieties. Between 50 and 92% of the asymptomatic tubers tested positive for Sss DNA, depending on the variety. Further research is required to understand the possibility and extent of these asymptomatic infections to the spread of Sss in the field. These findings highlight the complexity of Sss-host interactions and give precedence that the lack of disease expression does not necessarily indicate resistance of a variety to Sss.
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Affiliation(s)
- Ibrahim Kutay Ozturk
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
- Cooperative Extension, University of Maine, Presque Isle, ME 04769
| | - Elizabeth Buchholz
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
- Department of Plant and Environmental Sciences, University of Hawai'i at Mānoa, Honolulu, HI 96822
| | - Ally Bentley
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Dennis Halterman
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
- Vegetable Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Madison, WI 53706
| | - Renee Rioux
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
- BASF, Research Triangle Park, NC 27709
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Amponsah J, Tegg RS, Thangavel T, Wilson CR. Chemotaxis and Motility of Spongospora subterranea Zoospores in Response to Potato Root Exudate Constituents and pH. PHYTOPATHOLOGY 2023; 113:1233-1243. [PMID: 36774556 DOI: 10.1094/phyto-04-21-0176-r] [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: 06/18/2023]
Abstract
Spongospora subterranea f. sp. subterranea is an important pathogen of potato responsible for major losses in most potato growing regions of the world. Infection is initiated by biflagellated motile zoospores released from long-lived resting spores. Zoospore chemotaxis to the host plant root is widely believed to be stimulated by host root exudate compounds, although direct evidence is lacking. This study refined the traditional chemotaxis capillary assay, with which we provided the first empirical evidence of S. subterranea zoospore chemotaxis. Individual potato root exudate metabolites were either taxis neutral, inhibitory, or attractant to the zoospores. L-Glutamine was the strongest chemoattractant, while spermine was the most inhibitory. Zoospore motility and chemotaxis were constrained by strongly acidic or alkaline solutions of pH < 5.3 and >8.5, respectively. Beyond pH, ionic constituents of the test solution affected zoospore motility as Sorensen's phosphate buffer stalled zoospore motility, but HEPES buffer at the same concentration and pH had little or no negative motility effect. Zoospore motility, as characterized by several parameters, influenced chemotaxis. Among the parameters measured, total distance traveled was the best predictor of zoospore chemotaxis. The characterization of environmental and ecological effects on zoospore motility and chemotaxis highlights useful targets for S. subterranea disease control through manipulation of zoospore taxis or selection of host resistance traits.
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Affiliation(s)
- J Amponsah
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania 7008, Australia
- Biotechnology Centre, Ghana Atomic Energy Commission, Ghana
| | - R S Tegg
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania 7008, Australia
| | - T Thangavel
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania 7008, Australia
| | - C R Wilson
- Tasmanian Institute of Agriculture, New Town Research Laboratories, University of Tasmania, New Town, Tasmania 7008, Australia
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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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Jiang J, Feindel W, Harding M, Feindel D, Bajema S, Feng J. Development and Evaluation of a Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of the Potato Powdery Scab Pathogen Spongospora subterranea. PLANT DISEASE 2023; 107:136-141. [PMID: 35748732 DOI: 10.1094/pdis-05-22-1000-sr] [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: 06/15/2023]
Abstract
Spongospora subterranea is the causal agent of powdery scab of potato (Solanum tuberosum), which can significantly reduce potato quality. In this study, we developed and evaluated a loop-mediated isothermal amplification (LAMP) method for the detection of S. subterranea. A set of LAMP primers named PS-LAMP was designed and tested for specificity and sensitivity. In the specificity test, in silico analysis using the NCBI Primer-BLAST tool indicated that PS-LAMP was specific to S. subterranea. The in vitro tests confirmed specificity, showing that PS-LAMP could produce positive signals from DNA isolated from each of three potato tubers with powdery scab symptoms but did not produce positive signals from DNA isolated from 38 nontarget plant pathogens. The sensitivity of PS-LAMP was tested on both gBlocks and DNA isolated from potato samples with powdery scab symptoms. On gBlocks, the lowest number of copies for a positive LAMP reaction was six, which was similar to results obtained via qPCR, but it was 10 times more sensitive than conventional PCR. On a DNA sample from S. subterranea-infected potato, the lowest amount of template DNA for a positive LAMP reaction was 2 pg, which was incomparable with the sensitivity of qPCR. Considering the convenience of the LAMP technique, as well as the high specificity and sensitivity, this assay can be very useful for plant pathology practitioners and diagnostic labs interested in rapid, accurate, and routine detection of S. subterranea and confirmation of powdery scab disease.
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Affiliation(s)
- Junye Jiang
- Potato Growers of Alberta, Edmonton, AB, T5Y 6H3, Canada
| | - Will Feindel
- Potato Growers of Alberta, Edmonton, AB, T5Y 6H3, Canada
| | - Michael Harding
- Crop Diversification Centre South, Alberta Agriculture, Forestry and Rural Economic Development (AAFRED), Brooks, AB, T1R 1E6, Canada
| | - David Feindel
- Alberta Plant Health Lab, AAFRED, Edmonton, AB, T5Y 6H3, Canada
| | - Stacey Bajema
- Potato Growers of Alberta, Edmonton, AB, T5Y 6H3, Canada
| | - Jie Feng
- Alberta Plant Health Lab, AAFRED, Edmonton, AB, T5Y 6H3, Canada
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Stauber L, Badet T, Feurtey A, Prospero S, Croll D. Emergence and diversification of a highly invasive chestnut pathogen lineage across southeastern Europe. eLife 2021; 10:e56279. [PMID: 33666552 PMCID: PMC7935491 DOI: 10.7554/elife.56279] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 02/17/2021] [Indexed: 12/18/2022] Open
Abstract
Invasive microbial species constitute a major threat to biodiversity, agricultural production and human health. Invasions are often dominated by one or a small number of genotypes, yet the underlying factors driving invasions are poorly understood. The chestnut blight fungus Cryphonectria parasitica first decimated the North American chestnut, and a more recent outbreak threatens European chestnut stands. To unravel the chestnut blight invasion of southeastern Europe, we sequenced 230 genomes of predominantly European strains. Genotypes outside of the invasion zone showed high levels of diversity with evidence for frequent and ongoing recombination. The invasive lineage emerged from the highly diverse European genotype pool rather than a secondary introduction from Asia or North America. The expansion across southeastern Europe was mostly clonal and is dominated by a single mating type, suggesting a fitness advantage of asexual reproduction. Our findings show how an intermediary, highly diverse bridgehead population gave rise to an invasive, largely clonally expanding pathogen.
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Affiliation(s)
- Lea Stauber
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)BirmensdorfSwitzerland
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
| | - Alice Feurtey
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
- Plant Pathology, Institute of Integrative Biology, ETH ZürichZürichSwitzerland
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)BirmensdorfSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchâtelSwitzerland
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Muzhinji N, van der Waals JE. Population Biology and Genetic Variation of Spongospora subterranea f. sp. subterranea, the Causal Pathogen of Powdery Scab and Root Galls on Potatoes in South Africa. PHYTOPATHOLOGY 2019; 109:1957-1965. [PMID: 31237188 DOI: 10.1094/phyto-12-18-0467-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Spongospora subterranea f. sp. subterranea, causal agent of powdery scab and root galls of potatoes, occurs worldwide and is responsible for quality and yield losses in potato production in South Africa. Despite being one of the most important potato pathogens in South Africa, little information is available on the genetic structure and diversity of S. subterranea f. sp. subterranea, which could provide insight into the factors shaping its evolution and the role of inoculum sources in disease development. A total of 172 samples were collected from four potato growing regions in South Africa. An additional 27 samples obtained from Colombia were included for comparative purposes. The samples were screened against six informative microsatellite (simple-sequence repeat) markers. Of the 172 samples obtained from potato growing regions in South Africa, there were 75 multilocus genotypes (MLGs), only 16 of which were shared between potato growing regions, indicating substantial gene flow and countrywide dispersal of the pathogen. The presence of common MLGs among the root- and tuber-derived samples indicated a lack of specialization of S. subterranea f. sp. subterranea to either tuber or root infection. Nei's unbiased estimates of gene diversity for the clone-corrected data were low and ranged from 0.24 to 0.38. Analysis of molecular variance and discriminant analysis of principal components showed no population differentiation between different potato growing regions in South Africa and between root- and tuber-derived genotypes. The presence of MLGs, high considerable genotypic diversity, and failure to reject the null hypothesis of random mating in most populations are indicative of some kind of recombination, either sexual or asexual, in these S. subterranea f. sp. subterranea populations. Information from this study provides new insights into the genetic structure and diversity of S. subterranea f. sp. subterranea in South Africa. Continuous monitoring of the pathogen population dynamics will be helpful in implementing effective region-specific management strategies for the pathogen, especially in the development of resistant potato cultivars.
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Affiliation(s)
- Norman Muzhinji
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0028, South Africa
| | - Jacquie E van der Waals
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria 0028, South Africa
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Zhu X, Gopurenko D, Serrano M, Spencer MA, Pieterse PJ, Skoneczny D, Lepschi BJ, Reigosa MJ, Gurr GM, Callaway RM, Weston LA. Genetic evidence for plural introduction pathways of the invasive weed Paterson's curse (Echium plantagineum L.) to southern Australia. PLoS One 2019; 14:e0222696. [PMID: 31536564 PMCID: PMC6752891 DOI: 10.1371/journal.pone.0222696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
Paterson’s curse (Echium plantagineum L. (Boraginaceae)), is an herbaceous annual native to Western Europe and northwest Africa. It has been recorded in Australia since the 1800’s and is now a major weed in pastures and rangelands, but its introduction history is poorly understood. An understanding of its invasion pathway and subsequent genetic structure is critical to the successful introduction of biological control agents and for provision of informed decisions for plant biosecurity efforts. We sampled E. plantagineum in its native (Iberian Peninsula), non-native (UK) and invaded ranges (Australia and South Africa) and analysed three chloroplast gene regions. Considerable genetic diversity was found among E. plantagineum in Australia, suggesting a complex introduction history. Fourteen haplotypes were identified globally, 10 of which were co-present in Australia and South Africa, indicating South Africa as an important source population, likely through contamination of traded goods or livestock. Haplotype 4 was most abundant in Australia (43%), and in historical and contemporary UK populations (80%), but scarce elsewhere (< 17%), suggesting that ornamental and/or other introductions from genetically impoverished UK sources were also important. Collectively, genetic evidence and historical records indicate E. plantagineum in southern Australia exists as an admixture that is likely derived from introduced source populations in both the UK and South Africa.
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Affiliation(s)
- Xiaocheng Zhu
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, Australia
- * E-mail:
| | - David Gopurenko
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, Australia
| | - Miguel Serrano
- Department of Botany, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mark A. Spencer
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Petrus J. Pieterse
- Department of Agronomy, Stellenbosch University, Private bag X1, Matieland, South Africa
| | - Dominik Skoneczny
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Australia
| | - Brendan J. Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Canberra, Australia
| | - Manuel J. Reigosa
- Department of Plant Biology and Soil Science, Faculty of Biology, University of Vigo, Vigo, Pontevedra, Spain
| | - Geoff M. Gurr
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, Australia
| | - Ragan M. Callaway
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Leslie A. Weston
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, Australia
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Ciaghi S, Neuhauser S, Schwelm A. Draft Genome Resource for the Potato Powdery Scab Pathogen Spongospora subterranea. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1227-1229. [PMID: 29969057 PMCID: PMC6443038 DOI: 10.1094/mpmi-06-18-0163-a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The Plasmodiophorida (Phytomyxea, Rhizaria) are a group of protists that infect plants. Of this group, Spongospora subterranea causes major problems for the potato industry by causing powdery scab and root galling of potatoes and as vector for the Potato mop-top virus (PMTV) (genus Pomovirus, family Virgaviridae). A single tuber isolate (SSUBK13) of this uncultivable protist was used to generate DNA for Illumina sequencing. The data were assembled to a draft genome of 28.08 Mb consisting of 2,340 contigs and an L50 of 280. A total of 10,778 genes were predicted and 93% of the BUSCO genes were detected. The presented genome assembly is only the second genome of a plasmodiophorid. The data will accelerate functional genomics to study poorly understood interaction of plasmodiophorids and their hosts.
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Affiliation(s)
- Stefan Ciaghi
- University of Innsbruck, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Sigrid Neuhauser
- University of Innsbruck, Institute of Microbiology, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Arne Schwelm
- Swedish University of Agricultural Sciences, Department of Plant Biology, Uppsala BioCenter, Linnean Centre for Plant Biology, P.O. Box 7080, SE-75007 Uppsala, Sweden
- Corresponding author: Arne Schwelm;
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10
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Bertelsmeier C, Keller L. Bridgehead Effects and Role of Adaptive Evolution in Invasive Populations. Trends Ecol Evol 2018; 33:527-534. [DOI: 10.1016/j.tree.2018.04.014] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 11/25/2022]
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Schwelm A, Badstöber J, Bulman S, Desoignies N, Etemadi M, Falloon RE, Gachon CMM, Legreve A, Lukeš J, Merz U, Nenarokova A, Strittmatter M, Sullivan BK, Neuhauser S. Not in your usual Top 10: protists that infect plants and algae. MOLECULAR PLANT PATHOLOGY 2018; 19:1029-1044. [PMID: 29024322 PMCID: PMC5772912 DOI: 10.1111/mpp.12580] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 07/06/2017] [Accepted: 07/07/2017] [Indexed: 05/09/2023]
Abstract
Fungi, nematodes and oomycetes belong to the most prominent eukaryotic plant pathogenic organisms. Unicellular organisms from other eukaryotic lineages, commonly addressed as protists, also infect plants. This review provides an introduction to plant pathogenic protists, including algae infecting oomycetes, and their current state of research.
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Affiliation(s)
- Arne Schwelm
- Department of Plant Biology, Uppsala BioCentre, Linnean Centre for Plant BiologySwedish University of Agricultural SciencesUppsala SE‐75007Sweden
- Institute of Microbiology, University of InnsbruckInnsbruck 6020Austria
| | - Julia Badstöber
- Institute of Microbiology, University of InnsbruckInnsbruck 6020Austria
| | - Simon Bulman
- New Zealand Institute for Plant and Food Research LtdLincoln 7608New Zealand
| | - Nicolas Desoignies
- Applied Plant Ecophysiology, Haute Ecole Provinciale de Hainaut‐CondorcetAth 7800Belgium
| | - Mohammad Etemadi
- Institute of Microbiology, University of InnsbruckInnsbruck 6020Austria
| | - Richard E. Falloon
- New Zealand Institute for Plant and Food Research LtdLincoln 7608New Zealand
| | - Claire M. M. Gachon
- The Scottish Association for Marine ScienceScottish Marine InstituteOban PA37 1QAUK
| | - Anne Legreve
- Université catholique de Louvain, Earth and Life InstituteLouvain‐la‐Neuve 1348Belgium
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre37005 České Budějovice (Budweis)Czech Republic
- Faculty of SciencesUniversity of South Bohemia37005 České Budějovice (Budweis)Czech Republic
- Integrated Microbial Biodiversity, Canadian Institute for Advanced ResearchTorontoOntario M5G 1Z8Canada
| | - Ueli Merz
- Plant PathologyInstitute of Integrative Biology, ETH Zurich, Zurich 8092Switzerland
| | - Anna Nenarokova
- Institute of Parasitology, Biology Centre37005 České Budějovice (Budweis)Czech Republic
- Faculty of SciencesUniversity of South Bohemia37005 České Budějovice (Budweis)Czech Republic
| | - Martina Strittmatter
- The Scottish Association for Marine ScienceScottish Marine InstituteOban PA37 1QAUK
- Present address:
Station Biologique de Roscoff, CNRS – UPMC, UMR7144 Adaptation and Diversity in the Marine Environment, Place Georges Teissier, CS 90074, 29688 Roscoff CedexFrance
| | - Brooke K. Sullivan
- School of BiosciencesUniversity of Melbourne, Parkville, Vic. 3010Australia
- School of BiosciencesVictorian Marine Science ConsortiumQueenscliffVic. 3225Australia
| | - Sigrid Neuhauser
- Institute of Microbiology, University of InnsbruckInnsbruck 6020Austria
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12
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Kalyandurg P, Gil JF, Lukhovitskaya NI, Flores B, Müller G, Chuquillanqui C, Palomino L, Monjane A, Barker I, Kreuze J, Savenkov EI. Molecular and pathobiological characterization of 61 Potato mop-top virus full-length cDNAs reveals great variability of the virus in the centre of potato domestication, novel genotypes and evidence for recombination. MOLECULAR PLANT PATHOLOGY 2017; 18:864-877. [PMID: 28390168 PMCID: PMC6638219 DOI: 10.1111/mpp.12552] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/17/2017] [Accepted: 03/24/2017] [Indexed: 06/07/2023]
Abstract
The evolutionary divergence of Potato mop-top virus (PMTV), a tri-partite, single-stranded RNA virus, is exceptionally low, based on the analysis of sequences obtained from isolates from Europe, Asia and North America. In general, RNA viruses exist as dynamic populations of closely related and recombinant genomes that are subjected to continuous genetic variation. The reason behind the low genetic variation of PMTV remains unclear. The question remains as to whether the low variability is a shared property of all PMTV isolates or is a result of the limited number of isolates characterized so far. We hypothesized that higher divergence of the virus might exist in the Andean regions of South America, the centre of potato domestication. Here, we report high variability of PMTV isolates collected from 12 fields in three locations in the Andean region of Peru. To evaluate PMTV genetic variation in Peru, we generated full-length cDNA clones, which allowed reliable comparative molecular and pathobiological characterization of individual isolates. We found significant divergence of the CP-RT and 8K sequences. The 8K cistron, which encodes a viral suppressor of RNA silencing, was found to be under diversifying selection. Phylogenetic analysis determined that, based on the CP-RT sequence, all PMTV isolates could be categorized into three separate lineages (clades). Moreover, we found evidence for recombination between two clades. Using infectious cDNA clones of the representatives of these two clades, as well as reassortants for the RNA-CP genomic component, we determined the pathobiological differences between the lineages, which we coined as S (for severe) and M (for mild) types. Interestingly, all isolates characterized previously (from Europe, Asia and North America) fall into the S-type clade, whereas most of the Peruvian isolates belong to the M-type. Taken together, our results support the notion of the single introduction of PMTV from the centre of potato origin to Europe, and subsequent spread of the S-type into Asia and USA. This is also supported by the suggested novel classification of isolates based on genetic constellations.
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Affiliation(s)
- Pruthvi Kalyandurg
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jose Fernando Gil
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
| | - Nina I. Lukhovitskaya
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
- Present address:
Division of Virology, Department of PathologyUniversity of CambridgeHills RoadCambridgeCB2 0QQUK
| | - Betty Flores
- International Potato Center (CIP)Apartado 1558Lima12Peru
| | | | | | - Ladislao Palomino
- Instituto Nacional de Innovación Agraria (INIA)EEA – Andenes04540CuzcoPeru
| | - Aderito Monjane
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
- Present address:
Norwegian Veterinary Institute0106OsloNorway
| | - Ian Barker
- International Potato Center (CIP)Apartado 1558Lima12Peru
- Present address:
Syngenta Foundation for Sustainable Agriculture4002BaselSwitzerland
| | - Jan Kreuze
- International Potato Center (CIP)Apartado 1558Lima12Peru
| | - Eugene I. Savenkov
- Department of Plant Biology, Uppsala BioCenter SLUSwedish University of Agricultural Sciences, Linnean Center for Plant BiologyUppsala75007Sweden
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13
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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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14
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Abstract
Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.
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Affiliation(s)
- Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611;
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15
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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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16
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Diversity and evolution of potato mop-top virus. Arch Virol 2015; 160:1345-51. [PMID: 25753427 DOI: 10.1007/s00705-015-2381-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/24/2015] [Indexed: 10/23/2022]
Abstract
Nearly complete sequences of RNA-CP and 3'-proximal RNA-TGB were determined for 43 samples of potato mop-top virus (PMTV) originating from potato tubers and field soil from Sweden, Denmark and the USA. The results showed limited diversity and no strict geographical grouping, suggesting only a few original introductions of PMTV from the Andes. Two distinguishable types of RNA-CP and RNA-TGB were found in the samples, but no specific combination of them correlated with spraing symptoms in tubers. Lack of positive selection in the coding sequences indicates that there is no specific molecular adaptation of PMTV to new vectors or hosts.
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17
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Gutiérrez P, Bulman S, Alzate J, Ortíz MC, Marín M. Mitochondrial genome sequence of the potato powdery scab pathogen Spongospora subterranea. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:58-9. [PMID: 24438302 DOI: 10.3109/19401736.2013.873898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Spongospora subterranea is a soil-borne obligate parasite responsible for potato powdery scab disease. S. subterranea is a member of the order Plasmodiophorida, a protist taxa that is related to Cercozoa and Foraminifera but the fine details of these relationships remain unresolved. Currently there is only one available complete mtDNA sequence of a cercozoan, Bigelowiella natans. In this work, the mitochondrial sequence of a S. subterranea isolate infecting an Andean variety of S. tuberosum ssp. andigena (Diacol-Capiro) is presented. The mtDNA codes for 16 proteins of the respiratory chain, 11 ribosomal proteins, 3 ribosomal RNAs, 24 tRNAs, a RNA processing RNaseP, a RNA-directed polymerase, and two proteins of unknown function. This is the first report of a mtDNA genome sequence from a plasmodiophorid and will be useful in clarifying the phylogenetic relationship of this group to other members in the supergroup Rhizaria once more mtDNA sequences are available.
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Affiliation(s)
- Pablo Gutiérrez
- a Laboratorio de Microbiología Industrial, Facultad de Ciencias , Universidad Nacional de Colombia Sede Medellín , Medellín , Colombia
| | - Simon Bulman
- b New Zealand Institute for Plant & Food Research Ltd , Christchurch , New Zealand
| | - Juan Alzate
- c Centro Nacional de Secuenciación Genómica-CNSG, Facultad de Medicina, Universidad de Antioquia , Medellín , Colombia , and
| | - Mary Carmen Ortíz
- a Laboratorio de Microbiología Industrial, Facultad de Ciencias , Universidad Nacional de Colombia Sede Medellín , Medellín , Colombia
| | - Mauricio Marín
- d Laboratorio de Biología Celular y Molecular, Facultad de Ciencias , Universidad Nacional de Colombia Sede Medellín , Medellín , Colombia
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