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Abad Z, Burgess T, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl J, Verkleij G, Broders K, Schena L, Redford A. Phytophthora : taxonomic and phylogenetic revision of the genus. Stud Mycol 2023; 106:259-348. [PMID: 38298569 PMCID: PMC10825748 DOI: 10.3114/sim.2023.106.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/19/2023] [Indexed: 02/02/2024] Open
Abstract
Many members of the Oomycota genus Phytophthora cause economic and environmental impact diseases in nurseries, horticulture, forest, and natural ecosystems and many are of regulatory concern around the world. At present, there are 223 described species, including eight unculturable and three lost species. Twenty-eight species need to be redescribed or validated. A lectotype, epitype or neotype was selected for 20 species, and a redescription based on the morphological/molecular characters and phylogenetic placement is provided. In addition, the names of five species are validated: P. cajani, P. honggalleglyana (Synonym: P. hydropathica), P. megakarya, P. pisi and P. pseudopolonica for which morphology and phylogeny are given. Two species, P. ×multiformis and P. uniformis are presented as new combinations. Phytophthora palmivora is treated with a representative strain as both lecto- and epitypification are pending. This manuscript provides the updated multigene phylogeny and molecular toolbox with seven genes (ITS rDNA, β-tub, COI, EF1α, HSP90, L10, and YPT1) generated from the type specimens of 212 validly published, and culturable species (including nine hybrid taxa). The genome information of 23 types published to date is also included. Several aspects of the taxonomic revision and phylogenetic re-evaluation of the genus including species concepts, concept and position of the phylogenetic clades recognized within Phytophthora are discussed. Some of the contents of this manuscript, including factsheets for the 212 species, are associated with the "IDphy: molecular and morphological identification of Phytophthora based on the types" online resource (https://idtools.org/tools/1056/index.cfm). The first version of the IDphy online resource released to the public in September 2019 contained 161 species. In conjunction with this publication, we are updating the IDphy online resource to version 2 to include the 51 species recently described. The current status of the 223 described species is provided along with information on type specimens with details of the host (substrate), location, year of collection and publications. Additional information is provided regarding the ex-type culture(s) for the 212 valid culturable species and the diagnostic molecular toolbox with seven genes that includes the two metabarcoding genes (ITS and COI) that are important for Sanger sequencing and also very valuable Molecular Operational Taxonomic Units (MOTU) for second and third generation metabarcoding High-throughput sequencing (HTS) technologies. The IDphy online resource will continue to be updated annually to include new descriptions. This manuscript in conjunction with IDphy represents a monographic study and the most updated revision of the taxonomy and phylogeny of Phytophthora, widely considered one of the most important genera of plant pathogens. Taxonomic novelties: New species: Phytophthora cajani K.S. Amin, Baldev & F.J. Williams ex Abad, Phytophthora honggalleglyana Abad, Phytophthora megakarya Brasier & M.J. Griffin ex Abad, Phytophthora pisi Heyman ex Abad, Phytophthora pseudopolonica W.W. Li, W.X. Huai & W.X. Zhao ex Abad & Kasiborski; New combinations: Phytophthora ×multiformis (Brasier & S.A. Kirk) Abad, Phytophthora uniformis (Brasier & S.A. Kirk) Abad; Epitypifications (basionyms): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora inundata Brasier et al., Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Lectotypifications (basionym): Peronospora cactorum Lebert & Cohn, Pythiacystis citrophthora R.E. Sm. & E.H. Sm., Phytophthora colocasiae Racib., Phytophthora drechsleri Tucker, Phytophthora erythroseptica Pethybr., Phytophthora fragariae Hickman, Phytophthora hibernalis Carne, Phytophthora ilicis Buddenh. & Roy A. Young, Phytophthora megasperma Drechsler, Phytophthora mexicana Hotson & Hartge, Phytophthora nicotianae Breda de Haan, Phytophthora phaseoli Thaxt., Phytophthora porri Foister, Phytophthora primulae J.A. Toml., Phytophthora sojae Kaufm. & Gerd., Phytophthora vignae Purss, Pythiomorpha gonapodyides H.E. Petersen; Neotypifications (basionym): Phloeophthora syringae Kleb., Phytophthora meadii McRae Citation: Abad ZG, Burgess TI, Bourret T, Bensch K, Cacciola S, Scanu B, Mathew R, Kasiborski B, Srivastava S, Kageyama K, Bienapfl JC, Verkleij G, Broders K, Schena L, Redford AJ (2023). Phytophthora: taxonomic and phylogenetic revision of the genus. Studies in Mycology 106: 259-348. doi: 10.3114/sim.2023.106.05.
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Affiliation(s)
- Z.G. Abad
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - T.I. Burgess
- Phytophthora Science and Management, Harry Butler Institute, Murdoch University, Perth, WA, Australia;
| | - T. Bourret
- Department of Plant Pathology, University of California, Davis, CA, USA,
| | - K. Bensch
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - S.O. Cacciola
- Department of Agricultural, Food and Environment, University of Catania, Italy;
| | - B. Scanu
- Department of Agricultural Sciences, University of Sassari, Italy;
| | - R. Mathew
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - B. Kasiborski
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - S. Srivastava
- Department of Entomology & Plant Pathology, North Carolina State University, Raleigh, NC, USA;
| | - K. Kageyama
- River Basin Research Center, Gifu University, Japan,
| | - J.C. Bienapfl
- USDA APHIS PPQ S&T Plant Pathogen Confirmatory Diagnostics Laboratory, USA;
| | - G. Verkleij
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8, 3584 CT Utrecht, Netherlands,
| | - K. Broders
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL, 61604, USA;
| | - L. Schena
- Dipartimento di Agraria, Mediterranean University of Reggio Calabria, Italy,
| | - A.J. Redford
- USDA APHIS PPQ S&T Identification Technology Program, USA
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Chen X, Wen K, Zhou X, Zhu M, Liu Y, Jin J, Nellist CF. The devastating oomycete phytopathogen Phytophthora cactorum: Insights into its biology and molecular features. MOLECULAR PLANT PATHOLOGY 2023; 24:1017-1032. [PMID: 37144631 PMCID: PMC10423333 DOI: 10.1111/mpp.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
Phytophthora cactorum is one of the most economically important soilborne oomycete pathogens in the world. It infects more than 200 plant species spanning 54 families, most of which are herbaceous and woody species. Although traditionally considered to be a generalist, marked differences of P. cactorum isolates occur in degree of pathogenicity to different hosts. As the impact of crop loss caused by this species has increased recently, there has been a tremendous increase in the development of new tools, resources, and management strategies to study and combat this devastating pathogen. This review aims to integrate recent molecular biology analyses of P. cactorum with the current knowledge of the cellular and genetic basis of its growth, development, and host infection. The goal is to provide a framework for further studies of P. cactorum by highlighting important biological and molecular features, shedding light on the functions of pathogenicity factors, and developing effective control measures. TAXONOMY P. cactorum (Leb. & Cohn) Schröeter: kingdom Chromista; phylum Oomycota; class Oomycetes; order Peronosporales; family Peronosporaceae; genus Phytophthora. HOST RANGE Infects about 200 plant species in 154 genera representing 54 families. Economically important host plants include strawberry, apple, pear, Panax spp., and walnut. DISEASE SYMPTOMS The soilborne pathogen often causes root, stem, collar, crown, and fruit rots, as well as foliar infection, stem canker, and seedling damping off.
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Affiliation(s)
- Xiao‐Ren Chen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ke Wen
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Xue Zhou
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Ming‐Yue Zhu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Yang Liu
- College of Plant ProtectionYangzhou UniversityYangzhouChina
| | - Jing‐Hao Jin
- College of Plant ProtectionYangzhou UniversityYangzhouChina
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Marin MV, Seijo TE, Baggio JS, Whitaker VM, Peres NA. Resistance of Strawberry Cultivars and the Effects of Plant Ontogenesis on Phytophthora cactorum and P. nicotianae Causing Crown Rot. PLANT DISEASE 2023; 107:651-657. [PMID: 35801901 DOI: 10.1094/pdis-01-22-0203-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Phytophthora crown rot (PhCR) is an important disease of strawberry worldwide. Phytophthora cactorum is the most common causal agent, however, P. nicotianae was also recently reported causing PhCR in the U.S. Therefore, the goals of this study were to evaluate the resistance of strawberry cultivars from Florida and California, and to study the etiology of the two Phytophthora species causing PhCR. Sixteen strawberry cultivars were evaluated over three Florida seasons for susceptibility to P. cactorum, and P. nicotianae. Inoculations at different days after transplanting (DAT) were also carried out to evaluate the ability of both species to cause PhCR at different phenological stages of the plant. Plant wilting and mortality were assessed weekly, and disease incidence, and the area under the disease progress curve were calculated. Cultivars Sensation 'Florida127', 'Winterstar FL 05-107', and 'Florida Radiance' were susceptible, whereas 'Florida Elyana', 'Camarosa', 'Fronteras', 'Sweet Charlie', and 'Strawberry Festival' were highly resistant to both Phytophthora species. However, some cultivars exhibited stronger resistance to one species over the other. P. cactorum caused more PhCR when plants were inoculated at transplanting, 45, and 60 DAT, whereas P. nicotianae only caused disease when inoculated at transplanting. These results emphasize the importance of screening for disease resistance to guide management recommendations in commercial strawberry production as well as the need for proper pathogen identification since cultivar susceptibility might differ. Varying susceptibility to P. cactorum and P. nicotianae at different growth stages emphasizes the importance of considering both plant and pathogen biology when making management recommendations.
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Affiliation(s)
- Marcus V Marin
- IFAS Gulf Coast Research and Education Center, Department of Plant Pathology, University of Florida, Wimauma, FL 33598
| | - Teresa E Seijo
- IFAS Gulf Coast Research and Education Center, Department of Plant Pathology, University of Florida, Wimauma, FL 33598
| | - Juliana S Baggio
- IFAS Gulf Coast Research and Education Center, Department of Plant Pathology, University of Florida, Wimauma, FL 33598
| | - Vance M Whitaker
- IFAS Gulf Coast Research and Education Center, Department of Horticultural Science, University of Florida, Wimauma, FL 33598
| | - Natalia A Peres
- IFAS Gulf Coast Research and Education Center, Department of Plant Pathology, University of Florida, Wimauma, FL 33598
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Bourret TB, Fajardo SN, Frankel SJ, Rizzo DM. Cataloging Phytophthora Species of Agriculture, Forests, Horticulture, and Restoration Outplantings in California, U.S.A.: A Sequence-Based Meta-Analysis. PLANT DISEASE 2023; 107:67-75. [PMID: 35724315 DOI: 10.1094/pdis-01-22-0187-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
California contains a diverse flora, and knowledge of the pathogens that threaten those plants is essential to managing their long-term health. To better understand threats to California plant health, a meta-analysis of Phytophthora detections within the state was conducted using publicly available sequences as a primary source of data rather than published records. Accessions of internal transcribed spacer (ITS) ribosomal DNA were cataloged from 800 Californian Phytophthora isolates, analyzed, and determined to correspond to 80 taxa, including several phylogenetically distinct provisional species. A number of Phytophthora taxa not previously reported from California were identified, including 20 described species. Pathways of introduction and spread were analyzed by categorizing isolates' origins, grouped by land-use: (i) agriculture, (ii) forests and other natural ecosystems, (iii) horticulture and nurseries, or (iv) restoration outplantings. The pooled Phytophthora metacommunities of the restoration outplantings and horticulture land-use categories were the most similar, whereas the communities pooled from forests and agriculture were least similar. Phytophthora cactorum, P. pini, P. pseudocryptogea, and P. syringae were identified in all four land-use categories, while 13 species were found in three. P. gonapodyides was the most common species by number of ITS accessions and exhibited the greatest diversity of ITS haplotypes. P. cactorum, P. ramorum, and P. nicotianae were associated with the greatest number of host genera. In this analysis, the Phytophthora spp. most prevalent in California differ from those compiled from the scientific literature.
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Affiliation(s)
- Tyler B Bourret
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
| | - Sebastian N Fajardo
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
| | - Susan J Frankel
- Pacific Southwest Research Station, United States Department of Agriculture Forest Service, Albany, CA 94710
| | - David M Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, CA 95616
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Poimala A, Raco M, Haikonen T, Černý M, Parikka P, Hantula J, Vainio EJ. Bunyaviruses Affect Growth, Sporulation, and Elicitin Production in Phytophthora cactorum. Viruses 2022; 14:v14122596. [PMID: 36560602 PMCID: PMC9788385 DOI: 10.3390/v14122596] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/02/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
Phytophthora cactorum is an important oomycetous plant pathogen with numerous host plant species, including garden strawberry (Fragaria × ananassa) and silver birch (Betula pendula). P. cactorum also hosts mycoviruses, but their phenotypic effects on the host oomycete have not been studied earlier. In the present study, we tested polyethylene glycol (PEG)-induced water stress for virus curing and created an isogenic virus-free isolate for testing viral effects in pair with the original isolate. Phytophthora cactorum bunya-like viruses 1 and 2 (PcBV1 & 2) significantly reduced hyphal growth of the P. cactorum host isolate, as well as sporangia production and size. Transcriptomic and proteomic analyses revealed an increase in the production of elicitins due to bunyavirus infection. However, the presence of bunyaviruses did not seem to alter the pathogenicity of P. cactorum. Virus transmission through anastomosis was unsuccessful in vitro.
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Affiliation(s)
- Anna Poimala
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
- Correspondence: ; Tel.: +358-29-5322173
| | - Milica Raco
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 613 00 Brno, Czech Republic
| | - Tuuli Haikonen
- Natural Resources Institute Finland, Toivonlinnantie 518, FI-21500 Piikkiö, Finland
| | - Martin Černý
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 1, 613 00 Brno, Czech Republic
| | - Päivi Parikka
- Natural Resources Institute Finland, Humppilantie 18, FI-31600 Jokioinen, Finland
| | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
| | - Eeva J. Vainio
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, FI-00790 Helsinki, Finland
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Evaluation of the Ability of Seven Active Ingredients of Fungicides to Suppress Phytophthora cactorum at Diverse Life Stages, and Variability in Resistance Found among Isolates. J Fungi (Basel) 2022; 8:jof8101039. [PMID: 36294604 PMCID: PMC9605621 DOI: 10.3390/jof8101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Phytophthora cactorum is considered an important plant pathogen which is causing major damage to strawberry plants worldwide. In the current study, the ability of the active ingredients of seven different fungicides, azoxystrobin, cymoxanil, dimethomorph, fenamidone, fluopicolide, metalaxyl and propamocarb, to suppress the mycelial growth, sporangial formation and zoospore release of P. cactorum isolates, was tested. The variation in resistance against various fungicides was found among the isolates. The active ingredients are also unequally efficient against different life stages of P. cactorum, which is probably associated with their different modes of action. A significant level of resistance was recorded against metalaxyl and dimethomorph; however, these were totally inefficient against the zoospore release, while azoxystrobin did not inhibit mycelial growth. The only fungicide efficient against all three P. cactorum life stages tested was fluopicolide, although the calculated resistance factor gives evidence of the rise of resistance in the majority of isolates even against this fungicide. Significant differences were found between responses to fungicides of isolates from strawberry and from other host species. Based on the Mahalanobis distances calculated in the discriminant analysis comprising all of the assays performed, the similarities among isolates were estimated.
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