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Nowicki M, Hadziabdic D, Trigiano RN, Runge F, Thines M, Boggess SL, Ristaino J, Spring O. Microsatellite Markers from Peronospora tabacina, the Cause of Blue Mold of Tobacco, Reveal Species Origin, Population Structure, and High Gene Flow. PHYTOPATHOLOGY 2022; 112:422-434. [PMID: 34058860 DOI: 10.1094/phyto-03-21-0092-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
- Department of Life Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, D-60323 Frankfurt am Main, Germany
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Jean Ristaino
- Department of Entomology and Plant Pathology, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh 27650, U.S.A
| | - Otmar Spring
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
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Nowicki M, Hadziabdic D, Trigiano RN, Boggess SL, Kanetis L, Wadl PA, Ojiambo PS, Cubeta MA, Spring O, Thines M, Runge F, Scheffler BE. "Jumping Jack": Genomic Microsatellites Underscore the Distinctiveness of Closely Related Pseudoperonospora cubensis and Pseudoperonospora humuli and Provide New Insights Into Their Evolutionary Past. Front Microbiol 2021; 12:686759. [PMID: 34335513 PMCID: PMC8317435 DOI: 10.3389/fmicb.2021.686759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
Downy mildews caused by obligate biotrophic oomycetes result in severe crop losses worldwide. Among these pathogens, Pseudoperonospora cubensis and P. humuli, two closely related oomycetes, adversely affect cucurbits and hop, respectively. Discordant hypotheses concerning their taxonomic relationships have been proposed based on host-pathogen interactions and specificity evidence and gene sequences of a few individuals, but population genetics evidence supporting these scenarios is missing. Furthermore, nuclear and mitochondrial regions of both pathogens have been analyzed using microsatellites and phylogenetically informative molecular markers, but extensive comparative population genetics research has not been done. Here, we genotyped 138 current and historical herbarium specimens of those two taxa using microsatellites (SSRs). Our goals were to assess genetic diversity and spatial distribution, to infer the evolutionary history of P. cubensis and P. humuli, and to visualize genome-scale organizational relationship between both pathogens. High genetic diversity, modest gene flow, and presence of population structure, particularly in P. cubensis, were observed. When tested for cross-amplification, 20 out of 27 P. cubensis-derived gSSRs cross-amplified DNA of P. humuli individuals, but few amplified DNA of downy mildew pathogens from related genera. Collectively, our analyses provided a definite argument for the hypothesis that both pathogens are distinct species, and suggested further speciation in the P. cubensis complex.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Loukas Kanetis
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Phillip A Wadl
- USDA-ARS, Vegetable Research, Charleston, SC, United States
| | - Peter S Ojiambo
- Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC, United States
| | - Otmar Spring
- Institute of Botany 210, University of Hohenheim, Stuttgart, Germany
| | - Marco Thines
- Department of Biological Sciences, Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft fuer Naturforschung and Evolution and Diversity, Institute of Ecology, Goethe University, Frankfurt am Main, Germany
| | | | - Brian E Scheffler
- U.S. Department of Agriculture, Agricultural Research Service, Stoneville, MS, United States
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Blanco-Meneses M, Carbone I, Ristaino JB. Population structure and migration of the Tobacco Blue Mold Pathogen, Peronospora tabacina, into North America and Europe. Mol Ecol 2018; 27:737-751. [PMID: 29218863 DOI: 10.1111/mec.14453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 10/13/2017] [Accepted: 11/08/2017] [Indexed: 11/28/2022]
Abstract
Tobacco blue mold, caused by Peronospora tabacina, is an oomycete plant pathogen that causes yearly epidemics in tobacco (Nicotiana tabacum) in the United States and Europe. The genetic structure of P. tabacina was examined to understand genetic diversity, population structure and patterns of migration. Two nuclear loci, Igs2 and Ypt1, and one mitochondrial locus, cox2, were amplified, cloned and sequenced from fifty-four isolates of P. tabacina from the United States, Central America-Caribbean-Mexico (CCAM), Europe and the Middle East (EULE). Cloned sequences from the three genes showed high genetic variability across all populations. Nucleotide diversity and the population mean mutation parameter per site (Watterson's theta) were higher in EULE and CCAM and lower in U.S. POPULATIONS Neutrality tests were significant and the equilibrium model of neutral evolution was rejected, indicating an excess of recent mutations or rare alleles. Hudson's Snn tests were performed to examine population subdivision and gene flow among populations. An isolation-with-migration analysis (IM) supported the hypothesis of long-distance migration of P. tabacina from the Caribbean region, Florida and Texas into other states in the United States. Within the European populations, the model documented migration from North Central Europe into western Europe and Lebanon, and migration from western Europe into Lebanon. The migration patterns observed support historical observations about the first disease introductions and movement in Europe. The models developed are applicable to other aerial dispersed emerging pathogens and document that high-evolutionary-risk plant pathogens can move over long distances to cause disease due to their large effective population size, population expansion and dispersal.
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Affiliation(s)
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Jean B Ristaino
- Department of Entomology and Plant Pathology, NC State University, Raleigh, NC, USA
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Derevnina L, Chin-Wo-Reyes S, Martin F, Wood K, Froenicke L, Spring O, Michelmore R. Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1198-215. [PMID: 26196322 DOI: 10.1094/mpmi-05-15-0112-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain-containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.
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Affiliation(s)
- Lida Derevnina
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | | | - Frank Martin
- 2 United States Department of Agriculture-Agricultural Research Service, Salinas, CA U.S.A
| | - Kelsey Wood
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Lutz Froenicke
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Otmar Spring
- 3 Institute of Botany, University of Hohenheim, Germany
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Aguayo J, Adams GC, Halkett F, Catal M, Husson C, Nagy ZÁ, Hansen EM, Marçais B, Frey P. Strong genetic differentiation between North American and European populations of Phytophthora alni subsp. uniformis. PHYTOPATHOLOGY 2013; 103:190-199. [PMID: 23095465 DOI: 10.1094/phyto-05-12-0116-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Alder decline caused by Phytophthora alni has been one of the most important diseases of natural ecosystems in Europe during the last 20 years. The emergence of P. alni subsp. alni -the pathogen responsible for the epidemic-is linked to an interspecific hybridization event between two parental species: P. alni subsp. multiformis and P. alni subsp. uniformis. One of the parental species, P. alni subsp. uniformis, has been isolated in several European countries and, recently, in North America. The objective of this work was to assess the level of genetic diversity, the population genetic structure, and the putative reproduction mode and mating system of P. alni subsp. uniformis. Five new polymorphic microsatellite markers were used to contrast both geographical populations. The study comprised 71 isolates of P. alni subsp. uniformis collected from eight European countries and 10 locations in North America. Our results revealed strong differences between continental populations (Fst = 0.88; Rst = 0.74), with no evidence for gene flow. European isolates showed extremely low genetic diversity compared with the North American collection. Selfing appears to be the predominant mating system in both continental collections. The results suggest that the European P. alni subsp. uniformis population is most likely alien and derives from the introduction of a few individuals, whereas the North American population probably is an indigenous population.
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Affiliation(s)
- Jaime Aguayo
- INRA, UMR1136, INRA, Université de Lorraine, Interactions Arbres- Micro- organismes, IFR110 EFABA, Centre INRA de Nancy, 54280 Champenoux, France
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Dean DA, Wadl PA, Hadziabdic D, Wang X, Trigiano RN. Analyzing microsatellites using the QIAxcel system. Methods Mol Biol 2013; 1006:223-43. [PMID: 23546795 DOI: 10.1007/978-1-62703-389-3_16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Microsatellites are ubiquitous throughout eukaryotic genomes and are useful in analyzing populations and genetic diversity. The QIAxcel system, an automated capillary electrophoresis device, allows the user to determine the size of microsatellite fragments, to discern allelic polymorphisms among individuals, and to differentiate homozygous and heterozygous individuals. This system provides comparable base pair resolution to more expensive systems at a relatively affordable cost.
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Affiliation(s)
- Deborah A Dean
- Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
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