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Xu MS, Fu Q, Baxter A. The components and amylase activity of Massa Medicata Fermentata during the process of fermentation. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Reeser PW, Hansen EM, Sutton W. Phytophthora siskiyouensis, a new species from soil, water, myrtlewood (Umbellularia californica) and tanoak (Lithocarpus densiflorus) in southwestern Oregon. Mycologia 2017. [DOI: 10.1080/15572536.2007.11832528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | | | - Wendy Sutton
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
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3
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Man in ’t Veld WA, Rosendahl KC, Hong C. Phytophthora ×serendipita sp. nov. and P. ×pelgrandis, two destructive pathogens generated by natural hybridization. Mycologia 2017; 104:1390-6. [DOI: 10.3852/11-272] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Karin C.H.M. Rosendahl
- Plant Protection Service, Ministry of Economic Affairs, Agriculture and Innovation, P.O. Box 9102, 6700 HC Wageningen, the Netherlands
| | - Chuanxue Hong
- Virginia Polytechnic Institute and State University, Virginia Beach, Virginia 23455
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4
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Reeser PW, Sutton W, Hansen EM, Remigi P, Adams GC. Phytophthora species in forest streams in Oregon and Alaska. Mycologia 2017; 103:22-35. [DOI: 10.3852/10-013] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Everett M. Hansen
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331
| | | | - Gerry C. Adams
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan 48824
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5
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Bartels M, French R, Graybosch RA, Tatineni S. Triticum mosaic virus exhibits limited population variation yet shows evidence of parallel evolution after replicated serial passage in wheat. Virology 2016; 492:92-100. [PMID: 26914507 DOI: 10.1016/j.virol.2016.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 02/11/2016] [Accepted: 02/12/2016] [Indexed: 10/22/2022]
Abstract
An infectious cDNA clone of Triticum mosaic virus (TriMV) (genus Poacevirus; family Potyviridae) was used to establish three independent lineages in wheat to examine intra-host population diversity levels within protein 1 (P1) and coat protein (CP) cistrons over time. Genetic variation was assessed at passages 9, 18 and 24 by single-strand conformation polymorphism, followed by nucleotide sequencing. The founding P1 region genotype was retained at high frequencies in most lineage/passage populations, while the founding CP genotype disappeared after passage 18 in two lineages. We found that rare TriMV genotypes were present only transiently and lineages followed independent evolutionary trajectories, suggesting that genetic drift dominates TriMV evolution. These results further suggest that experimental populations of TriMV exhibit lower mutant frequencies than that of Wheat streak mosaic virus (genus Tritimovirus; family Potyviridae) in wheat. Nevertheless, there was evidence for parallel evolution at a synonymous site in the TriMV CP cistron.
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Affiliation(s)
- Melissa Bartels
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Roy French
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Robert A Graybosch
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Satyanarayana Tatineni
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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6
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Copes WE, Yang X, Hong C. Phytophthora Species Recovered From Irrigation Reservoirs in Mississippi and Alabama Nurseries and Pathogenicity of Three New Species. PLANT DISEASE 2015; 99:1390-1395. [PMID: 30690996 DOI: 10.1094/pdis-11-14-1197-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
From a survey for Phytophthora spp. in containment basins at one nursery each in Alabama and Mississippi, eight species and one taxon were recovered, with Phytophthora gonapodyides dominant in cooler months and P. hydropathica in warmer months, accounting for 39.6 and 46.6% overall recovery, respectively. Among the recoveries were P. macilentosa, P. mississippiae, and P. stricta, three new species recently described from a small lake (labeled M4) that serves as a primary water source for irrigation and to feed another irrigation pond (M5) at the Mississippi nursery. Neither of ponds M4 and M5 directly receives runoff from any production area. The three new species were tested for pathogenicity with Catharanthus roseus, Gardenia jasminoides 'August Beauty,' Hydrangea quercifolia 'Semmes Beauty,' Ilex magland 'Oakland,' Pieris japonica 'Mountain Snow,' and Rhododendron × 'Brandi Michele Raley.' None of the three species infected any of the test plants or became established in peat or pine bark growing media. Based on the result of pathogenicity trials as well as the field observation that none of the nine Phytophthora taxa recovered from irrigation reservoirs have caused episodic disease in the nurseries, they appear to not present a high risk to ornamental plants at those nurseries.
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Affiliation(s)
- Warren E Copes
- Agricultural Research Service, US Department of Agriculture, Poplarville, Mississippi, 39470
| | - Xiao Yang
- Department of Plant Pathology, Physiology and Weed Science, Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, Virginia, 23455
| | - Chuanxue Hong
- Department of Plant Pathology, Physiology and Weed Science, Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, Virginia, 23455
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7
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Hussain T, Singh BP, Anwar F. A quantitative Real Time PCR based method for the detection of Phytophthora infestans causing Late blight of potato, in infested soil. Saudi J Biol Sci 2014; 21:380-6. [PMID: 25183949 PMCID: PMC4150230 DOI: 10.1016/j.sjbs.2013.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 09/21/2013] [Accepted: 09/29/2013] [Indexed: 11/25/2022] Open
Abstract
A fast and simple polymerase chain reaction method has been developed for detection of Phytophthora infestans oospores, the causal agent of Late blight of Potato in soil. The method involves the disruption of oospores by grinding dry soil, using abrasive properties, in the presence of glass powder and skimmed milk powder within a short time. The latter prevents loss of DNA by adsorption to soil particles or by degradation and reduces the co-extraction of PCR inhibitors with the DNA. After phenol/chloroform extraction; the DNA is suitable for direct PCR amplification without a precipitation step. This amplification leads to detection of pathogen in infested soils before planting of crop. The real-time PCR assay we describe is highly sensitive and specific, and has several advantages over conventional PCR assays used for P. infestans detection to confirm positive inoculum level in potato seeds and elsewhere. With increasing amounts of standard DNA templates, the respective threshold cycle (Ct) values were determined and a linear relationship was established between these Ct values and the logarithm of initial template amounts. The method is rapid, cost efficient, and when combined with suitable internal controls can be applied to the detection and quantification of P. infestans oospores on a large-scale basis.
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Affiliation(s)
- Touseef Hussain
- Plant Pathology Lab., CPRI Campus, Modipuram 250110, Meerut City, U.P., India
| | - Bir Pal Singh
- Central Potato Research Institute, Shimla 171001, H.P., India
| | - Firoz Anwar
- Siddhartha Institute of Pharmacy, Uttarakhand Technical University, Dehradun 248001, U.K., India
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8
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Yang X, Gallegly ME, Hong C. A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov. Mycologia 2014; 106:57-65. [PMID: 24396104 DOI: 10.3852/13-043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A previously unknown Phytophthora species was isolated from irrigation water in Virginia, USA. This novel species produces abundant noncaducous and nonpapillate sporangia in soil water extract solution. It sometimes produces chlamydospores and hyphal swellings in aged cultures and in Petri's solution. This species has optimum vegetative growth at 30 C and grows well at 35 C. The lowest and highest temperatures for growth are 5 and 40 C. All isolates examined in this study are compatibility type A1 and produce mostly plerotic oospores when paired with an A2 mating-type tester of P. cinnamomi. Sequence analyses of the rDNA internal transcribed spacer (ITS) regions and the mitochondrially encoded cytochrome c oxidase 1 (cox 1) gene placed this species in clade 9 of the genus Phytophthora. These characteristics support the description of this taxon as a new species for which we propose the name P. hydrogena sp. nov. Further phylogenetic and physiological investigations of clade 9 species revealed a high-temperature tolerant cluster including P. hydrogena, P. aquimorbida, P. hydropathica, P. irrigata, P. chrysanthemi, P. insolita, P. polonica and P. parsiana. These species all grow well at 35 C. The monophyly of the species in this heat-tolerant cluster except P. insolita and P. polonica is highly supported by the maximum-likelihood analyses of the ITS and cox 1 sequences.
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Affiliation(s)
- Xiao Yang
- Department of Plant Pathology, Physiology and Weed Science, Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, Virginia 23455
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9
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Heat treatment induced bacterial changes in irrigation water and their implications for plant disease management. World J Microbiol Biotechnol 2013; 30:1591-601. [PMID: 24343781 DOI: 10.1007/s11274-013-1583-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 12/12/2013] [Indexed: 10/25/2022]
Abstract
A new heat treatment for recycled irrigation water using 48 °C for 24 h to inactivate Phytophthora and bacterial plant pathogens is estimated to reduce fuel cost and environmental footprint by more than 50 % compared to current protocol (95 °C for 30 s). The objective of this study was to determine the impact of this new heat treatment temperature regime on bacterial community structure in water and its practical implications. Bacterial communities in irrigation water were analyzed before and after heat treatment using both culture-dependent and -independent strategies based on the 16S ribosomal DNA. A significant shift was observed in the bacterial community after heat treatment. Most importantly, bacteria with biological control potential--Bacillus and Paenibacillus, and Pseudomonas species became more abundant at both 48 and 42 °C. These findings imply that the new heat treatment procedure not only controls existing plant pathogens but also may make the heat-treated irrigation water a more antagonistic environment against plant pathogens, promoting sustainable disease management.
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Yang X, Copes WE, Hong C. Two novel species representing a new clade and cluster of Phytophthora. Fungal Biol 2013; 118:72-82. [PMID: 24433678 DOI: 10.1016/j.funbio.2013.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/24/2013] [Accepted: 11/05/2013] [Indexed: 11/25/2022]
Abstract
Phytophthora stricta sp. nov. and Phytophthora macilentosa sp. nov. are described based on morphological, physiological and molecular characters in this study. Phytophthora stricta represents a previously unknown clade in the rRNA internal transcribed spacer (ITS)-based phylogeny. Phytophthora macilentosa, along with nine other species, consistently forms a high temperature-tolerant cluster within ITS clade 9. These observations are supported by the sequence analysis of the mitochondrial cytochrome c oxidase 1 gene. Both species are heterothallic and all examined isolates are A1 mating type. Phytophthora stricta produces nonpapillate and slightly caducous sporangia. This species is named after its characteristic constrictions on sporangiophores. Phytophthora macilentosa produces nonpapillate and noncaducous sporangia, which are mostly elongated obpyriform with a high length to breadth ratio. Both species were recovered from irrigation water of an ornamental plant nursery in Mississippi, USA and P. stricta was also recovered from stream water in Virginia, USA.
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Affiliation(s)
- Xiao Yang
- Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, VA, USA.
| | - Warren E Copes
- Agricultural Research Service, United States Department of Agriculture, Thad Cochran Southern Horticultural Laboratory, Poplarville, MS, USA
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, VA, USA
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Schroeder KL, Martin FN, de Cock AWAM, Lévesque CA, Spies CFJ, Okubara PA, Paulitz TC. Molecular Detection and Quantification of Pythium Species: Evolving Taxonomy, New Tools, and Challenges. PLANT DISEASE 2013; 97:4-20. [PMID: 30722255 DOI: 10.1094/pdis-03-12-0243-fe] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Pythium is one of the most important groups of soilborne plant pathogens, present in almost every agricultural soil and attacking the roots of thousands of hosts, reducing crop yield and quality. Most species are generalists, necrotrophic pathogens that infect young juvenile tissue. In fact, Cook and Veseth have called Pythium the "common cold" of wheat, because of its chronic nature and ubiquitous distribution. Where Pythium spp. are the cause of seedling damping-off or emergence reduction, the causal agent can easily be identified based on symptoms and culturing. In more mature plants, however, infection by Pythium spp. is more difficult to diagnose, because of the nonspecific symptoms that could have abiotic causes such as nutrient deficiencies or be due to other root rotting pathogens. Molecular methods that can accurately identify and quantify this important group are needed for disease diagnosis and management recommendations and to better understand the epidemiology and ecology of this important group. The purpose of this article is to outline the current state-of-the-art in the detection and quantification of this important genus. In addition, we will introduce the reader to new changes in the taxonomy of this group.
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Affiliation(s)
| | | | | | - C André Lévesque
- Agriculture and Agri-Food Canada, Central Experimental Farm, Ottawa, ON
| | | | - Patricia A Okubara
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
| | - Timothy C Paulitz
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
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12
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del Castillo-Múnera J, Cárdenas M, Pinzón A, Castañeda A, Bernal AJ, Restrepo S. Developing a taxonomic identification system of Phytophthora species based on microsatellites. Rev Iberoam Micol 2012. [PMID: 23202806 DOI: 10.1016/j.riam.2012.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Phytophthora is the most important genus of the Oomycete plant pathogens. Nowadays, there are 117 described species in this genus, most of them being primary invaders of plant tissues. The different species are causal agents of diseases in a wide range of crops and plants in natural environments. In order to develop control strategies against Phytophthoraspecies, it is important to know the biology, ecology and evolutionary processes of these important pathogens. AIMS The aim of this study was to propose and validate a low cost identification system for Phytophthora species based on a set of polymorphic microsatellite (SSRs) markers. METHODS Thirty-three isolates representing Phytophthora infestans, Phytophthora andina, Phytophthora sojae, Phytophthora cryptogea, Phytophthora nicotianae, Phytophthora capsici and Phytophthora cinnamomi species were obtained, and 13 SSRs were selected as potentially transferable markers between these species. Amplification conditions, including annealing temperatures, were standardized for several markers. RESULTS A subset of these markers amplified in all species, showing species-specific alleles. CONCLUSIONS The adaptability and impact of the identification system in Colombia, an Andean agricultural country where different Phytophthora species co-exist in the same or in several hosts grown together, are discussed.
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Affiliation(s)
- Johanna del Castillo-Múnera
- Laboratorio de Micología y Fitopatología, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá D.C., Colombia
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13
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Martin FN, Abad ZG, Balci Y, Ivors K. Identification and Detection of Phytophthora: Reviewing Our Progress, Identifying Our Needs. PLANT DISEASE 2012; 96:1080-1103. [PMID: 30727075 DOI: 10.1094/pdis-12-11-1036-fe] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
With the increased attention given to the genus Phytophthora in the last decade in response to the ecological and economic impact of several invasive species (such as P. ramorum, P. kernoviae, and P. alni), there has been a significant increase in the number of described species. In part, this is due to the extensive surveys in historically underexplored ecosystems (e.g., forest and stream ecosystems) undertaken to determine the spread of invasive species and the involvement of Phytophthora species in forest decline worldwide (e.g., oak decline). The past decade has seen an approximate doubling in the number of described species within the genus Phytophthora, and the number will likely continue to increase as more surveys are completed and greater attention is devoted to clarifying phylogenetic relationships and delineating boundaries in species complexes. The development of molecular resources, the availability of credible sequence databases to simplify identification of new species, and the sequencing of several genomes have provided a solid framework to gain a better understanding of the biology, diversity, and taxonomic relationships within the genus. This information is much needed considering the impact invasive or exotic Phytophthora species have had on natural ecosystems and the regulatory issues associated with their management. While this work is improving our ability to identify species based on phylogenetic grouping, it has also revealed that the genus has a much greater diversity than previously appreciated.
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Affiliation(s)
- Frank N Martin
- USDA, ARS, Crop Improvement and Protection Research Unit, Salinas, CA
| | - Z Gloria Abad
- USDA, APHIS, PPQ, Center for Plant Health Science and Technology (CPHST), Beltsville Laboratory, MD
| | - Yilmaz Balci
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD
| | - Kelly Ivors
- Department of Plant Pathology, NC State University, Mountain Hort. Crops Research & Extension Center, Mills River, NC
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Abstract
The Key to the Common Phytophthora species (Lucid v 3.4) is a matrix-based computerized identification key and includes important morphological and molecular characters that are useful for identification of 55 common species of Phytophthora. A set of 20 features are used to make a correct species identification. Once a culture is obtained, the user enters responses to known character state options into Lucid Player, and the correct species is identified. Illustrations of each character state for a feature are included in the key. The main morphological features included in the key are: asexual structures, sexual structures, and chlamydospore, hyphae, and cultural characteristics. The user can read an illustrated "Fact Sheet" on each species that includes pictures of morphological characters, disease symptoms, host range, and relevant references. A cross-linked glossary of terminology is included in each fact sheet. In addition, a DNA search function that contains a simple search of internal transcribed spacer (ITS) and Barcode of Life (BOL, 5' end of the cox 1 gene) sequences for each species can be queried. The key was created to provide teachers, diagnosticians, and regulatory personnel with easily accessible tools to distinguish common species in the genus Phytophthora based on a number of important morphological and molecular characteristics. The key is available for purchase from APS Press and should provide another useful tool for the identification of members of this destructive group of Oomycete plant pathogens.
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Affiliation(s)
- Jean Beagle Ristaino
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695
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Zhang Y, Zhang S, Wang M, Bai F, Liu X. High diversity of the fungal community structure in naturally-occurring Ophiocordyceps sinensis. PLoS One 2010; 5:e15570. [PMID: 21179540 PMCID: PMC3002287 DOI: 10.1371/journal.pone.0015570] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Accepted: 11/13/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Ophiocordyceps sinensis (syn. Cordyceps sinensis), which is a parasite of caterpillars and is endemic to alpine regions on the Tibetan Plateau, is one of the most valuable medicinal fungi in the world. "Natural O. sinensis specimens" harbor various other fungi. Several of these other fungi that have been isolated from natural O. sinensis specimens have similar chemical components and/or pharmaceutical effects as O. sinensis. Nevertheless, the mycobiota of natural O. sinensis specimens has not been investigated in detail. METHODOLOGY/PRINCIPAL FINDINGS Based on the technique of PCR-single-strand conformation polymorphism (PCR-SSCP), the mycobiota of three different sections (stromata, sclerotia, and mycelial cortices) from natural O. sinensis specimens were investigated using both culture-dependent and -independent methods. For the culture-dependent method, 572 fungal strains were isolated, and 92 putative operational taxonomic units (OTUs) were identified from 226 sequenced strains with the threshold of 97%. For the culture-independent method, 490 fungal clones were identified from about 3000 clones of ITS fragments from the whole-community DNA; based on PCR-SSCP analyses, 266 of these clones were selected to be sequenced, and 118 putative OTUs were detected. The overwhelming majority of isolates/clones and OTUs were detected from mycelial cortices; only a few were detected from stromata and sclerotia. The most common OTUs detected with both methods belonged to Ascomycota; however, only 13 OTUs were detected simultaneously by both methods. Potential novel lineages were detected by each of the two methods. CONCLUSIONS/SIGNIFICANCE A great number of fungal species present in the mycobiota of naturally-occurring O. sinensis specimens were detected, and many of them may represent undescribed lineages. That only a few of the same OTUs were detected by both methods indicated that different methods should be used. This study increased our understanding about the fungal community structure of this valuable medicinal herb.
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Affiliation(s)
- Yongjie Zhang
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Shu Zhang
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Mu Wang
- School of Plant Sciences and Technology, Agriculture and Animal Husbandry College of Tibet, Nyingchi, Tibet, China
| | - Fengyan Bai
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Key Laboratory of Systematic Mycology and Lichenology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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16
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Bezuidenhout C, Denman S, Kirk S, Botha W, Mostert L, McLeod A. Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov. PERSOONIA 2010; 25:32-49. [PMID: 21339965 PMCID: PMC3028514 DOI: 10.3767/003158510x538371] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/03/2010] [Indexed: 11/25/2022]
Abstract
Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports their identity, mating type, and pathogenicity to young Agathosma plants. Using morphological and sequence data seven Phytophthora taxa were identified: the A1 mating type of P. cinnamomi var. cinnamomi, P. cinnamomi var. parvispora and P. cryptogea, the A2 mating type of P. drechsleri and P. nicotianae, and two homothallic taxa from the P. citricola complex. The identity of isolates in the P. citricola complex was resolved using reference isolates of P. citricola CIT groups 1 to 5 sensu Oudemans et al. (1994) along with multi-locus phylogenies (three nuclear and two mitochondrial regions), isozyme analyses, morphological characteristics and temperature-growth studies. These analyses revealed the isolates from Agathosma to include P. multivora and a putative novel species, P. taxon emzansi. Furthermore, among the P. citricola reference isolates the presence of a new species was revealed, described here as P. capensis. Findings of our study, along with some recent other studies, have contributed to resolving some of the species complexity within the P. citricola complex, resulting in the identification of a number of phylogenetically distinct taxa. The pathogenicity of representative isolates of the taxa from Agathosma was tested on A. betulina seedlings. The putative novel species, P. taxon emzansi, and P. cinnamomi var. parvispora were non-pathogenic, whereas the other species were pathogenic to this host.
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Affiliation(s)
- C.M. Bezuidenhout
- Agricultural Research Council, Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa
| | - S. Denman
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU104LH, England
| | - S.A. Kirk
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU104LH, England
| | - W.J. Botha
- Agricultural Research Council, Plant Protection Research Institute, P. Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, P. Bag X1, Matieland, 7602, South Africa
| | - A. McLeod
- Department of Plant Pathology, University of Stellenbosch, P. Bag X1, Matieland, 7602, South Africa
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Parkunan V, Johnson CS, Bowman BC, Hong CX. Population Structure, Mating Type, and Mefenoxam Sensitivity of Phytophthora nicotianae in Virginia Tobacco Fields. PLANT DISEASE 2010; 94:1361-1365. [PMID: 30743626 DOI: 10.1094/pdis-05-10-0338] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Black shank is an important disease of tobacco (Nicotiana tabacum) caused by the fungus-like organism, Phytophthora nicotianae. Three physiological races (0, 1, and 3) have been documented in the United States. Shifts in the pathogen population structure have become a concern due to the widespread use of cultivars possessing resistance to race 0 arising from a single gene (Php or Phl). A comprehensive statewide survey conducted throughout major tobacco-growing areas during summer 2006 and supplemented by additional isolates in 2007 and 2008 yielded 217 isolates from flue-cured, burley, and dark fire-cured tobacco fields. After determining species identity using a single-strand conformational polymorphism fingerprinting technique, the race identity of isolates was assessed via greenhouse tests using three differential cultivars (Hicks, L8, and NC1071). Approximately 76% of the isolates belonged to race 1, 21% to race 0, and the remaining 3% were race 3. This race structure was comparable with those in the other tobacco-producing states in the United States. Approximately 94% of isolates belonged to A2 mating type and merely 6% were A1. These data suggest that it is unlikely that sexual recombination serves as a major mechanism enhancing the genetic diversity of the pathogen in Virginia. All isolates were also evaluated against mefenoxam at 5 μg/ml. None were insensitive; 98% of isolates were either highly sensitive or sensitive and the remaining 2% were intermediately sensitive. These results indicate that mefenoxam remains effective for control of black shank in Virginia. The results of this study can assist breeders to develop cultivars possessing the most appropriate set of disease resistance traits, as well as extension specialists, county agents, and tobacco growers in their decision-making process to manage tobacco black shank in Virginia.
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Affiliation(s)
- V Parkunan
- Virginia Tech Southern Piedmont Agricultural Research and Extension Center, Blackstone 23824
| | - C S Johnson
- Virginia Tech Southern Piedmont Agricultural Research and Extension Center, Blackstone 23824
| | - B C Bowman
- Virginia Tech Southern Piedmont Agricultural Research and Extension Center, Blackstone 23824
| | - C X Hong
- Virginia Tech Hampton Roads Agricultural Research and Extension Center, Virginia Beach 23455
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Siah A, Tisserant B, El Chartouni L, Duyme F, Deweer C, Roisin-Fichter C, Sanssené J, Durand R, Reignault P, Halama P. Mating type idiomorphs from a French population of the wheat pathogen Mycosphaerella graminicola: widespread equal distribution and low but distinct levels of molecular polymorphism. Fungal Biol 2010; 114:980-90. [DOI: 10.1016/j.funbio.2010.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 09/06/2010] [Accepted: 09/15/2010] [Indexed: 10/19/2022]
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19
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Hong C, Gallegly ME, Richardson PA, Kong P. Phytophthora pini Leonian resurrected to distinct species status. Mycologia 2010; 103:351-60. [PMID: 21415291 DOI: 10.3852/10-058] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phytophthora pini was named by Leonian in 1925, but this species was largely ignored until 1956 and then merged with P. citricola by Waterhouse in 1963. This study compared the ex-type and ex-authentic cultures of these two species with isolates of P. plurivora and the P. citricola subgroups Cil I and III reported previously. Examination of these isolates revealed that the ex-type culture of P. pini is identical to P. citricola I. Phytophthora pini Leonian therefore is resurrected to distinct species status and redescribed here with a Latin description, replacing P. citricola I. Molecular, physiological and morphological descriptions of this species are presented. The molecular description includes DNA sequences of five nuclear and mitochondrial regions as well as PCR-SSCP fingerprints. The relationship among the above species and other species recently segregated from the P. citricola complex also is discussed.
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Affiliation(s)
- Chuanxue Hong
- Virginia Polytechnic Institute and State University, Virginia Beach, Virginia 23455, USA.
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20
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Weiland JE, Nelson AH, Hudler GW. Aggressiveness of Phytophthora cactorum, P. citricola I, and P. plurivora from European Beech. PLANT DISEASE 2010; 94:1009-1014. [PMID: 30743488 DOI: 10.1094/pdis-94-8-1009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora cactorum, P. citricola I, and P. plurivora cause bleeding cankers on mature European beech (Fagus sylvatica) trees in the northeastern United States. Inoculation experiments were conducted to compare the aggressiveness of the three Phytophthora spp. on stems, leaf disks, and roots of European beech and common lilac (Syringa vulgaris) seedlings. Isolates were obtained from bleeding cankers on European beech from five cities in New York (Albany, Ithaca, Oyster Bay, Plainview, and Rochester) and from a bleeding canker on sugar maple in Ithaca, NY. Stems were inoculated with colonized agar plugs, leaf disks with a zoospore suspension, and roots via infested soil at three inoculum levels. All organs of inoculated beech and lilac developed disease except for lilac roots inoculated with zoospores of P. cactorum. Disease incidence, severity, and plant survival were dependent on isolate and were also influenced by the tissue inoculated and host. Isolates of P. cactorum were the least aggressive and caused less necrosis than isolates of P. citricola I and P. plurivora. Results emphasize the utility of stem and root inoculation for evaluation of this canker disease and underscore critical differences in species aggressiveness.
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Affiliation(s)
- Jerry E Weiland
- United States Department of Agriculture-Agriculture Research Service, Horticultural Crops Research Laboratory, and Oregon State University, Department of Botany and Plant Pathology, Corvallis 97331
| | - Angela H Nelson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14850
| | - George W Hudler
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14850
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21
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Hu J, Hong C, Stromberg EL, Moorman GW. Mefenoxam Sensitivity in Phytophthora cinnamomi Isolates. PLANT DISEASE 2010; 94:39-44. [PMID: 30754386 DOI: 10.1094/pdis-94-1-0039] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora cinnamomi is a destructive root pathogen of numerous woody plant species in the ornamental plant nursery. Sixty-five isolates of P. cinnamomi were evaluated for mefenoxam sensitivity on 20% clarified V8 agar amended with mefenoxam at 0 or 100 μg/ml. In the presence of mefenoxam at 100 μg/ml, eight isolates were intermediately sensitive, with mycelium growth ranging between 11 and 18% of the nonamended control, and 57 isolates were highly sensitive, with little or no mycelium growth. Five intermediately sensitive and five sensitive isolates were chosen to characterize their responses to mefenoxam at 0, 0.1, 1, 10, and 100 μg/ml. For intermediately sensitive isolates, the mefenoxam concentration causing 50% inhibition of mycelium growth (EC50 values) ranged between 0.03 and 0.08 μg/ml; EC50 values for sensitive isolates varied from 0.01 to 0.02 μg/ml. Five intermediately sensitive and seven sensitive isolates were selected further to assess in vivo sensitivity to mefenoxam using Lupinus angustifolius 'Russell Hybrids'. Lupine seedlings were treated with distilled water or mefenoxam at label rate (Subdue MAXX, 1 fl. oz. of product per 100 gal.) and then, 2 days later, inoculated with a 5-mm-diameter mycelial plug of P. cinnamomi on each cotyledon. Mefenoxam-treated plants averaged more than 96% less disease than water-treated plants. Mefenoxam provided adequate protection of lupines from infection by all 12 isolates regardless of their in vitro levels of sensitivity to mefenoxam. The ability to develop mefenoxam resistance was assessed in P. cinnamomi isolates with different mefenoxam sensitivity by UV mutagenesis and adapting mycelium to increasing concentrations of mefenoxam. Both UV mutagenesis and mycelium adaptation generated isolates with reduced sensitivity to mefenoxam. These isolates, however, did not grow as quickly as their corresponding parent. This study suggests that P. cinnamomi populations from ornamental nurseries in Virginia are sensitive to mefenoxam.
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Affiliation(s)
- Jiahuai Hu
- Hampton Roads Agricultural Research and Extension Center, Virginia Beach, VA 23455
| | - Chuanxue Hong
- Hampton Roads Agricultural Research and Extension Center, Virginia Beach, VA 23455
| | - Erik L Stromberg
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg 24061
| | - Gary W Moorman
- Department of Plant Pathology, The Pennsylvania State University, University Park 16802
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Hong CX, Gallegly ME, Browne GT, Bhat RG, Richardson PA, Kong P. The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp. nov. Mycologia 2009; 101:833-40. [PMID: 19927748 DOI: 10.3852/08-214] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Isolates from avocado tree cankers have been recognized as a distinct subgroup within the P. citricola complex since 1974, both morphologically and molecularly (isozyme and amplified fragment length polymorphism [AFLP] analyses). This subgroup is formally separated from P. citricola after comparative DNA fingerprinting and sequence analyses of the ITS region, as well as by morphological examinations. This new taxon is homothallic, produces plerotic oospores with paragynous antheridia and noncaducous semipapillate sporangia. Morphologically it differs from other species of Waterhouse group III by producing many large bizarre-shaped sporangia and smaller oogonia with asymmetric capitate antheridia. It belongs to clade 2 and is phylogenetically closer to P. siskiyouensis, P. capsici and P. tropicalis than to P. citricola. P. mengei can be easily differentiated from its relatives in the same clade and other species of this morpho-group by DNA fingerprints and sequence analysis. This new taxon is named Phytophthora mengei sp. nov.
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Affiliation(s)
- C X Hong
- Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, Department of Plant Pathology, Physiology and Weed Science, 1444 Diamond Springs Road, Virginia Beach, Virginia 23455, USA.
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23
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Broders KD, Wallhead MW, Austin GD, Lipps PE, Paul PA, Mullen RW, Dorrance AE. Association of soil chemical and physical properties with Pythium species diversity, community composition, and disease incidence. PHYTOPATHOLOGY 2009; 99:957-67. [PMID: 19594315 DOI: 10.1094/phyto-99-8-0957] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A high-throughput baiting and identification process identified more than 7,000 isolates of Pythium from 88 locations in Ohio. Isolates were identified using direct-colony polymerase chain reaction followed by single-strand conformational polymorphism, and communities were assembled using the Jaccard similarity coefficient and cluster analysis. Both univariate and multivariate statistics were used to evaluate differences in soil properties between communities, and canonical discriminant analysis (CDA) was used to assess the strength of the association of soil variables within communities from 83 of the locations. In all, 21 species of Pythium were identified but only 6 were recovered from >40% of the locations. Five communities were formed using the cluster analysis, and significant differences were observed in disease incidence, as well as soil pH, calcium, magnesium, and cation exchange capacity between communities. Stepwise multiple discriminant analysis and CDA identified pH, calcium, magnesium, and field capacity as contributing the most to the separation of the five Pythium communities. There was a strong association between abiotic soil components and the structure of Pythium communities, as well as diversity of Pythium spp. collected from agronomic production fields in Ohio.
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Affiliation(s)
- K D Broders
- Department of Plant Pathology, School of Natural Resources, The Ohio State University, Wooster, OH 44691, USA
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24
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Kong P, Moorman GW, Lea-Cox JD, Ross DS, Richardson PA, Hong C. Zoosporic tolerance to pH stress and its implications for Phytophthora species in aquatic ecosystems. Appl Environ Microbiol 2009; 75:4307-14. [PMID: 19429548 PMCID: PMC2704844 DOI: 10.1128/aem.00119-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2009] [Accepted: 05/04/2009] [Indexed: 11/20/2022] Open
Abstract
Phytophthora species, a group of destructive plant pathogens, are commonly referred to as water molds, but little is known about their aquatic ecology. Here we show the effect of pH on zoospore survival of seven Phytophthora species commonly isolated from irrigation reservoirs and natural waterways and dissect zoospore survival strategy. Zoospores were incubated in a basal salt liquid medium at pH 3 to 11 for up to 7 days and then plated on a selective medium to determine their survival. The optimal pHs differed among Phytophthora species, with the optimal pH for P. citricola at pH 9, the optimal pH for P. tropicalis at pH 5, and the optimal pH for the five other species, P. citrophthora, P. insolita, P. irrigata, P. megasperma, and P. nicotianae, at pH 7. The greatest number of colonies was recovered from zoospores of all species plated immediately after being exposed to different levels of pH. At pH 5 to 11, the recovery rate decreased sharply (P < or = 0.0472) after 1-day exposure for five of the seven species. In contrast, no change occurred (P > or = 0.1125) in the recovery of any species even after a 7-day exposure at pH 3. Overall, P. megasperma and P. citricola survived longer at higher rates in a wider range of pHs than other species did. These results are generally applicable to field conditions as indicated by additional examination of P. citrophthora and P. megasperma in irrigation water at different levels of pH. These results challenge the notion that all Phytophthora species inhabit aquatic environments as water molds and have significant implications in the management of plant diseases resulting from waterborne microbial contamination.
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Affiliation(s)
- Ping Kong
- Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, Virginia Beach, 23455, USA
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25
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Jung T, Burgess T. Re-evaluation of Phytophthora citricola isolates from multiple woody hosts in Europe and North America reveals a new species, Phytophthora plurivora sp. nov. PERSOONIA 2009; 22:95-110. [PMID: 20198142 PMCID: PMC2789536 DOI: 10.3767/003158509x442612] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 03/26/2009] [Indexed: 11/25/2022]
Abstract
During large-scale surveys for soilborne Phytophthora species in forests and semi-natural stands and nurseries in Europe during the last decade, homothallic Phytophthora isolates with paragynous antheridia, semipapillate persistent sporangia and a growth optimum around 25 degrees C which did not form catenulate hyphal swellings, were recovered from 39 host species in 16 families. Based on their morphological and physiological characters and the similarity of their ITS DNA sequences with P. citricola as designated on GenBank, these isolates were routinely identified as P. citricola. In this study DNA sequence data from the internal transcribed spacer regions (ITS1 and ITS2) and 5.8S gene of the rRNA operon, the mitochondrial cox1 and beta-tubulin genes were used in combination with morphological and physiological characteristics to characterise these isolates and compare them to the ex-type and the authentic type isolates of P. citricola, and two other taxa of the P. citricola complex, P. citricola I and the recently described P. multivora. Due to their unique combination of morphological, physiological and molecular characters these semipapillate homothallic isolates are described here as a new species, P. plurivora sp. nov.
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Affiliation(s)
- T. Jung
- Centre for Phytophthora Science and Management, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
- Phytophthora Research and Consultancy, Thomastrasse 75, 83098 Brannenburg, Germany
| | - T.I. Burgess
- Centre for Phytophthora Science and Management, School of Biological Sciences and Biotechnology, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
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26
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Martin FN, Coffey MD, Zeller K, Hamelin RC, Tooley P, Garbelotto M, Hughes KJD, Kubisiak T, Bilodeau GJ, Levy L, Blomquist C, Berger PH. Evaluation of molecular markers for Phytophthora ramorum detection and identification: testing for specificity using a standardized library of isolates. PHYTOPATHOLOGY 2009; 99:390-403. [PMID: 19271981 DOI: 10.1094/phyto-99-4-0390] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Given the importance of Phytophthora ramorum from a regulatory standpoint, it is imperative that molecular markers for pathogen detection are fully tested to evaluate their specificity in detection of the pathogen. In an effort to evaluate 11 reported diagnostic techniques, we assembled a standardized DNA library using accessions from the World Phytophthora Genetic Resource Collection for 315 isolates representing 60 described Phytophthora spp. as well as 11 taxonomically unclassified isolates. These were sent blind to collaborators in seven laboratories to evaluate published diagnostic procedures using conventional (based on internal transcribed spacer [ITS] and cytochrome oxidase gene [cox]1 and 2 spacer regions) and real-time polymerase chain reaction (based on ITS and cox1 and 2 spacer regions as well as beta-tubulin and elicitin genes). Single-strand conformation polymorphism (SSCP) analysis using an automated sequencer for data collection was also evaluated for identification of all species tested. In general, the procedures worked well, with varying levels of specificity observed among the different techniques. With few exceptions, all assays correctly identified all isolates of P. ramorum and low levels of false positives were observed for the mitochondrial cox spacer markers and most of the real-time assays based on nuclear markers (diagnostic specificity between 96.9 and 100%). The highest level of false positives was obtained with the conventional nested ITS procedure; however, this technique is not stand-alone and is used in conjunction with two other assays for diagnostic purposes. The results indicated that using multiple assays improved the accuracy of the results compared with looking at a single assay alone, in particular when the markers represented different genetic loci. The SSCP procedure accurately identified P. ramorum and was helpful in classification of a number of isolates to a species level. With one exception, all procedures accurately identified P. ramorum in blind evaluations of 60 field samples that included examples of plant infection by 11 other Phytophthora spp. The SSCP analysis identified eight of these species, with three identified to a species group.
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Affiliation(s)
- F N Martin
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, CA, USA.
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Quesada-Ocampo LM, Fulbright DW, Hausbeck MK. Susceptibility of Fraser Fir to Phytophthora capsici. PLANT DISEASE 2009; 93:135-141. [PMID: 30764108 DOI: 10.1094/pdis-93-2-0135] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora cinnamomi, P. drechsleri, P. citricola, and P. cactorum limit Fraser fir production, whereas P. capsici affects Solanaceous, Cucurbitaceous, and Fabaceous crops. Some vegetable growers in Michigan plant conifers for the Christmas tree market in fields infested with P. capsici. To determine the susceptibility of Fraser fir to P. capsici, stems (no wound or 1- or 3-mm-diameter wound) or roots (2 or 4 g of infested millet seed or 2 or 5 × 103 zoospores/ml of a zoospore suspension) of seedlings were inoculated with each of four P. capsici isolates and incubated in growth chambers (20 or 25°C). In addition, Fraser fir seedlings were planted in two commercial fields naturally infested with P. capsici. All P. capsici isolates tested incited disease in the seedlings regardless of incubation temperature or inoculation method. Seedlings (72%) planted in P. capsici-infested fields developed disease symptoms and died. Most of the P. capsici isolates obtained from the Fraser fir seedlings infected while in the field were recovered from root tissue. Identification was confirmed by species-specific direct colony polymerase chain reaction. The pathogen was successfully recovered from stems of all stem-inoculated seedlings, and from roots and stems of all root-inoculated seedlings; the phenotype of the recovered isolate matched the phenotype of the inoculum. This study suggests that planting Fraser fir in fields infested with P. capsici could result in infection and that adjustments in current rotational schemes are needed.
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Affiliation(s)
| | | | - M K Hausbeck
- Professor, Department of Plant Pathology, Michigan State University, East Lansing 48824
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Kuo HC, Su YL, Yang HL, Chen TY. Establishment and Application of PCR-SSCP Profile for Molecular Typing ofCordycepsFungi. FOOD BIOTECHNOL 2008. [DOI: 10.1080/08905430802458354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Gómez-Alpizar L, Hu CH, Oliva R, Forbes G, Ristaino JB. Phylogenetic relationships of Phytophthora andina, a new species from the highlands of Ecuador that is closely related to the Irish potato famine pathogen Phytophthora infestans. Mycologia 2008; 100:590-602. [PMID: 18833752 DOI: 10.3852/07-074r1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phylogenetic relationships of Phytophthora infestans sensu lato in the Andean highlands of South America were examined. Three clonal lineages (US-1, EC-1, EC-3) and one heterogeneous lineage (EC-2) were found in association with different host species in genus Solanum. The EC-2 lineage includes two mitochondrial (mtDNA) haplotypes, Ia and Ic. Isolates of P. infestans sensu lato EC-2 fit the morphological description of P. infestans but are different from any genotypes of P. infestans described to date. All isolates of P. infestans sensu lato from Ecuador were amplified by a P. infestans specific primer (PINF), and restriction fragment length patterns were identical in isolates amplified with ITS primers 4 and 5. The EC-1 clonal lineage of P. infestans sensu lato from S. andreanum, S. columbianum, S. paucijugum, S. phureja, S. regularifolium, S. tuberosum and S. tuquerense was confirmed to be P. infestans based on sequences of the cytochrome oxidase I (cox I) gene and intron 1 of ras gene. The EC-2 isolates with the Ic haplotype formed a distinct branch in the same clade with P. infestans and P. mirabilis, P. phaseoli and P. ipomoeae for both cox I and ras intron 1 phylogenies and were identified as the newly described species P. andina. Ras intron 1 sequence data suggests that P. andina might have arisen via hybridization between P. infestans and P. mirabilis.
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Affiliation(s)
- Luis Gómez-Alpizar
- Agronomic Research Center, Box 2060, University of Costa Rica, San Pedro, Montes de Oca, Costa Rica
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Hong C, Gallegly ME, Richardson PA, Kong P, Moorman GW. Phytophthora irrigata, a new species isolated from irrigation reservoirs and rivers in Eastern United States of America. FEMS Microbiol Lett 2008; 285:203-11. [DOI: 10.1111/j.1574-6968.2008.01226.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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31
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Hong C, Richardson PA, Kong P. Pathogenicity to Ornamental Plants of Some Existing Species and New Taxa of Phytophthora from Irrigation Water. PLANT DISEASE 2008; 92:1201-1207. [PMID: 30769481 DOI: 10.1094/pdis-92-8-1201] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Eighteen isolates from 12 species of Phytophthora, including several new taxa, were tested for pathogenicity to six ornamental and four vegetable species. The following three inoculation methods were used depending on infection court targeted: vermiculite culture inoculation for roots, agar block inoculation for fruit, and zoospore inoculation for foliage. All six new taxa (P. irrigata, P. hydropathica, Dre III, Cil I, Cip-like, and Gon I) are pathogenic to one or more test plants. Specifically, taxon Cil I was identified as a growing threat to horticultural crops, particularly ornamental crops in container production nurseries. The potential host list of P. tropicalis was expanded to four new families (Apocynaceae, Asteraceae, Begoniaceae, and Fabaceae) and one additional genus within each of three existing families (Ericaceae, Cucurbitaceae, and Solanaceae). New potential hosts were also identified for other existing species of Phytophthora. The practical implications of these results in crop health management programs for both ornamental and vegetable crops locally, and for development and implementation of agricultural biosecurity programs globally, are discussed.
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Affiliation(s)
- Chuanxue Hong
- Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, Department of Plant Pathology, Physiology and Weed Science, Virginia Beach, VA 23455
| | - Patricia A Richardson
- Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, Department of Plant Pathology, Physiology and Weed Science, Virginia Beach, VA 23455
| | - Ping Kong
- Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, Department of Plant Pathology, Physiology and Weed Science, Virginia Beach, VA 23455
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32
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Rapid differentiation of phenotypically similar yeast species by single-strand conformation polymorphism analysis of ribosomal DNA. Appl Environ Microbiol 2008; 74:2604-11. [PMID: 18344345 DOI: 10.1128/aem.02223-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including Saccharomyces species, medically important Candida species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.
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33
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Li J, Bai FY. Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans. Med Mycol 2008; 45:629-35. [PMID: 17885945 DOI: 10.1080/13693780701530950] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.
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Affiliation(s)
- Juan Li
- Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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Bowers JH, Martin FN, Tooley PW, Luz EDMN. Genetic and Morphological Diversity of Temperate and Tropical Isolates of Phytophthora capsici. PHYTOPATHOLOGY 2007; 97:492-503. [PMID: 18943290 DOI: 10.1094/phyto-97-4-0492] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Phytophthora capsici is a diverse species causing disease on a broad range of both temperate and tropical plants. In this study, we used cultural characteristics, amplified fragment length polymorphism (AFLP), and DNA sequence analyses of the ribosomal internal transcribed spacer (ITS) region and mitochondrial cytochrome oxidase II (cox II) genes to characterize temperate and tropical isolates from a wide range of host species. All but one temperate isolate grew at 35 degrees C, while all tropical isolates did not. All but two tropical isolates formed chlamydospores, while temperate isolates did not. There was strong bootstrap support for separation of temperate and tropical isolates using AFLP analysis; however, the temperate isolates appeared as a subgroup within the observed variation of the tropical isolates. The majority of temperate isolates clustered within a single clade with low variation regardless of host or geographical origin, while the tropical isolates were more variable and grouped into three distinct clades. Two clades of tropical isolates grouped together and were affiliated closely with the temperate isolates, while the third tropical clade was more distantly related. Phylogenetic analysis of the ITS regions resulted in similar groupings and variation within and between the temperate and tropical isolates as with the AFLP results. Sequence divergence among isolates and clades was low, with more variation within the tropical isolates than within the temperate isolates. Analysis of other species revealed shorter branch lengths separating temperate and tropical isolates than were observed in comparisons among other phylogenetically closely related species in the genus. Analysis of cox II sequence data was less clear. Although the temperate and tropical isolates grouped together apart from other species, there was no bootstrap support for separating these isolates. Restriction fragment length polymorphism (RFLP) analysis of the ITS regions separated the temperate and tropical isolates, as in the AFLP and ITS phylogenetic analyses. However, RFLP analysis of the cox I and II gene cluster did not distinguish between temperate and tropical isolates. The differences in grouping of isolates in these two RFLP studies should be helpful in identifying isolate subgroups. Our data do not fully clarify whether or not temperate and tropical isolates should be separated into different species. The available worldwide data are incomplete and the full range of variation in the species is not yet known. We suggest refraining from using the epithet P. tropicalis until more data are available.
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Abstract
SUMMARY Phytophthora cinnamomi Rands was first isolated from cinnamon trees in Sumatra in 1922. The pathogen is believed to have originated near Papua New Guinea but now has a worldwide distribution. P. cinnamomi is heterothallic with A1 and A2 mating types; however, even in areas in which both mating types are present, it appears that genetic diversity arises asexually rather than as a result of sexual recombination. P. cinnamomi can grow saprophytically in the soil for long periods, rapidly capitalizing on the advent of favourable conditions to sporulate and produce vast numbers of asexual, biflagellate zoospores. The motile zoospores are attracted to suitable infection sites, where they attach and invade the plant. Within a few days, hyphae ramify throughout the tissues of susceptible plants, forming sporangia on the plant surface and rapidly amplifying the disease inoculum. Over the last 10-15 years, molecular analyses have clarified details of the phylogeny of P. cinnamomi and other Oomycetes. Research on P. cinnamomi has given rise to a more comprehensive understanding of the structure and function of the motile zoospores. New methods have been developed for P. cinnamomi identification and diagnosis. Long-term studies of diseased sites, particular those in southern Australia, have produced a better understanding of the epidemiology of P. cinnamomi diseases. Research has also increased our knowledge of the mode of action and efficacy of inhibitors of P. cinnamomi diseases, especially the phosphonates. This review will present an overview of the advances these studies have made in our understanding of P. cinnamomi pathogenicity, epidemiology and control. TAXONOMY Phytophthora cinnamomi Rands; kingdom Chromista; phylum Oomycota; order Peronosporales; family Peronosporaceae; genus Phytophthora. HOST RANGE Likely to infect in excess of 3000 species of plants including over 2500 Australian native species, and crops such as avocado, pineapple, peach, chestnut and macadamia. Disease symptoms: A root pathogen which usually causes rotting of fine and fibrous roots but which can also cause stem cankers. Often causes dieback of young shoots and is thought to do so as a result of interference with transpiration from roots to shoots. USEFUL WEBSITES http://genome.jgi-psf.org/physo00.info.html; http://phytophthora.vbi.vt.edu.
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Affiliation(s)
- Adrienne R Hardham
- Plant Cell Biology Group, Research School of Biological Sciences, The Australian National University, Canberra, ACT 2601, Australia
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Kuhn DN, Schnell RJ. Use of capillary array electrophoresis single-strand conformational polymorphism analysis to estimate genetic diversity of candidate genes in germplasm collections. Methods Enzymol 2005; 395:238-58. [PMID: 15865971 DOI: 10.1016/s0076-6879(05)95015-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Capillary array electrophoresis single-strand conformation polymorphism (CAE-SSCP) analysis provides a reliable high-throughput method to genotype plant germplasm collections. Primers designed for highly conserved regions of candidate genes can be used to amplify DNA from plants in the collection. These amplified DNA fragments of identical length are turned into useful markers by assaying sequence differences by CAE-SSCP analysis. Sequence differences affect the electrophoretic mobility of single-stranded DNA under non-denaturing conditions. By collecting the mobility data for both strands assayed at two temperatures, alleles can be defined by mobility alone. For a germplasm collection with an unknown number of alleles at a locus, such mobility data of homozygotes can be used to determine the number of unique alleles without the necessity of cloning and sequencing each allele.
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Affiliation(s)
- David N Kuhn
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA
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Kong P, Richardson PA, Moorman GW, Hong C. Single-strand conformational polymorphism analysis of the ribosomal internal transcribed spacer 1 for rapid species identification within the genus Pythium. FEMS Microbiol Lett 2005; 240:229-36. [PMID: 15522512 DOI: 10.1016/j.femsle.2004.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2004] [Revised: 09/21/2004] [Accepted: 09/23/2004] [Indexed: 11/29/2022] Open
Abstract
Single-strand conformational polymorphism (SSCP) of the ribosomal internal transcribed spacer 1 (ITS-1) was characterized for 58 isolates of Pythium, representing 41 species from the five groups of Plaats-Niterink. Thirty-one species each produced a distinct SSCP pattern. Three species produced more than one unique pattern, corresponding to morphological subgrouping. The remaining seven species produced three distinct patterns with two or three morphologically similar species sharing a pattern. A successful blind test with four samples and the identification of eight previously unknown isolates from irrigation water demonstrated the reliability of this technique for species identification. Each SSCP pattern was defined and described by the positions of the top and bottom bands and the number of bands in between, which allows laboratories to use this technique without need to access the type isolates of Pythium species.
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Affiliation(s)
- Ping Kong
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, 1444 Diamond Springs Road, Virginia Beach, VA 23455, USA
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Kong P, Richardson PA, Hong C. Direct colony PCR-SSCP for detection of multiple pythiaceous oomycetes in environmental samples. J Microbiol Methods 2005; 61:25-32. [PMID: 15676193 DOI: 10.1016/j.mimet.2004.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2004] [Revised: 10/26/2004] [Accepted: 10/27/2004] [Indexed: 11/18/2022]
Abstract
Colony PCR was developed for detection of pythiaceous species recovered on selective agar plates without DNA extraction. A minute amount of mycelia from a single colony was picked up with a pipette tip and added directly to the PCR mix as template for DNA amplification. Successful amplification was achieved in over 95% of the colonies recovered from plant tissues, irrigation water and soil with species-specific primers or oomycete ITS-1 primers. PCR was inhibited in the case of colonies emerging from unwashed pine bark potting mix plates. Direct colony PCR with ITS-1 primers combined with single-strand conformation polymorphism analysis (SSCP) was used to determine population levels of single and multiple species in plant and environmental samples. Application of this technique for disease diagnosis and monitoring pathogen sources was explored, and the potential for studying diversity and population dynamics of other cultivated microbial communities in the environment is discussed.
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Affiliation(s)
- Ping Kong
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Hampton Roads Agricultural Research and Extension Center, 1444 Diamond Springs Road, Virginia Beach, VA 23455, USA.
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Martin FN, Tooley PW. Identification of phytophthora isolates to species level using restriction fragment length polymorphism analysis of a polymerase chain reaction-amplified region of mitochondrial DNA. PHYTOPATHOLOGY 2004; 94:983-991. [PMID: 18943075 DOI: 10.1094/phyto.2004.94.9.983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Polymerase chain reaction primers spanning the mitochondrially encoded coxI and II genes have been identified that were capable of amplifying target DNA from all 152 isolates of 31 species in the genus Phytophthora that were tested. Digestion of the amplicons with restriction enzymes generated species-specific restriction fragment length polymorphism banding profiles that were effective for isolate classification to a species level. Of the 24 species in which multiple isolates were examined, intraspecific polymorphisms were not observed for 16 species, while 5 species exhibited limited intraspecific polymorphism that could be explained by the addition/loss of a single restriction site. Intraspecific polymorphisms were observed for P. megakarya, P. megasperma, and P. syringae; however, these differences may be a reflection of the variation that exists in these species as reported in the literature. Although digestion with AluI alone could differentiate most species tested, single digests with a total of four restriction enzymes were used in this investigation to enhance the accuracy of the technique and minimize the effect of intraspecific variability on correct isolate identification. The use of the computer program BioNumerics simplified data analysis and identification of isolates. Successful template amplification was obtained with DNA recovered from hyphae using a boiling miniprep procedure, thereby reducing the time and materials needed for conducting this analysis.
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McKee DR, Thomson MS. Nucleic acid stain-dependent single strand conformation polymorphisms. Biotechniques 2004; 37:46, 48, 50. [PMID: 15283199 DOI: 10.2144/04371bm04] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- David R McKee
- University of Wisconsin-Parkside, Kenosha, IL 53141, USA
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Kroon LPNM, Verstappen ECP, Kox LFF, Flier WG, Bonants PJM. A Rapid Diagnostic Test to Distinguish Between American and European Populations of Phytophthora ramorum. PHYTOPATHOLOGY 2004; 94:613-620. [PMID: 18943486 DOI: 10.1094/phyto.2004.94.6.613] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT A new devastating disease in the United States, commonly known as Sudden Oak Death, is caused by Phytophthora ramorum. This pathogen, which previously was described attacking species of Rhododendron and Viburnum in Germany and the Netherlands, has established itself in forests on the central coast of California and is killing scores of native oak trees (Lithocarpus densiflora, Quercus agrifolia, Q. kelloggii, and Q. parvula var. shrevei). The phytosanitary authorities in the European Union consider non-European isolates of P. ramorum as a threat to forest trees in Europe. To date, almost all European isolates are mating type A1 while those from California and Oregon are type A2. The occurrence of both mating types in the same region could lead to a population capable of sexual recombination, which could generate a new source of diversity. To prevent contact between these two populations, a rapid, reliable, and discriminating diagnostic test was developed to easily distinguish the two populations. Based on a DNA sequence difference in the mitochondrial Cytochrome c oxidase subunit 1 (Cox1) gene, we developed a single-nucleotide polymorphism (SNP) protocol to distinguish between isolates of P. ramorum originating in Europe and those originating in the United States. A total of 83 isolates of P. ramorum from Europe and 51 isolates from the United States were screened and all isolates could be consistently and correctly allocated to either the European or the U.S. populations using the SNP protocol.
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Kong P, Hong CX, Tooley PW, Ivors K, Garbelotto M, Richardson PA. Rapid identification of Phytophthora ramorum using PCR-SSCP analysis of ribosomal DNA ITS-1. Lett Appl Microbiol 2004; 38:433-9. [PMID: 15059217 DOI: 10.1111/j.1472-765x.2004.01510.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The primary objectives of this study were to determine if a single-strand conformation polymorphism (SSCP) analysis can be used for rapid identification of Phytophthora ramorum, an important quarantine plant pathogen worldwide, and to further assess the potential of the SSCP technique as a taxonomic tool for the genus Phytophthora. METHODS AND RESULTS SSCP of ribosomal DNA internal transcribed spacer 1 was characterized for 12 isolates of P. ramorum, using a recently reported protocol. The SSCP patterns of this species then were compared with those of 18 closely related Phytophthora species. Phytophthora ramorum had a unique pattern and was easily distinguished from genetically, morphologically and ecologically close relatives. CONCLUSION An immediate benefit of this study is provision of a highly effective and efficient identification tool for P. ramorum in the quarantine process. SIGNIFICANCE AND IMPACT OF THE STUDY This study also provides additional evidence demonstrating that the SSCP is an ideal DNA marker for species differentiation within the genus Phytophthora.
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Affiliation(s)
- P Kong
- Department of Plant Pathology, Hampton Roads Agricultural Research and Extension Center, Virginia Polytechnic Institute and State University, Virginia Beach, VA 23455, USA
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