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Tovar-Pedraza JM, Solano-Báez AR, Leyva-Mir SG, Tlapal-Bolaños B, Camacho-Tapia M, García-León E, Ayala-Escobar V, Nava-Díaz C, Quezada-Salinas A, Santiago-Santiago V, Beltrán-Peña H, Hernandez-Hernandez MA, Juárez-Cruz KJ, Márquez-Licona G. The Need and Opportunity to Update the Inventory of Plant Pathogenic Fungi and Oomycetes in Mexico. J Fungi (Basel) 2024; 10:395. [PMID: 38921381 PMCID: PMC11204560 DOI: 10.3390/jof10060395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Mexico generates specific phytosanitary regulations for each product and origin to prevent the entry of quarantine pests and/or delay their spread within the national territory, including fungi and oomycetes. Phytosanitary regulations are established based on available information on the presence or absence of these pathogens in the country; however, the compilation and precise analysis of reports is a challenging task due to many publications lacking scientific rigor in determining the presence of a taxon of phytosanitary interest in the country. This review evaluated various studies reporting the presence of plant pathogenic fungi and oomycetes in Mexico and concluded that some lists of diseases and phytopathogenic organisms lack technical-scientific basis. Thus, it highlights the need and presents an excellent opportunity to establish a National Collection of Fungal Cultures and a National Herbarium for obligate parasites, as well as to generate a National Database of Phytopathogenic Fungi and Oomycetes present in Mexico, supported by the combination of morphological, molecular, epidemiological, pathogenicity, symptom, and micrograph data. If realized, this would have a direct impact on many future applications related to various topics, including quarantines, risk analysis, biodiversity studies, and monitoring of fungicide resistance, among others.
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Affiliation(s)
- Juan Manuel Tovar-Pedraza
- Laboratorio de Fitopatología, Centro de Investigación en Alimentación y Desarrollo, Coordinación Culiacán, Culiacán 80110, Sinaloa, Mexico;
| | - Alma Rosa Solano-Báez
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Santos Gerardo Leyva-Mir
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Bertha Tlapal-Bolaños
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Moisés Camacho-Tapia
- Departamento de Parasitología Agrícola, Universidad Autónoma Chapingo, Texcoco 56230, Estado de México, Mexico; (S.G.L.-M.); (B.T.-B.); (M.C.-T.)
| | - Elizabeth García-León
- Campo Experimental Valle del Fuerte, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Guasave 81110, Sinaloa, Mexico;
| | - Victoria Ayala-Escobar
- Fitopatología, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Estado de México, Mexico; (V.A.-E.); (C.N.-D.)
| | - Cristian Nava-Díaz
- Fitopatología, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Estado de México, Mexico; (V.A.-E.); (C.N.-D.)
| | - Andrés Quezada-Salinas
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Tecámac 55740, Estado de México, Mexico;
| | - Víctor Santiago-Santiago
- Departamento de Agronomía, Instituto Tecnológico del Altiplano de Tlaxcala, San Diego Xocoyucán 90122, Tlaxcala, Mexico;
| | - Hugo Beltrán-Peña
- Departamento de Ciencias Biológicas, Unidad Los Mochis, Universidad Autónoma de Occidente, Los Mochis 81223, Sinaloa, Mexico;
| | - Maria Alondra Hernandez-Hernandez
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Karla Jenifer Juárez-Cruz
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
| | - Guillermo Márquez-Licona
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Yautepec 62731, Morelos, Mexico; (A.R.S.-B.); (M.A.H.-H.); (K.J.J.-C.)
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Nielsen KAG, Skårn MN, Talgø V, Pettersson M, Fløistad IS, Strømeng GM, Brurberg MB, Stensvand A. Fungicide-Resistant Botrytis in Forest Nurseries May Impact Disease Control in Norway Spruce. PLANT DISEASE 2024; 108:139-148. [PMID: 37578357 DOI: 10.1094/pdis-01-23-0037-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: 08/15/2023]
Abstract
Gray mold, caused by Botrytis spp., is a serious problem in Norway spruce seedling production in forest nurseries. From 2013 to 2019, 125 isolates of Botrytis were obtained from eight forest nurseries in Norway: 53 from Norway spruce seedlings, 16 from indoor air, 52 from indoor surfaces, and four from weeds growing close to seedlings. The majority of isolates were identified as B. cinerea, and over 60% of these were characterized as Botrytis group S. B. pseudocinerea isolates were obtained along with isolates with DNA sequence similarities to B. prunorum. Fungicide resistance was assessed with a mycelial growth assay, and resistance was found for the following: boscalid (8.8%), fenhexamid (33.6%), fludioxonil (17.6%), pyraclostrobin (36.0%), pyrimethanil (13.6%), and thiophanate-methyl (50.4%). Many isolates (38.4%) were resistant to two to six different fungicides. A selection of isolates was analyzed for the presence of known resistance-conferring mutations in the cytb, erg27, mrr1, sdhB, and tubA genes, and mutations leading to G143A, F412S, ΔL497, H272R, and E198A/F200Y were detected, respectively. Detection of fungicide resistance in Botrytis from Norway spruce and forest nursery facilities reinforces the necessity of employing resistance management strategies to improve control and delay development of fungicide resistance in the gray mold pathogens.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Katherine Ann Gredvig Nielsen
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Magne Nordang Skårn
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Venche Talgø
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Martin Pettersson
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Inger Sundheim Fløistad
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - Gunn Mari Strømeng
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
| | - May Bente Brurberg
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
| | - Arne Stensvand
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås 1431, Norway
- Department of Plant Sciences (IPV), Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås 1432, Norway
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Moparthi S, Parikh LP, Gunnink Troth EE, Burrows ME. Identification and Prevalence of Seedborne Botrytis spp. in Dry Pea, Lentil, and Chickpea in Montana. PLANT DISEASE 2023; 107:382-392. [PMID: 35822889 DOI: 10.1094/pdis-05-22-1236-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Botrytis spp. cause gray mold and are significant pathogens of pulse crops (dry pea, lentil, and chickpea). Seedling infection can result in plant stunting and death. In this study, 100 Botrytis isolates were recovered from pulse crop seed samples that were submitted to the Regional Pulse Crop Diagnostic Laboratory at Montana State University. Nine Botrytis spp. were found to be associated with pulse seeds in Montana based on a combination of cultural characteristics; the amplification of partial sequences of the G3PDH, HSP60, and RPB2 genes; and phylogenetic analysis. Botrytis cinerea (n = 54) was the predominant species, followed by B. euroamericana (n = 22) and B. prunorum (n = 11). There were a few isolates of B. mali and five novel Botrytis spp. that included one cryptic species. To determine the pathogenicity and aggressiveness of the isolates, dry pea cultivar Lifter, lentil cultivar Richlea, and chickpea cultivar Sierra, detached leaves were inoculated using mycelial plugs. Lesion diameter produced by Botrytis isolates on three hosts differed (P < 0.05). Aggressiveness of B. cinerea was high in all three hosts and varied among the tested isolates. Spore inoculations were conducted on greenhouse-grown dry pea, lentil and chickpea plants using one sporulating isolate each of B. cinerea, B. prunorum, and Botrytis sp. 1. Results indicated that these isolates were pathogenic on the tested hosts. This study illustrates that many species of Botrytis are associated with pulse crop seed in Montana and can be aggressive on multiple crops, which may have implications for disease management.
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Affiliation(s)
- Swarnalatha Moparthi
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT 59717
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613
| | - Lipi P Parikh
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Erin E Gunnink Troth
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT 59717
| | - Mary E Burrows
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT 59717
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Dal’Sasso TCS, Rody HVS, Oliveira LO. Genome-Wide Analysis and Evolutionary History of the Necrosis- and Ethylene-Inducing Peptide 1-Like Protein (NLP) Superfamily Across the Dothideomycetes Class of Fungi. Curr Microbiol 2023; 80:44. [DOI: 10.1007/s00284-022-03125-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
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Makris G, Nikoloudakis N, Samaras A, Karaoglanidis GS, Kanetis LI. Under Pressure: A Comparative Study of Botrytis cinerea Populations from Conventional and Organic Farms in Cyprus and Greece. PHYTOPATHOLOGY 2022; 112:2236-2247. [PMID: 35671479 DOI: 10.1094/phyto-12-21-0510-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The highly heterogeneous nature of Botrytis cinerea provides adaptive benefits to variable environmental regimes. Disentangling pathogen population structure in anthropogenic agroecosystems is crucial to designing more effective management schemes. Herein, we studied how evolutionary forces exerted in different farming systems, in terms of agrochemicals-input, shape B. cinerea populations. In total, 360 B. cinerea isolates were collected from conventional and organic, strawberry and tomato farms in Cyprus and Greece. The occurrence and frequency of sensitivities to seven botryticides were estimated. Results highlighted widespread fungicide resistance in conventional farms since only 15.5% of the isolates were sensitive. A considerable frequency of fungicide-resistant isolates was also detected in the organic farms (14.9%). High resistance frequencies were observed for boscalid (67.7%), pyraclostrobin (67.3%), cyprodinil (65.9%), and thiophanate-methyl (61.4%) in conventional farms, while high levels of multiple fungicide resistance were also evident. Furthermore, B. cinerea isolates were genotyped using a set of seven microsatellite markers (simple sequence repeat [SSR] markers). Index of association analyses (Ia and rBarD) suggest asexual reproduction of the populations, even though the mating-type idiomorphs were equally distributed, indicating frequency-dependent selection. Fungicide resistance was correlated with farming systems across countries and crops, while SSRs were able to detect population structure associated with resistance to thiophanate-methyl, pyraclostrobin, boscalid, and cyprodinil. The expected heterozygosity in organic farms was significantly higher than in conventional, suggesting the absence of selective pressure that may change the allelic abundance in organic farms. However, genetic variance among strawberry and tomato populations was high, ranking host specificity higher than other selection forces studied.
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Affiliation(s)
- Georgios Makris
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Nikolaos Nikoloudakis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
| | - Anastasios Samaras
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Georgios S Karaoglanidis
- Department of Agriculture, Plant Pathology Laboratory, Aristotle University of Thessaloniki, Greece
| | - Loukas I Kanetis
- Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
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Dal'Sasso TCDS, Rocha VDD, Rody HVS, Costa MDBL, Oliveira LOD. The necrosis- and ethylene-inducing peptide 1-like protein (NLP) gene family of the plant pathogen Corynespora cassiicola. Curr Genet 2022; 68:645-659. [PMID: 36098767 DOI: 10.1007/s00294-022-01252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022]
Abstract
Effectors are secreted by plant-associated microorganisms to modify the host cell physiology. As effectors, the Necrosis- and Ethylene-inducing peptide 1-like proteins (NLPs) are involded in the early phases of plant infection and may trigger host immune responses. Corynespora cassiicola is a polyphagous plant pathogen that causes target spot on many agriculturally important crops. Using genome assembly, gene prediction, and proteome annotation tools, we retrieved 135 NLP-encoding genes from proteomes of 44 isolates. We explored the evolutionary history of NLPs using Bayesian phylogeny, gene genealogies, and selection analyses. We accessed the expression profiles of the NLP genes during the early phase of C. cassiicola-soybean interaction. Three NLP putative-effector genes (Cc_NLP1.1, Cc_NLP1.2A, and Cc_NLP1.2B) were maintained in the genomes of all isolates tested. An NLP putative-non-effector gene (Cc_NLP1.3) was found in three isolates that had been originally obtained from soybean. Putative-effector NLPs were under different selective constraints: Cc_NLP1.1 was under stronger selective pressure, while Cc_NLP1.2A was under a more relaxed constraint. Meanwhile, Cc_NLP1.2B likely evolved under either positive or balancing selection. Despite highly divergent, the putative-effector NLPs maintain conserved the residues necessary to trigger plant immune responses, suggesting they are potentially functional. Only the Cc_NLP1.1 putative-effector gene was significantly expressed at the early hours of soybean colonization, while Cc_NLP1.2A and Cc_NLP1.2B showed much lower levels of gene expression.
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Affiliation(s)
| | | | - Hugo Vianna Silva Rody
- Departamento de Genética, Universidade de São Paulo/Escola Superior de Agricultura "Luiz de Queiroz", Piracicaba, Brazil
| | | | - Luiz Orlando de Oliveira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil.
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Steentjes MBF, Herrera Valderrama AL, Fouillen L, Bahammou D, Leisen T, Albert I, Nürnberger T, Hahn M, Mongrand S, Scholten OE, van Kan JAL. Cytotoxic activity of Nep1-like proteins on monocots. THE NEW PHYTOLOGIST 2022; 235:690-700. [PMID: 35383933 PMCID: PMC9320973 DOI: 10.1111/nph.18146] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are found throughout several plant-associated microbial taxa and are typically considered to possess cytolytic activity exclusively on dicot plant species. However, cytolytic NLPs are also produced by pathogens of monocot plants such as the onion (Allium cepa) pathogen Botrytis squamosa. We determined the cytotoxic activity of B. squamosa BsNep1, as well as other previously characterized NLPs, on various monocot plant species and assessed the plant plasma membrane components required for NLP sensitivity. Leaf infiltration of NLPs showed that onion cultivars are differentially sensitive to NLPs, and analysis of their sphingolipid content revealed that the GIPC series A : series B ratio did not correlate to NLP sensitivity. A tri-hybrid population derived from a cross between onion and two wild relatives showed variation in NLP sensitivity within the population. We identified a quantitative trait locus (QTL) for NLP insensitivity that colocalized with a previously identified QTL for B. squamosa resistance and the segregating trait of NLP insensitivity correlated with the sphingolipid content. Our results demonstrate the cytotoxic activity of NLPs on several monocot plant species and legitimize their presence in monocot-specific plant pathogens.
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Affiliation(s)
| | | | - Laetitia Fouillen
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Delphine Bahammou
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Thomas Leisen
- Department of Biology, Plant PathologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Isabell Albert
- Molecular Plant PhysiologyFAU Erlangen‐NürnbergErlangen91058Germany
| | | | - Matthias Hahn
- Department of Biology, Plant PathologyUniversity of KaiserslauternKaiserslautern67663Germany
| | - Sébastien Mongrand
- Laboratoire de Biogènese MembranaireUMR 5200CNRSUniversity of BordeauxF‐33140Villenave d’OrnonFrance
| | - Olga E. Scholten
- Plant BreedingWageningen University & ResearchWageningen6708 PBthe Netherlands
| | - Jan A. L. van Kan
- Laboratory of PhytopathologyWageningen UniversityWageningen6708 PBthe Netherlands
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De Miccolis Angelini RM, Landi L, Raguseo C, Pollastro S, Faretra F, Romanazzi G. Tracking of Diversity and Evolution in the Brown Rot Fungi Monilinia fructicola, Monilinia fructigena, and Monilinia laxa. Front Microbiol 2022; 13:854852. [PMID: 35356516 PMCID: PMC8959702 DOI: 10.3389/fmicb.2022.854852] [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: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Monilinia species are among the most devastating fungi worldwide as they cause brown rot and blossom blight on fruit trees. To understand the molecular bases of their pathogenic lifestyles, we compared the newly assembled genomes of single strains of Monilinia fructicola, M. fructigena and M. laxa, with those of Botrytis cinerea and Sclerotinia sclerotiorum, as the closest species within Sclerotiniaceae. Phylogenomic analysis of orthologous proteins and syntenic investigation suggest that M. laxa is closer to M. fructigena than M. fructicola, and is closest to the other investigated Sclerotiniaceae species. This indicates that M. laxa was the earliest result of the speciation process. Distinct evolutionary profiles were observed for transposable elements (TEs). M. fructicola and M. laxa showed older bursts of TE insertions, which were affected (mainly in M. fructicola) by repeat-induced point (RIP) mutation gene silencing mechanisms. These suggested frequent occurrence of the sexual process in M. fructicola. More recent TE expansion linked with low RIP action was observed in M. fructigena, with very little in S. sclerotiorum and B. cinerea. The detection of active non-syntenic TEs is indicative of horizontal gene transfer and has resulted in alterations in specific gene functions. Analysis of candidate effectors, biosynthetic gene clusters for secondary metabolites and carbohydrate-active enzymes, indicated that Monilinia genus has multiple virulence mechanisms to infect host plants, including toxins, cell-death elicitor, putative virulence factors and cell-wall-degrading enzymes. Some species-specific pathogenic factors might explain differences in terms of host plant and organ preferences between M. fructigena and the other two Monilinia species.
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Affiliation(s)
| | - Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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Jones DAB, Moolhuijzen PM, Hane JK. Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi. Microb Genom 2021; 7. [PMID: 34468307 PMCID: PMC8715435 DOI: 10.1099/mgen.0.000637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between 'effector' molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.
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Affiliation(s)
- Darcy A B Jones
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - Paula M Moolhuijzen
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia
| | - James K Hane
- Centre for Crop & Disease Management, School of Molecular & Life Sciences, Curtin University, Perth, Australia.,Curtin Institute for Computation, Curtin University, Perth, Australia
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Riquelme D, Aravena Z, Valdés-Gómez H, Latorre BA, Díaz GA, Zoffoli JP. Characterization of Botrytis cinerea and B. prunorum From Healthy Floral Structures and Decayed 'Hayward' Kiwifruit During Post-Harvest Storage. PLANT DISEASE 2021; 105:2129-2140. [PMID: 33258430 DOI: 10.1094/pdis-04-20-0878-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Gray mold is the primary postharvest disease of 'Hayward' kiwifruit (Actinidia deliciosa) in Chile, with a prevalence of 33.1% in 2016 and 7.1% in 2017. Gray mold develops during postharvest storage, which is characterized by a soft, light to brown watery decay that is caused by Botrytis cinerea and B. prunorum. However, there is no information on the role of B. prunorum during the development and storage of kiwifruit in Chile. For this purpose, asymptomatic flowers and receptacles were collected throughout fruit development and harvest from five orchards over two seasons in the Central Valley of Chile. Additionally, diseased kiwifruits were selected after storage for 100 days at 0°C and 2 days at 20°C. Colonies of Botrytis sp. with high and low conidial production were consistently obtained from apparently healthy petals, sepals, receptacles, and styles and diseased kiwifruit. Morphological and phylogenetic analysis of three partial gene sequences encoding glyceraldehyde-3-phosphate dehydrogenase, heat shock protein 60, and DNA-dependent RNA polymerase subunit II were able to identify and separate B. cinerea and B. prunorum species. Consistently, B. cinerea was predominantly isolated from all floral parts and fruit in apparently healthy tissue and diseased kiwifruit. During full bloom, the highest colonization by B. cinerea and B. prunorum was obtained from petals, followed by sepals. In storage, both Botrytis species were isolated from the diseased fruit (n = 644), of which 6.8% (n = 44) were identified as B. prunorum. All Botrytis isolates grew from 0°C to 30°C in vitro and were pathogenic on kiwifruit leaves and fruit. Notably, B. cinerea isolates were always more virulent than B. prunorum isolates. This study confirms the presence of B. cinerea and B. prunorum colonizing apparently healthy flowers and floral parts in fruit and causing gray mold during kiwifruit storage in Chile. Therefore, B. prunorum plays a secondary role in the epidemiology of gray mold developing in kiwifruit during cold storage.
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Affiliation(s)
- Danae Riquelme
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Fruticultura y Enología, Santiago 7820244, Chile
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santiago 8831314, Chile
| | - Zdenka Aravena
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Fruticultura y Enología, Santiago 7820244, Chile
| | - Héctor Valdés-Gómez
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Fruticultura y Enología, Santiago 7820244, Chile
| | - Bernardo A Latorre
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Fruticultura y Enología, Santiago 7820244, Chile
| | - Gonzalo A Díaz
- Universidad de Talca, Facultad de Ciencias Agrarias, Departamento de Producción Agrícola, Talca 3460000, Chile
| | - Juan Pablo Zoffoli
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Fruticultura y Enología, Santiago 7820244, Chile
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Derbyshire MC, Harper LA, Lopez-Ruiz FJ. Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene. Genome Biol Evol 2021; 13:6325025. [PMID: 34289036 PMCID: PMC8379374 DOI: 10.1093/gbe/evab167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 01/18/2023] Open
Abstract
Tests based on the dN/dS statistic are used to identify positive selection of nonsynonymous polymorphisms. Using these tests on alignments of all orthologs from related species can provide insights into which gene categories have been most frequently positively selected. However, longer alignments have more power to detect positive selection, creating a detection bias that could create misleading results from functional enrichment tests. Most studies of positive selection in plant pathogens focus on genes with specific virulence functions, with little emphasis on broader molecular processes. Furthermore, no studies in plant pathogens have accounted for detection bias due to alignment length when performing functional enrichment tests. To address these research gaps, we analyze 12 genomes of the phytopathogenic fungal genus Botrytis, including two sequenced in this study. To establish a temporal context, we estimated fossil-calibrated divergence times for the genus. We find that Botrytis likely originated 16–18 Ma in the Miocene and underwent continuous radiation ending in the Pliocene. An untargeted scan of Botrytis single-copy orthologs for positive selection with three different statistical tests uncovered evidence for positive selection among proteases, signaling proteins, CAZymes, and secreted proteins. There was also a strong overrepresentation of transcription factors among positively selected genes. This overrepresentation was still apparent after two complementary controls for detection bias due to sequence length. Positively selected sites were depleted within DNA-binding domains, suggesting changes in transcriptional responses to internal and external cues or protein–protein interactions have undergone positive selection more frequently than changes in promoter fidelity.
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Affiliation(s)
- Mark C Derbyshire
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Lincoln A Harper
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
| | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, Curtin University, Perth, Western Australia, Australia
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12
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Application of plant natural products for the management of postharvest diseases in fruits. FOLIA HORTICULTURAE 2021. [DOI: 10.2478/fhort-2021-0016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Prevention of postharvest losses has been a very important concern in the scientific world for many centuries, since adoption of an effective means to curtail such losses is believed to help in reaching sustainability in horticultural production and prevention of hunger around the world. The main means of deterioration in fruits, which may occur after harvest, include physiological changes/losses, physical losses, biochemical changes, changes in enzymatic activities and pathological deterioration. Among these, diseases cover the most important part; the losses due to diseases range from 5% to 20%, and this figure may extend up to >50% in the cases of certain susceptible cultivars. Fungicides have been the most important tool for the management of postharvest diseases for many years, together with hygiene, cold storage and packaging. However, due to the scientifically confirmed hazards of agro-chemicals on environment and human health, the acceptability of agro-chemicals decreased and scientists turned their attention towards natural alternatives. Most tropical and subtropical fruits contain a superficial cuticle, which helps them to regulate respiration and transpiration and protects against microbial decay. However, the waxy cuticle is generally being removed or damaged during washing or other handling practices. Therefore, the application of protective coatings (including wax) has been used in the fruit industry since the twelfth century, against microbial decay and for maintaining an acceptable standard of postharvest quality. This review aims to summarise and discuss the main natural products used for this purpose, to provide a broad-in-scope guide to farmers and the fruit storage sector.
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13
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Plesken C, Pattar P, Reiss B, Noor ZN, Zhang L, Klug K, Huettel B, Hahn M. Genetic Diversity of Botrytis cinerea Revealed by Multilocus Sequencing, and Identification of B. cinerea Populations Showing Genetic Isolation and Distinct Host Adaptation. FRONTIERS IN PLANT SCIENCE 2021; 12:663027. [PMID: 34025700 PMCID: PMC8131559 DOI: 10.3389/fpls.2021.663027] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Botrytis cinerea is a world-wide occurring plant pathogen, causing pre- and post-harvest gray mold rot on a large number of fruit, vegetable, and flower crops. B. cinerea is closely related to Botrytis pseudocinerea, another broad host range species which often occurs in sympatry with B. cinerea, and to several host-specific species including Botrytis fabae and Botrytis calthae. B. cinerea populations have been shown to be genetically heterogeneous, and attempts have been made to correlate genetic markers to virulence and host adaptation. Here, we present the development of a multilocus sequence typing (MLST) scheme, with 10 genes selected for high variability and phylogenetic congruence, to evaluate the genetic diversity of B. cinerea, B. fabae, and B. pseudocinerea. Using PacBio-assisted simultaneous mass sequencing of PCR products, MLST analysis of about 100 strains from diverse geographical origins and years of isolation was performed, which resulted in high-resolution strain differentiation and robust species separation. Several B. cinerea strains formed an as yet unknown population, referred to as group B, which was well separated from all other B. cinerea strains. Furthermore, the gene cluster for biosynthesis of the phytotoxin botcinic acid was missing in B. cinerea B strains. B. cinerea strains from the monocot Iris pseudacorus were found to form a genetically distinct population, and contained an intact gene cluster for production of the red pigment bikaverin, which is usually degenerated in B. cinerea. Remarkably, these strains were much more aggressive on Iris than other B. cinerea strains, which is the first unequivocal example for host specialization in B. cinerea. Our data reveal new insights into the genetic diversity of B. cinerea and provide evidence for intraspecific differentiation and different degrees of host adaptation of this polyphagous necrotrophic pathogen.
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Affiliation(s)
- Cecilia Plesken
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Patrick Pattar
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Bianka Reiss
- Department of Plant Physiology, RWTH Aachen University, Aachen, Germany
| | - Zinnia Naoshin Noor
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lisha Zhang
- Center of Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Klaus Klug
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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14
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Naegele RP, DeLong J, Alzohairy SA, Saito S, Abdelsamad N, Miles TD. Population Genetic Analyses of Botrytis cinerea Isolates From Michigan Vineyards Using a High-Throughput Marker System Approach. Front Microbiol 2021; 12:660874. [PMID: 33959117 PMCID: PMC8093758 DOI: 10.3389/fmicb.2021.660874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/09/2021] [Indexed: 11/29/2022] Open
Abstract
As sequencing costs continue to decrease, new tools are being developed for assessing pathogen diversity and population structure. Traditional marker types, such as microsatellites, are often more cost effective than single-nucleotide polymorphism (SNP) panels when working with small numbers of individuals, but may not allow for fine scale evaluation of low or moderate structure in populations. Botrytis cinerea is a necrotrophic plant pathogen with high genetic variability that can infect more than 200 plant species worldwide. A panel of 52 amplicons were sequenced for 82 isolates collected from four Michigan vineyards representing 2 years of collection and varying fungicide resistance. A panel of nine microsatellite markers previously described was also tested across 74 isolates from the same population. A microsatellite and SNP marker analysis of B. cinerea populations was performed to assess the genetic diversity and population structure of Michigan vineyards, and the results from both marker types were compared. Both methods were able to detect population structure associated with resistance to the individual fungicides thiabendazole and boscalid, and multiple fungicide resistance (MFR). Microsatellites were also able to differentiate population structure associated with another fungicide, fluopyram, while SNPs were able to additionally differentiate structure based on year. For both methods, AMOVA results were similar, with microsatellite results explaining a smaller portion of the variation compared with the SNP results. The SNP-based markers presented here were able to successfully differentiate population structure similar to microsatellite results. These SNP markers represent new tools to discriminate B. cinerea isolates within closely related populations using multiple targeted sequences.
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Affiliation(s)
- Rachel P Naegele
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Jeff DeLong
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Safa A Alzohairy
- Small Fruit and Hop Pathology Laboratory, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Seiya Saito
- Commodity Protection and Quality Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Noor Abdelsamad
- Crop Diseases, Pests and Genetics Unit, United States Department of Agriculture, Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Timothy D Miles
- Small Fruit and Hop Pathology Laboratory, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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15
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Richards JK, Xiao CL, Jurick WM. Botrytis spp.: A Contemporary Perspective and Synthesis of Recent Scientific Developments of a Widespread Genus that Threatens Global Food Security. PHYTOPATHOLOGY 2021; 111:432-436. [PMID: 33231498 DOI: 10.1094/phyto-10-20-0475-ia] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This perspective presents a synopsis of the topics contained in the Phytopathology Pathogen Spotlight on Botrytis spp. causing gray mold, including pathogen biology and systematics, genomic characterization of new species, perspectives on genome editing, and fungicide resistance. A timely breakthrough to engineer host plant resistance against the gray mold fungus has been demonstrated in planta and may augment chemical controls in the near future. While B. cinerea has garnered much of the research attention, other economically important Botrytis spp. have been identified and characterized via morphological and genome-based approaches. Gray mold control is achieved primarily through fungicide applications but resistance to various chemical classes is a major concern that threatens global plant health and food security. In this issue, new information on molecular mechanism(s) of fungicide resistance and ways to manage control failures are presented. Finally, a significant leap in fundamental pathogen biology has been achieved via development of CRISPR/Cas9 to assess gene function in the fungus which likely will spawn new control mechanisms and facilitate gene discovery studies.
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Affiliation(s)
- Jonathan K Richards
- Assistant Professor, Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA
| | - Chang-Lin Xiao
- Supervisory Research Plant Pathologist, Commodity Protection and Quality Research Unit, USDA-ARS, Parlier, CA
| | - Wayne M Jurick
- Lead Scientist and Research Plant Pathologist, Food Quality Laboratory, USDA-ARS, Beltsville, MD
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16
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Garfinkel AR. The History of Botrytis Taxonomy, the Rise of Phylogenetics, and Implications for Species Recognition. PHYTOPATHOLOGY 2021; 111:437-454. [PMID: 32976058 DOI: 10.1094/phyto-06-20-0211-ia] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Botrytis is one of the oldest, most well studied, and most economically important fungal taxa. Nonetheless, many species in this genus have remained obscured for nearly 300 years because of the difficulty in distinguishing these species by conventional mycological methods. Aided by the use of phylogenetic tools, the genus is currently undergoing a taxonomic revolution. The number of putative species in the genus has nearly doubled over the last 10 years and more species are likely to be discovered in the future. The implementation of phylogenetic species recognition concepts in Botrytis is providing for more resolution on the relatedness among species than ever before, and this has helped to overcome issues in historical species recognition using morphology, sexual crosses, and pathogenicity tests. Meanwhile, the use of genetic tools is helping to reveal surprising insight into this archetypal necrotroph's behavior, making these approaches increasingly important in species recognition and identification. As Botrytis taxonomy continues to evolve at a rapid pace, researchers should be encouraged to continue to employ the powerful tool of phylogenetics while considering how it fits into a larger framework of classical Botrytis species recognition. Starting points for discussion on how to move forward with Botrytis species recognition are included herein, with an emphasis on the implications and utility of new species descriptions.
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17
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He SQ, Wen ZH, Bai B, Jing ZQ, Wang XW. Botrytis polygoni, a new species of the genus Botrytis infecting Polygonaceae in Gansu, China. Mycologia 2020; 113:78-91. [PMID: 33125292 DOI: 10.1080/00275514.2020.1809288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A new species, Botrytis polygoni, was isolated from several species of Polygonaceae in 2011 and 2012 in Tongwei County, Gansu Province, China. The species infects Fagopyrum esculentum, F. tataricum, and Fallopia convolvulus, causing brown leaf spots and large blotches with concentric rings in the field. Botrytis polygoni is morphologically characterized by conidia spherical, unicellular, hyaline to pale brown or brown, (10.2-)14.3-21.4(-23.5) μm; and sclerotia black, spherical to subspherical, allantoid, or irregular-shaped, 0.2-4.1 × 0.1-3.0 mm. Comparison of the nuc rDNA internal transcribed spacer region (ITS1-5.8S-ITS2) sequences confirmed its placement in the genus Botrytis. Phylogenetic analysis based on the protein-coding genes glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60), and DNA-dependent RNA polymerase subunit II (RPB2) showed that the new species is clustered close but separate from Botrytis pyriformis, which was distant from 37 other Botrytis species and 17 undescribed species. Pathogenicity tests showed that the new species has aggressive pathogenicity to four species of Polygonaceae, specifically Fag. tataricum, Fal. convolvulus, Polygonum sibiricum, and Pol. aviculare, weak pathogenicity to Vicia faba in the Fabaceae, and no pathogenicity to eight other tested plants: Amaranthus retroflexus, Cirsium arvense, Convolvulus arvensis, Kalanchoe blossfeldiana, Lagopsis supine, Mentha canadensis, Plantago asiatica, and Raphanus sativus.
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Affiliation(s)
- S Q He
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences , Lanzhou 730070, China.,Scientific Observing and Experimental Station of Crop Pests in Tianshui, Ministry of Agriculture and Rural Affairs, P. R. China , Tianshui 741200, Gansu, China
| | - Z H Wen
- Technical Center, Lanzhou Customs , Lanzhou, 730010, China
| | - B Bai
- Institute of Agricultural Quality Standards and Testing Technology, Gansu Academy of Agricultural Sciences , Lanzhou 730070, China.,Laboratory of Quality & Safety Risk Assessment for Agro-products (Lanzhou), Ministry of Agriculture and Rural Affairs , P. R. China, Lanzhou 730070, China
| | - Z Q Jing
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences , Lanzhou 730070, China.,Scientific Observing and Experimental Station of Crop Pests in Tianshui, Ministry of Agriculture and Rural Affairs, P. R. China , Tianshui 741200, Gansu, China
| | - X W Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences , Beijing 100101, China
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18
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Esterio M, Osorio-Navarro C, Carreras C, Azócar M, Copier C, Estrada V, Rubilar M, Auger J. Botrytis prunorum Associated to Vitis vinifera Blossom Blight in Chile. PLANT DISEASE 2020; 104:2324-2329. [PMID: 32609075 DOI: 10.1094/pdis-09-19-2055-sc] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Table grapes are highly susceptible to Botrytis cinerea infections during the bloom period. After reaching the flower development stage, B. cinerea remains quiescent until berry ripening or gives rise to blossom blight under specific climate conditions. A research study was conducted on the Chilean Central Valley during the 2018-2019 growing season. Flowers of Vitis vinifera cv. Thompson Seedless were collected and B. cinerea was isolated together to a second and morphologically different species, characterized by white mycelium and low to no sporulation (11.4% of total isolates). Three randomly selected isolates within this population were genetically examined and identified as Botrytis prunorum based on a phylogenetic multilocus approach using partial regions of genes RPB2, HSP60, and G3PDH or NEP1 and NEP2. Pathogenicity tests showed that B. prunorum infects and causes wilting in healthy table grape flowers. B. prunorum isolates were able to infect Thompson Seedless berries, inducing lesions between 13.11 and 41.53% with respect to the lesion diameter generated by B. cinerea B05.10. The fungicide sensitivity was evaluated. The three genetically characterized isolates were sensitive to boscalid and to cyprodinil/fludioxonil mixture with a mean EC50 value of 5.5 µg/ml and 0.065 µg/ml, respectively. However, loss of sensitivity to fenhexamid was determined, with a mean EC50 value of 5.13 µg/ml. Our understanding about blossom blight in V. vinifera has been limited to B. cinerea. Here we associated B. prunorum as a second causal agent of this disease in Chile. This data represents a first approach to the epidemiological characteristics of B. prunorum associated with blossom blight in table grapes.
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Affiliation(s)
- Marcela Esterio
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Claudio Osorio-Navarro
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Claudia Carreras
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Madelaine Azócar
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Charleen Copier
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Verónica Estrada
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Mauricio Rubilar
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Jaime Auger
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
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19
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Derbyshire MC. Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action. Front Microbiol 2020; 11:644. [PMID: 32328056 PMCID: PMC7160247 DOI: 10.3389/fmicb.2020.00644] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.
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Affiliation(s)
- Mark C. Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
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20
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Lee RC, Farfan-Caceres LM, Debler JW, Syme RA. Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean ( Vicia faba L.). Front Microbiol 2020; 11:217. [PMID: 32132988 PMCID: PMC7040437 DOI: 10.3389/fmicb.2020.00217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/30/2020] [Indexed: 11/13/2022] Open
Abstract
Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.
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Affiliation(s)
- Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Lina M Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Johannes W Debler
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Robert A Syme
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
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21
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Wang L, Hu W, Deng J, Liu X, Zhou J, Li X. Antibacterial activity of Litsea cubeba essential oil and its mechanism against Botrytis cinerea. RSC Adv 2019; 9:28987-28995. [PMID: 35528448 PMCID: PMC9071840 DOI: 10.1039/c9ra05338g] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/31/2019] [Indexed: 12/22/2022] Open
Abstract
Litsea cubeba essential oil (LCEO) extracted from the fruit of the Litsea tree is a broad-spectrum bacteriostatic agent that has been used to treat ailments for thousands of years in China. The objective of our study was to assess the inhibitory effect of LCEO on Botrytis cinerea, a fungus that causes the putrification of fruits and vegetables. After being treated with 1.0% LCEO, the electrical conductivity of the fungal cells increased, and the contents of soluble reducing sugars and proteins slowly increased over treatment time. After being treated for 48 h with 1.0% LCEO, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images clearly showed damage to hyphae cells when compared with the normal growth of the control groups. Additional studies showed that the ergosterol content in the cell membrane significantly decreased with an increase in the LCEO concentration, and the electrophoretic bands of the proteins assayed using the sodium dodecyl sulfate-polyacrylamide gel electrophoresis method significantly changed at different LCEO concentrations. LCEO damaged the cell membrane and changed the cell membrane permeability, leading to the changes in some components in the cytoplasm, such as soluble reducing sugars, proteins, and ergosterol. In general, the antimicrobial activity of LCEO is attributable to a unique pathway and involves a series of events both on the surface and within the cytoplasm of the fungal cell.
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Affiliation(s)
- Liqun Wang
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
| | - Wei Hu
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
| | - Jiao Deng
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
| | - Xin Liu
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
| | - Jun Zhou
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
- Insititute of Natural Product Research and Development, Central South University of Forestry and Technology Changsha 410004 Hunan China
| | - Xiangzhou Li
- College of Materials Science and Engineering, Central South University of Forestry and Technology Changsha 410004 Hunan China
- National Engineering Laboratory for Applied Technology of Forestry & Ecology in South China Changsha 410004 Hunan China
- Insititute of Natural Product Research and Development, Central South University of Forestry and Technology Changsha 410004 Hunan China
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22
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Garfinkel AR, Coats KP, Sherry DL, Chastagner GA. Genetic analysis reveals unprecedented diversity of a globally-important plant pathogenic genus. Sci Rep 2019; 9:6671. [PMID: 31040332 PMCID: PMC6491473 DOI: 10.1038/s41598-019-43165-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/16/2019] [Indexed: 01/22/2023] Open
Abstract
Genus Botrytis contains approximately 35 species, many of which are economically-important and globally-distributed plant pathogens which collectively infect over 1,400 plant species. Recent efforts to genetically characterize genus Botrytis have revealed new species on diverse host crops around the world. In this study, surveys and subsequent genetic analysis of the glyceraldehyde-3-phosate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60), DNA-dependent RNA polymerase subunit II (RPB2), and necrosis and ethylene-inducing proteins 1 and 2 (NEP1 and NEP2) genes indicated that Botrytis isolates collected from peony fields in the United States contained more species diversity than ever before reported on a single host, including up to 10 potentially novel species. Together, up to 16 different phylogenetic species were found in association with peonies in the Pacific Northwest, which is over a third of the total number of species that are currently named. Furthermore, species were found on peonies in Alaska that have been described on other host plants in different parts of the world, indicating a wider geographic and host distribution than previously thought. Lastly, some isolates found on peony share sequence similarity with unnamed species found living as endophytes in weedy hosts, suggesting that the isolates found on peony have flexible lifestyles as recently discovered in the genus. Selected pathogenicity, growth, and morphological characteristics of the putatively new Botrytis species were also assessed to provide a basis for future formal description of the isolates as new species.
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Affiliation(s)
- Andrea R Garfinkel
- Washington State University Puyallup Research and Extension Center, 2606 W, Pioneer, Puyallup, WA, 98371, USA.
| | - Katie P Coats
- Washington State University Puyallup Research and Extension Center, 2606 W, Pioneer, Puyallup, WA, 98371, USA
| | - Don L Sherry
- Washington State University Puyallup Research and Extension Center, 2606 W, Pioneer, Puyallup, WA, 98371, USA
| | - Gary A Chastagner
- Washington State University Puyallup Research and Extension Center, 2606 W, Pioneer, Puyallup, WA, 98371, USA
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Valero-Jiménez CA, Veloso J, Staats M, van Kan JAL. Comparative genomics of plant pathogenic Botrytis species with distinct host specificity. BMC Genomics 2019; 20:203. [PMID: 30866801 PMCID: PMC6417074 DOI: 10.1186/s12864-019-5580-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 03/03/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Fungi of the genus Botrytis (presently containing ~ 35 species) are able to infect more than 1400 different plant species and cause losses in a wide range of crops of economic importance. The best studied species is B. cinerea, which has a broad host range and is one of the best studied necrotrophic plant pathogenic fungi. Most other Botrytis spp. have a narrow host range and have been studied in less detail. To characterize genomic variation among different representatives of Botrytis spp., we sequenced and annotated the draft genomes of nine Botrytis species: B. calthae, B. convoluta, B. elliptica, B. galanthina, B. hyacinthi, B. narcissicola, B. paeoniae, B. porri and B. tulipae. RESULTS Bioinformatics and comparative genomics tools were applied to determine a core of 7668 shared protein families in all Botrytis species, which grouped them in two distinct phylogenetic clades. The secretome of all nine Botrytis spp. was similar in number (ranging from 716 to 784 predicted proteins). A detailed analysis of the molecular functions of the secretome revealed that shared activities were highly similar. Orthologs to effectors functionally studied in B. cinerea were also present in the other Botrytis species. A complex pattern of presence/absence of secondary metabolite biosynthetic key enzymes was observed. CONCLUSIONS Comparative genomics of Botrytis show that overall, species share the main signatures and protein families in the secreted proteins, and of known effectors. Our study provides leads to study host range determinants in the genus Botrytis and provides a stepping stone to elucidate the roles of effector candidates in the infection process of these species.
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Affiliation(s)
| | - Javier Veloso
- Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, the Netherlands
- Department of Biology, Faculty of Sciences, University of A Coruña, A Coruña, Spain
| | - Martijn Staats
- Biosystematics Group, Wageningen University, 6708PB Wageningen, the Netherlands
- Present address: RIKILT Wageningen University and Research, 6708WB Wageningen, the Netherlands
| | - Jan A. L. van Kan
- Laboratory of Phytopathology, Wageningen University, 6708PB Wageningen, the Netherlands
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Cobos R, Calvo-Peña C, Álvarez-Pérez JM, Ibáñez A, Diez-Galán A, González-García S, García-Angulo P, Acebes JL, Coque JJR. Necrotic and Cytolytic Activity on Grapevine Leaves Produced by Nep1-Like Proteins of Diplodia seriata. FRONTIERS IN PLANT SCIENCE 2019; 10:1282. [PMID: 31749815 PMCID: PMC6843023 DOI: 10.3389/fpls.2019.01282] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/13/2019] [Indexed: 05/22/2023]
Abstract
Many phytopathogenic fungi produce necrosis and ethylene inducing peptide 1 (Nep1-like proteins or NLP) that trigger leaf necrosis and the activation of defense mechanisms. These proteins have been widely studied in plant pathogens as Moniliophthora perniciosa or Botrytis cinerea between others, but little is known about their biological roles in grapevine trunk pathogens. Advances in the sequencing of genomes of several fungi involved in grapevine trunk diseases have revealed that these proteins are present in several copies in their genomes. The aim of this project was to analyze the presence of genes encoding NLP proteins in the Diplodia seriata genome and to characterize their putative role as virulence factors associated to grapevine trunk diseases. In this study, we characterized four NLPs from Diplodia seriata. All proteins showed highly similar amino acid sequences and contained the characteristic peptide motifs of NLPs. DserNEPs slightly reduced the viability of Vitis vinifera L. cell cultures. The cytolytic activity from DserNEP1 was stronger than that from DserNEP2, even at low concentrations. Purified DserNEPs also produced necrosis in leaves when they were inoculated into micropropagules of V. vinifera L. This is the first record of Nep1-like proteins from a fungus associated with grapevine trunk diseases and also from a member of the Botryosphaeriaceae family.
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Affiliation(s)
- Rebeca Cobos
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
- RGA-bioinvestigación S.L., León, Spain
- *Correspondence: Rebeca Cobos, ; Juan José Rubio Coque,
| | - Carla Calvo-Peña
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | | | - Ana Ibáñez
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | | | | | | | - Jose Luis Acebes
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
| | - Juan José R. Coque
- Instituto de Investigación de la Viña y el Vino, Universidad de León, León, Spain
- RGA-bioinvestigación S.L., León, Spain
- *Correspondence: Rebeca Cobos, ; Juan José Rubio Coque,
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25
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Wang R, Dong L, He R, Wang Q, Chen Y, Qu L, Zhang YA. Comparative genomic analyses reveal the features for adaptation to nematodes in fungi. DNA Res 2018; 25:4791394. [PMID: 29315395 PMCID: PMC6014366 DOI: 10.1093/dnares/dsx053] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 12/06/2017] [Indexed: 12/20/2022] Open
Abstract
Nematophagous (NP) fungi are ecologically important components of the soil microbiome in natural ecosystems. Esteya vermicola (Ev) has been reported as a NP fungus with a poorly understood evolutionary history and mechanism of adaptation to parasitism. Furthermore, NP fungal genomic basis of lifestyle was still unclear. We sequenced and annotated the Ev genome (34.2 Mbp) and integrated genetic makeup and evolution of pathogenic genes to investigate NP fungi. The results revealed that NP fungi had some abundant pathogenic genes corresponding to their niche. A number of gene families involved in pathogenicity were expanded, and some pathogenic orthologous genes underwent positive selection. NP fungi with diverse morphological features exhibit similarities of evolutionary convergence in attacking nematodes, but their genetic makeup and microscopic mechanism are different. Endoparasitic NP fungi showed similarity in large number of transporters and secondary metabolite coding genes. Noteworthy, expanded families of transporters and endo-beta-glucanase implied great genetic potential of Ev in quickly perturbing nematode metabolism and parasitic behavior. These results facilitate our understanding of NP fungal genomic features for adaptation to nematodes and lay a solid theoretical foundation for further research and application.
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Affiliation(s)
- Ruizhen Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Leiming Dong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Ran He
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Institute of Botany, Beijing Botanical Garden, Beijing 100093, China
| | - Qinghua Wang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yuequ Chen
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
- Forestry Resources Protection Institute, Jilin Provincial Academy of Forestry Sciences, Changchun 130031, China
| | - Liangjian Qu
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yong-An Zhang
- The Key Laboratory of Forest Protection, State Forestry Administration of China, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
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26
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Dowling ME, Hu MJ, Schnabel G. Identification and Characterization of Botrytis fragariae Isolates on Strawberry in the United States. PLANT DISEASE 2017; 101:1769-1773. [PMID: 30676928 DOI: 10.1094/pdis-03-17-0316-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gray mold is a devastating disease on strawberry, and may be caused by several species of Botrytis. The goal of this study was to better understand and characterize the species of Botrytis with reduced sensitivity to the fungicide Polyoxin D, particularly Botrytis fragariae. In total, 78 Botrytis isolates of unknown species that were sensitive (28 isolates; S), moderately sensitive (22 isolates; MS), or reduced sensitive (28 isolates; RS) to Polyoxin-D were collected from commercial strawberry fields of five states in the United States, identified to the species level, and characterized. The majority (75%) of S isolates were Botrytis cinerea and the majority (79%) of RS isolates were the recently described species B. fragariae, indicating an innate ability of B. fragariae to tolerate Polyoxin-D. B. fragariae produced fluffy, white mycelium and was less likely to sporulate on potato dextrose agar than B. cinerea. Isolates from a commercial field recovered from blossoms in early spring were all B. fragariae, those from leaves of the same plants in late spring were a mixture of B. fragariae and B. cinerea, and those from fruit in early summer were all B. cinerea, indicating that B. fragariae may preferentially colonize blossom tissue. A polymerase chain reaction-based assay was developed based on NEP2 sequence variability to distinguish B. fragariae from other Botrytis spp. that have been reported on strawberry, including B. cinerea, B. mali, B. caroliniana, and B. ricini. None of the isolates collected from Canada, California, or North Carolina nurseries were B. fragariae, indicating that the newly described species may not exist or not be widely distributed in planting stock.
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Affiliation(s)
- Madeline E Dowling
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Meng-Jun Hu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Guido Schnabel
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
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27
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Garfinkel AR, Lorenzini M, Zapparoli G, Chastagner GA. Botrytis euroamericana, a new species from peony and grape in North America and Europe. Mycologia 2017; 109:495-507. [PMID: 28849988 DOI: 10.1080/00275514.2017.1354169] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A novel species of Botrytis isolated from peony in Alaska, USA, and grape in Trento District, Italy, was identified based on morphology, pathogenicity, and sequence data. The grape and peony isolates share sequence homology in the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60), DNA-dependent RNA polymerase subunit II (RPB2), and necrosis- and ethylene-inducing protein 1 and 2 (NEP1 and NEP2) genes that place them in a distinct group closely related to B. aclada, a globally distributed pathogen of onions. Genetic results were corroborated with morphological and pathogenicity trials that included two isolates of B. cinerea and two isolates of B. paeoniae from peony in Alaska and one isolate of B. aclada. The authors observed differences in colony and conidia morphology and ability to cause lesions on different host tissues that suggest that the grape and peony isolates represent a distinct species. Most notably, the grape and peony isolates did not colonize onion bulbs, whereas B. aclada readily produced lesions and prolific sporulation on onion tissue. The new species Botrytis euroamericana is described herein.
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Affiliation(s)
- Andrea R Garfinkel
- a Washington State University Puyallup Research and Extension Center , Puyallup , Washington 98371
| | - Marilinda Lorenzini
- b Dipartimento di Biotecnologie , Università degli Studi di Verona , 37134 Verona , Italy
| | - Giacomo Zapparoli
- b Dipartimento di Biotecnologie , Università degli Studi di Verona , 37134 Verona , Italy
| | - Gary A Chastagner
- a Washington State University Puyallup Research and Extension Center , Puyallup , Washington 98371
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28
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Abstract
The interactions between fungi and plants encompass a spectrum of ecologies ranging from saprotrophy (growth on dead plant material) through pathogenesis (growth of the fungus accompanied by disease on the plant) to symbiosis (growth of the fungus with growth enhancement of the plant). We consider pathogenesis in this article and the key roles played by a range of pathogen-encoded molecules that have collectively become known as effectors.
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29
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Botrytis eucalypti, a novel species isolated from diseased Eucalyptus seedlings in South China. Mycol Prog 2016. [DOI: 10.1007/s11557-016-1229-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Zhang J, Yang H, Yu QY, Wu MD, Yang L, Zhuang WY, Chen WD, Li GQ. Botrytis pyriformis sp. nov., a novel and likely saprophytic species of Botrytis. Mycologia 2016; 108:682-96. [PMID: 27153884 DOI: 10.3852/15-340] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/20/2016] [Indexed: 02/02/2023]
Abstract
A novel species of Botrytis from Sedum sarmentosum was described based on morphology and analyses of DNA sequences of nuc rDNA ITS regions and three nuclear genes (G3PDH, HSP60, RPB2). Meanwhile pathogenicity in 32 plant species, response to temperature for growth and conidial germination for the species were determined. The Botrytis species was named Botrytis pyriformis sp. nov. It was characterized by formation of grayish mycelia, brownish conidia and melanized sclerotia on PDA. The conidia are pear-shaped, melanized and covered with abundant villiform appendages on the conidial surface. Comparison of the ITS sequences confirmed its placement in the genus Botrytis Phylogenetic analysis based on DNA sequences of G3PDH, HSP60 and RPB2 genes indicated that B. pyriformis and other 30 Botrytis species form a monophyletic clade, which was further divided into three subclades. Subclade I comprised B. pyriformis alone, whereas subclades II and III comprised six and 24 Botrytis species, respectively. Botrytis pyriformis could not infect 32 plant species including S. sarmentosum, possibly due to deficiency in formation of infection cushions. This study presents a formal description and illustrations for B. pyriformis and provides experimental evidence, indicating that B. pyriformis might be a saprophytic species.
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Affiliation(s)
- J Zhang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - H Yang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Q Y Yu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - M D Wu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - L Yang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - W Y Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - W D Chen
- USDA Agricultural Research Service, Washington State University, Pullman, Washington
| | - G Q Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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31
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Corwin JA, Subedy A, Eshbaugh R, Kliebenstein DJ. Expansive Phenotypic Landscape of Botrytis cinerea Shows Differential Contribution of Genetic Diversity and Plasticity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2016; 29:287-298. [PMID: 26828401 DOI: 10.1094/mpmi-09-15-0196-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The modern evolutionary synthesis suggests that both environmental variation and genetic diversity are critical determinants of pathogen success. However, the relative contribution of these two sources of variation is not routinely measured. To estimate the relative contribution of plasticity and genetic diversity for virulence-associated phenotypes in a generalist plant pathogen, we grew a population of 15 isolates of Botrytis cinerea from throughout the world, under a variety of in vitro and in planta conditions. Under in planta conditions, phenotypic differences between the isolates were determined by the combination of genotypic variation within the pathogen and environmental variation. In contrast, phenotypic differences between the isolates under in vitro conditions were predominantly determined by genetic variation in the pathogen. Using a correlation network approach, we link the phenotypic variation under in vitro experimental conditions to phenotypic variation during plant infection. This study indicates that there is a high level of phenotypic variation within B. cinerea that is controlled by a mixture of genetic variation, environment, and genotype × environment. This argues that future experiments into the pathogenicity of B. cinerea must account for the genetic and environmental variation within the pathogen to better sample the potential phenotypic space of the pathogen.
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Affiliation(s)
- Jason A Corwin
- 1 Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A.; and
| | - Anushriya Subedy
- 1 Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A.; and
| | - Robert Eshbaugh
- 1 Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A.; and
| | - Daniel J Kliebenstein
- 1 Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, U.S.A.; and
- 2 DynaMo Center of Excellence, University of Copenhagen, Thorvaldsensvej 40, DK-1871, Frederiksberg C, Denmark
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32
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Ferrada EE, Latorre BA, Zoffoli JP, Castillo A. Identification and Characterization of Botrytis Blossom Blight of Japanese Plums Caused by Botrytis cinerea and B. prunorum sp. nov. in Chile. PHYTOPATHOLOGY 2016; 106:155-65. [PMID: 26474331 DOI: 10.1094/phyto-06-15-0143-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Blossom blight is a destructive disease of plums (Prunus salicina) when humid and temperate weather conditions occur in Chile. Disease incidence ranging from 4 to 53% has been observed. Symptoms include light brown petal necrosis, starting as light brown mottles or V-shaped necrosis at the margins of the petals, progressing to the stamen and pistils. In this study, the etiology of blossom blight of plums was determined. High- and low-sporulating isolates of Botrytis were obtained consistently from blighted blossoms and apparently healthy flowers of plums. Based on colony morphology, conidial production and molecular phylogenetic analysis, these high- and low-sporulating isolates were identified as B. cinerea and B. prunorum sp. nov., respectively. Phylogenetic analysis of the genes glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60), and DNA-dependent RNA polymerase subunit II (RPB2) grouped B. prunorum isolates in a single cluster, distantly from B. cinerea and other Botrytis species. The phylogenetic analysis of necrosis and ethylene-inducing protein (NEP1 and NEP2) genes corroborated these results. Analysis of the internal transcribed spacer region and large-subunit (26S) ribosomal DNA and detection of Boty and Flipper transposable elements, were not useful to differentiate between these Botrytis species. Both species were pathogenic on plum flowers and the fruit of plums, apples, and kiwifruits. However, B. prunorum was less virulent than B. cinerea. These pathogens were re-isolated from inoculated and diseased tissues; thus, Koch's postulates were fulfilled, confirming its role in blossom blight of plums. B. cinerea was predominant, suggesting that B. prunorum may play a secondary role in the epidemiology of blossom blight in plums in Chile. This study clearly demonstrated that the etiology of blossom blight of plums is caused by B. cinerea and B. prunorum, which constitute a species complex living in sympatry on plums and possibly on other stone fruit trees.
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Affiliation(s)
- Enrique E Ferrada
- First, second, and third authors: Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile; and fourth author: Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago
| | - Bernardo A Latorre
- First, second, and third authors: Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile; and fourth author: Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago
| | - Juan P Zoffoli
- First, second, and third authors: Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile; and fourth author: Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago
| | - Antonio Castillo
- First, second, and third authors: Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Santiago, Chile; and fourth author: Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago
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33
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Anderson JP, Hane JK, Stoll T, Pain N, Hastie ML, Kaur P, Hoogland C, Gorman JJ, Singh KB. Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts. Mol Cell Proteomics 2016; 15:1188-203. [PMID: 26811357 PMCID: PMC4824849 DOI: 10.1074/mcp.m115.054502] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Indexed: 11/22/2022] Open
Abstract
Rhizoctonia solani is an important root infecting pathogen of a range of food staples worldwide including wheat, rice, maize, soybean, potato and others. Conventional resistance breeding strategies are hindered by the absence of tractable genetic resistance in any crop host. Understanding the biology and pathogenicity mechanisms of this fungus is important for addressing these disease issues, however, little is known about how R. solani causes disease. This study capitalizes on recent genomic studies by applying mass spectrometry based proteomics to identify soluble, membrane-bound and culture filtrate proteins produced under wheat infection and vegetative growth conditions. Many of the proteins found in the culture filtrate had predicted functions relating to modification of the plant cell wall, a major activity required for pathogenesis on the plant host, including a number found only under infection conditions. Other infection related proteins included a high proportion of proteins with redox associated functions and many novel proteins without functional classification. The majority of infection only proteins tested were confirmed to show transcript up-regulation during infection including a thaumatin which increased susceptibility to R. solani when expressed in Nicotiana benthamiana. In addition, analysis of expression during infection of different plant hosts highlighted how the infection strategy of this broad host range pathogen can be adapted to the particular host being encountered. Data are available via ProteomeXchange with identifier PXD002806.
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Affiliation(s)
- Jonathan P Anderson
- From the ‡CSIRO Agriculture, Floreat, Western Australia; §The University of Western Australia Institute of Agriculture, Crawley, Western Australia
| | - James K Hane
- From the ‡CSIRO Agriculture, Floreat, Western Australia
| | - Thomas Stoll
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Nicholas Pain
- From the ‡CSIRO Agriculture, Floreat, Western Australia
| | - Marcus L Hastie
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | | | - Jeffrey J Gorman
- ¶QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Karam B Singh
- From the ‡CSIRO Agriculture, Floreat, Western Australia; §The University of Western Australia Institute of Agriculture, Crawley, Western Australia;
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34
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Description of a taxonomically undefined Sclerotiniaceae strain from withered rotten-grapes. Antonie van Leeuwenhoek 2015; 109:197-205. [PMID: 26581438 DOI: 10.1007/s10482-015-0621-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/12/2015] [Indexed: 10/22/2022]
Abstract
A necrotrophic member of the Sclerotiniaceae family (herewith named strain C10) isolated from withered rotten-grapes, is described. Interestingly, the fungus has no defined taxonomic position since it has been impossible to attribute it to an existing genus. Phylogenetic analysis of partial sequences of glyceraldehyde 3-phosphate dehydrogenase (G3PDH), heat shock protein 60 (HSP60) and DNA-directed RNA polymerase II subunit (RPB2), revealed that strain C10 is distantly related to Amphobotrys and Botrytis. This evidence clearly distinguishes this new Sclerotiniaceae member from other taxa of the family. Moreover, its morphological characteristics did not match those of Amphobotrys and Botrytis. Infectivity assays demonstrated that strain C10 could be a potential postharvest pathogen of withered grapes. This study revealed the taxonomic importance of this strain suggesting the existence of a possible new genus, a theory that requires further investigation.
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35
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Ho CL, Tan YC. Molecular defense response of oil palm to Ganoderma infection. PHYTOCHEMISTRY 2015; 114:168-77. [PMID: 25457484 DOI: 10.1016/j.phytochem.2014.10.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 10/01/2014] [Accepted: 10/16/2014] [Indexed: 05/15/2023]
Abstract
Basal stem rot (BSR) of oil palm roots is due to the invasion of fungal mycelia of Ganoderma species which spreads to the bole of the stem. In addition to root contact, BSR can also spread by airborne basidiospores. These fungi are able to break down cell wall components including lignin. BSR not only decreases oil yield, it also causes the stands to collapse thus causing severe economic loss to the oil palm industry. The transmission and mode of action of Ganoderma, its interactions with oil palm as a hemibiotroph, and the molecular defence responses of oil palm to the infection of Ganoderma boninense in BSR are reviewed, based on the transcript profiles of infected oil palms. The knowledge gaps that need to be filled in oil palm-Ganoderma molecular interactions i.e. the associations of hypersensitive reaction (HR)-induced cell death and reactive oxygen species (ROS) kinetics to the susceptibility of oil palm to Ganoderma spp., the interactions of phytohormones (salicylate, jasmonate and ethylene) at early and late stages of BSR, and cell wall strengthening through increased production of guaiacyl (G)-type lignin, are also discussed.
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Affiliation(s)
- C-L Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia; Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia.
| | - Y-C Tan
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM-Serdang, Selangor, Malaysia
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Fan X, Zhang J, Yang L, Wu M, Chen W, Li G. Development of PCR-Based Assays for Detecting and Differentiating Three Species of Botrytis Infecting Broad Bean. PLANT DISEASE 2015; 99:691-698. [PMID: 30699675 DOI: 10.1094/pdis-07-14-0701-re] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Botrytis cinerea, B. fabae, and B. fabiopsis are known to cause chocolate spot on broad bean. This study was conducted to develop polymerase chain reaction (PCR)-based assays to detect and differentiate these three species. Two sets of primers, Bc-f/Bc-r for B. cinerea and Bfab-f/Bfab-r for B. fabiopsis, were designed based on two sequence-characterized amplified region markers derived from two random amplified polymorphic DNA assays. The other primer set, Bfa-f/Bfa-r for B. fabae, was designed based on the necrosis and ethylene-inducing protein 1 gene sequence. The three primer sets were highly specific for the corresponding species of Botrytis in both single and multiplex PCR assays. The PCR detection limit was 40, 40, and 400 pg of DNA per 25-μl reaction mixture for B. fabae, B. fabiopsis, and B. cinerea, respectively. Presence of the broad bean DNA in the PCR reactions at 1:1000 (Botrytis DNA/broad bean DNA [wt/wt]) had negligible effects on detection of the targeted Botrytis spp. The multiplex PCR assay was able to detect three Botrytis spp. in artificially infected and naturally infected broad bean leaves. These results suggest that the multiplex PCR assay developed in this study could be used to monitor the epidemics of chocolate spot of broad bean in the field.
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Affiliation(s)
- Xuan Fan
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingde Wu
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Weidong Chen
- United States Department of Agriculture-Agricultural Research Service, Washington State University, Pullman; and
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology and Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University
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Muñoz G, Campos F, Salgado D, Galdames R, Gilchrist L, Chahin G, Andrade O. Molecular identification of Botrytis cinerea, Botrytis paeoniae and Botrytis pseudocinerea associated with gray mould disease in peonies (Paeonia lactiflora Pall.) in Southern Chile. Rev Iberoam Micol 2015; 33:43-7. [PMID: 25982419 DOI: 10.1016/j.riam.2015.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/22/2015] [Accepted: 02/03/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND In Chile, the peony is the most important ornamental flower exported from the country. Gray mould is a phytopathological problem of this crop. This disease is caused by Botrytis cinerea and Botrytis paeoniae. AIMS We carried out the first survey of Botrytis species associated with peony gray mould in Southern Chile to estimate the diversity of these pathogens. METHODS Diseased peony leaves were collected from seven locations in Southern Chile covering a distance of 300km. The Botrytis isolates obtained were studied by morphological and molecular methods. Finally, a PCR assay using primers based on the necrosis and ethylene-inducing protein gene (nep1) was used to specifically identify B. paeoniae. RESULTS Seventeen isolates belonging to Botrytis genus were obtained, and all of them were pathogenic to peonies when inoculated in plants grown in a greenhouse. Morphological analyses showed that four isolates shared common characteristics, which distinguish them from the rest. Homology and phylogenetic analysis of G3PDH, as well as determination of the Bc-hch allele, allowed us to identify 12 isolates as B. cinerea, 4 as B. paeoniae and one isolate as Botrytis pseudocinerea. The PCR assay was found to be specific to B. paeoniae, amplifying a single band of 470bp. CONCLUSIONS Three Botrytis species involved in peony gray mould disease are present in Chile. This is the first time that both B. paeoniae and B. pseudocinerea have been reported to be present in the country and also that they affect peonies. Finally, to our knowledge, the PCR based method herein described is the first of its kind to be used to identify B. paeoniae.
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Affiliation(s)
- Gastón Muñoz
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Talcahuano, Chile.
| | - Felipe Campos
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Talcahuano, Chile
| | - Daisy Salgado
- Instituto de Investigaciones Agropecuarias (INIA) Carillanca, Temuco, Chile
| | - Rafael Galdames
- Instituto de Investigaciones Agropecuarias (INIA) Carillanca, Temuco, Chile
| | - Lucy Gilchrist
- Instituto de Investigaciones Agropecuarias (INIA) Carillanca, Temuco, Chile
| | - Gabriela Chahin
- Instituto de Investigaciones Agropecuarias (INIA) Carillanca, Temuco, Chile
| | - Orlando Andrade
- Escuela de Agronomía, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:40-50. [PMID: 27839074 DOI: 10.1094/mpmi-10-13-0313-ta.testissue] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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Vleeshouwers VGAA, Oliver RP. Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 2015:17-27. [PMID: 27839075 DOI: 10.1094/mpmi-10-13-0313-cr.testissue] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Affiliation(s)
- Vivianne G A A Vleeshouwers
- 1 Wageningen UR Plant Breeding, Wageningen University and Research Centre, P.O. Box 386, 6700 AJ, Wageningen, The Netherlands
| | - Richard P Oliver
- 2 Australian Centre for Necrotrophic Fungal Pathogens, Curtin University, Perth WA 6845, Australia
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Grant-Downton RT, Terhem RB, Kapralov MV, Mehdi S, Rodriguez-Enriquez MJ, Gurr SJ, van Kan JAL, Dewey FM. A novel Botrytis species is associated with a newly emergent foliar disease in cultivated Hemerocallis. PLoS One 2014; 9:e89272. [PMID: 24887415 PMCID: PMC4041564 DOI: 10.1371/journal.pone.0089272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 10/30/2013] [Indexed: 11/19/2022] Open
Abstract
Foliar tissue samples of cultivated daylilies (Hemerocallis hybrids) showing the symptoms of a newly emergent foliar disease known as 'spring sickness' were investigated for associated fungi. The cause(s) of this disease remain obscure. We isolated repeatedly a fungal species which proved to be member of the genus Botrytis, based on immunological tests. DNA sequence analysis of these isolates, using several different phyogenetically informative genes, indicated that they represent a new Botrytis species, most closely related to B. elliptica (lily blight, fire blight) which is a major pathogen of cultivated Lilium. The distinction of the isolates was confirmed by morphological analysis of asexual sporulating cultures. Pathogenicity tests on Hemerocallis tissues in vitro demonstrated that this new species was able to induce lesions and rapid tissue necrosis. Based on this data, we infer that this new species, described here as B. deweyae, is likely to be an important contributor to the development of 'spring sickness' symptoms. Pathogenesis may be promoted by developmental and environmental factors that favour assault by this necrotrophic pathogen. The emergence of this disease is suggested to have been triggered by breeding-related changes in cultivated hybrids, particularly the erosion of genetic diversity. Our investigation confirms that emergent plant diseases are important and deserve close monitoring, especially in intensively in-bred plants.
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Affiliation(s)
| | - Razak B. Terhem
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | | | - Saher Mehdi
- Department of Plant Sciences, University of Oxford, Oxford, England
| | | | - Sarah J. Gurr
- Department of Plant Sciences, University of Oxford, Oxford, England
| | - Jan A. L. van Kan
- Wageningen University, Laboratory of Phytopathology, Wageningen, The Netherlands
| | - Frances M. Dewey
- Department of Plant Sciences, University of Oxford, Oxford, England
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Vleeshouwers VGAA, Oliver RP. Effectors as tools in disease resistance breeding against biotrophic, hemibiotrophic, and necrotrophic plant pathogens. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:196-206. [PMID: 24405032 DOI: 10.1094/mpmi-10-13-0313-ia] [Citation(s) in RCA: 204] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
One of most important challenges in plant breeding is improving resistance to the plethora of pathogens that threaten our crops. The ever-growing world population, changing pathogen populations, and fungicide resistance issues have increased the urgency of this task. In addition to a vital inflow of novel resistance sources into breeding programs, the functional characterization and deployment of resistance also needs improvement. Therefore, plant breeders need to adopt new strategies and techniques. In modern resistance breeding, effectors are emerging as tools to accelerate and improve the identification, functional characterization, and deployment of resistance genes. Since genome-wide catalogues of effectors have become available for various pathogens, including biotrophs as well as necrotrophs, effector-assisted breeding has been shown to be successful for various crops. "Effectoromics" has contributed to classical resistance breeding as well as for genetically modified approaches. Here, we present an overview of how effector-assisted breeding and deployment is being exploited for various pathosystems.
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Leroch M, Plesken C, Weber RWS, Kauff F, Scalliet G, Hahn M. Gray mold populations in german strawberry fields are resistant to multiple fungicides and dominated by a novel clade closely related to Botrytis cinerea. Appl Environ Microbiol 2013; 79:159-67. [PMID: 23087030 PMCID: PMC3536109 DOI: 10.1128/aem.02655-12] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/10/2012] [Indexed: 11/20/2022] Open
Abstract
The gray mold fungus Botrytis cinerea is a major threat to fruit and vegetable production. Strawberry fields usually receive several fungicide treatments against Botrytis per season. Gray mold isolates from several German strawberry-growing regions were analyzed to determine their sensitivity against botryticides. Fungicide resistance was commonly observed, with many isolates possessing resistance to multiple (up to six) fungicides. A stronger variant of the previously described multidrug resistance (MDR) phenotype MDR1, called MDR1h, was found to be widely distributed, conferring increased partial resistance to two important botryticides, cyprodinil and fludioxonil. A 3-bp deletion mutation in a transcription factor-encoding gene, mrr1, was found to be correlated with MDR1h. All MDR1h isolates and the majority of isolates with resistance to multiple fungicides were found to be genetically distinct. Multiple-gene sequencing confirmed that they belong to a novel clade, called Botrytis group S, which is closely related to B. cinerea and the host-specific species B. fabae. Isolates of Botrytis group S genotypes were found to be widespread in all German strawberry-growing regions but almost absent from vineyards. Our data indicate a clear subdivision of gray mold populations, which are differentially distributed according to their host preference and adaptation to chemical treatments.
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Affiliation(s)
- Michaela Leroch
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Cecilia Plesken
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Frank Kauff
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | | | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, Kaiserslautern, Germany
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Dong S, Kong G, Qutob D, Yu X, Tang J, Kang J, Dai T, Wang H, Gijzen M, Wang Y. The NLP toxin family in Phytophthora sojae includes rapidly evolving groups that lack necrosis-inducing activity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:896-909. [PMID: 22397404 DOI: 10.1094/mpmi-01-12-0023-r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Necrosis- and ethylene-inducing-like proteins (NLP) are widely distributed in eukaryotic and prokaryotic plant pathogens and are considered to be important virulence factors. We identified, in total, 70 potential Phytophthora sojae NLP genes but 37 were designated as pseudogenes. Sequence alignment of the remaining 33 NLP delineated six groups. Three of these groups include proteins with an intact heptapeptide (Gly-His-Arg-His-Asp-Trp-Glu) motif, which is important for necrosis-inducing activity, whereas the motif is not conserved in the other groups. In total, 19 representative NLP genes were assessed for necrosis-inducing activity by heterologous expression in Nicotiana benthamiana. Surprisingly, only eight genes triggered cell death. The expression of the NLP genes in P. sojae was examined, distinguishing 20 expressed and 13 nonexpressed NLP genes. Real-time reverse-transcriptase polymerase chain reaction results indicate that most NLP are highly expressed during cyst germination and infection stages. Amino acid substitution ratios (Ka/Ks) of 33 NLP sequences from four different P. sojae strains resulted in identification of positive selection sites in a distinct NLP group. Overall, our study indicates that expansion and pseudogenization of the P. sojae NLP family results from an ongoing birth-and-death process, and that varying patterns of expression, necrosis-inducing activity, and positive selection suggest that NLP have diversified in function.
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Affiliation(s)
- Suomeng Dong
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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Li X, Kerrigan J, Chai W, Schnabel G. Botrytis caroliniana, a new species isolated from blackberry in South Carolina. Mycologia 2012; 104:650-8. [PMID: 22314589 DOI: 10.3852/11-218] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Blackberry fruits symptomatic for gray mold were collected from three commercial blackberry fields in northwestern South Carolina. Single-spore isolates were generated and two distinct phenotypes were discovered in each location; one sporulated on PDA and one did not. One isolate of each phenotype and location (six isolates total) were selected for in depth molecular and morphological characterization. Glyceraldehyde-3-phosphate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60) and DNA-dependent RNA polymerase subunit II (RPB2) coding sequence alignment revealed Botrytis cinerea as the sporulating phenotype and a new yet undescribed species as the non-sporulating phenotype. The new Botrytis sp., described herein as Botrytis caroliniana, was most closely related genetically to B. fabiopsis and B. galanthina, the causal agents of gray mold disease of broad bean and snowdrop, respectively. It produces smaller conidia than either B. fabiopsis or B. galanthina, and sequence analysis of genes encoding necrosis and ethylene-inducing proteins (NEPs) also indicated that the Botrytis isolates represent a separate and distinct species. The new species is pathogenic on blackberry fruits and broad bean leaves, which distinguishes it further from B. galanthina. The new species formed white to pale gray colonies with short, tufted aerial mycelium and produced black sclerotia on PDA at 20 C. To our knowledge this is only the third Botrytis species discovered to cause disease on blackberry in the United States.
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Affiliation(s)
- Xingpeng Li
- School of Agricultural, Forest, & Environmental Sciences, Clemson University, Clemson, SC 9634, USA
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Abstract
Plants inhabit environments crowded with infectious microbes that pose constant threats to their survival. Necrotrophic pathogens are notorious for their aggressive and wide-ranging virulence strategies that promote host cell death and acquire nutrients for growth and reproduction from dead cells. This lifestyle constitutes the axis of their pathogenesis and virulence strategies and marks contrasting immune responses to biotrophic pathogens. The diversity of virulence strategies in necrotrophic species corresponds to multifaceted host immune response mechanisms. When effective, the plant immune system disarms the infectious necrotroph of its pathogenic arsenal or attenuates its effect, restricting further ingress and disease symptom development. Simply inherited resistance traits confer protection against host-specific necrotrophs (HSNs), whereas resistance to broad host-range necrotrophs (BHNs) is complex. Components of host genetic networks, as well as the molecular and cellular processes that mediate host immune responses to necrotrophs, are being identified. In this review, recent advances in our understanding of plant immune responses to necrotrophs and comparison with responses to biotrophic pathogens are summarized, highlighting common and contrasting mechanisms.
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Affiliation(s)
- Tesfaye Mengiste
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA.
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Rossi FR, Gárriz A, Marina M, Romero FM, Gonzalez ME, Collado IG, Pieckenstain FL. The sesquiterpene botrydial produced by Botrytis cinerea induces the hypersensitive response on plant tissues and its action is modulated by salicylic acid and jasmonic acid signaling. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:888-96. [PMID: 21751851 DOI: 10.1094/mpmi-10-10-0248] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Botrytis cinerea, as a necrotrophic fungus, kills host tissues and feeds on the remains. This fungus is able to induce the hypersensitive response (HR) on its hosts, thus taking advantage on the host's defense machinery for generating necrotic tissues. However, the identity of HR effectors produced by B. cinerea is not clear. The aim of this work was to determine whether botrydial, a phytotoxic sesquiterpene produced by B. cinerea, is able to induce the HR on plant hosts, using Arabidopsis thaliana as a model. Botrydial induced the expression of the HR marker HSR3, callose deposition, and the accumulation of reactive oxygen species and phenolic compounds. Botrydial also induced the expression of PR1 and PDF1.2, two pathogenesis-related proteins involved in defense responses regulated by salicylic acid (SA) and jasmonic acid (JA), respectively. A. thaliana and tobacco plants defective in SA signaling were more resistant to botrydial than wild-type plants, as opposed to A. thaliana plants defective in JA signaling, which were more sensitive. It can be concluded that botrydial induces the HR on its hosts and its effects are modulated by host signaling pathways mediated by SA and JA.
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Stewart JE, Kawabe M, Abdo Z, Arie T, Peever TL. Contrasting codon usage patterns and purifying selection at the mating locus in putatively asexual alternaria fungal species. PLoS One 2011; 6:e20083. [PMID: 21625561 PMCID: PMC3098265 DOI: 10.1371/journal.pone.0020083] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 04/18/2011] [Indexed: 12/25/2022] Open
Abstract
Sexual reproduction in heterothallic ascomycete fungi is controlled by a single mating-type locus called MAT1 with two alternate alleles or idiomorphs, MAT1-1 and MAT1-2. These alleles lack sequence similarity and encode different transcriptional regulators. A large number of phytopathogenic fungi including Alternaria spp. are considered asexual, yet still carry expressed MAT1 genes. The molecular evolution of Alternaria MAT1 was explored using nucleotide diversity, nonsynonymous vs. synonymous substitution (dn/ds) ratios and codon usage statistics. Likelihood ratio tests of site-branch models failed to detect positive selection on MAT1-1-1 or MAT1-2-1. Codon-site models demonstrated that both MAT1-1-1 and MAT1-2-1 are under purifying selection and significant differences in codon usage were observed between MAT1-1-1 and MAT1-2-1. Mean GC content at the third position (GC3) and effective codon usage (ENC) were significantly different between MAT1-1-1 and MAT1-2-1 with values of 0.57 and 48 for MAT1-1-1 and 0.62 and 46 for MAT1-2-1, respectively. In contrast, codon usage of Pleospora spp. (anamorph Stemphylium), a closely related Dothideomycete genus, was not significantly different between MAT1-1-1 and MAT1-2-1. The purifying selection and biased codon usage detected at the MAT1 locus in Alternaria spp. suggest a recent sexual past, cryptic sexual present and/or that MAT1 plays important cellular role(s) in addition to mating.
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Affiliation(s)
- Jane E Stewart
- Department of Plant Pathology, Washington State University, Pullman, Washington, United States of America.
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Boava LP, Cristofani-Yaly M, Mafra VS, Kubo K, Kishi LT, Takita MA, Ribeiro-Alves M, Machado MA. Global gene expression of Poncirus trifoliata, Citrus sunki and their hybrids under infection of Phytophthora parasitica. BMC Genomics 2011; 12:39. [PMID: 21241495 PMCID: PMC3033816 DOI: 10.1186/1471-2164-12-39] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 01/17/2011] [Indexed: 11/14/2022] Open
Abstract
Background Gummosis and root rot caused by Phytophthora are among the most economically important diseases in citrus. Four F1 resistant hybrids (Pool R), and four F1 susceptible hybrids (Pool S) to P. parasitica, were selected from a cross between susceptible Citrus sunki and resistant Poncirus trifoliata cv. Rubidoux. We investigated gene expression in pools of four resistant and four susceptible hybrids in comparison with their parents 48 hours after P. parasitica inoculation. We proposed that genes differentially expressed between resistant and susceptible parents and between their resistant and susceptible hybrids provide promising candidates for identifying transcripts involved in disease resistance. A microarray containing 62,876 UniGene transcripts selected from the CitEST database and prepared by NimbleGen Systems was used for analyzing global gene expression 48 hours after infection with P. parasitica. Results Three pairs of data comparisons (P. trifoliata/C. sunki, Pool R/C. sunki and Pool R/Pool S) were performed. With a filter of false-discovery rate less than 0.05 and fold change greater than 3.0, 21 UniGene transcripts common to the three pairwise comparative were found to be up-regulated, and 3 UniGene transcripts were down-regulated. Among them, our results indicated that the selected transcripts were probably involved in the whole process of plant defense responses to pathogen attack, including transcriptional regulation, signaling, activation of defense genes participating in HR, single dominant genes (R gene) such as TIR-NBS-LRR and RPS4 and switch of defense-related metabolism pathway. Differentially expressed genes were validated by RT-qPCR in susceptible and resistant plants and between inoculated and uninoculated control plants Conclusions Twenty four UniGene transcripts were identified as candidate genes for Citrus response to P. parasitica. UniGene transcripts were likely to be involved in disease resistance, such as genes potentially involved in secondary metabolite synthesis, intracellular osmotic adjustment, signal transduction pathways of cell death, oxidative burst and defense gene expression. Furthermore, our microarray data suggest another type of resistance in Citrus-Phytophthora interaction conferred by single dominant genes (R gene) since we encountered two previously reported R genes (TIR-NBS-LRR and RPS4) upregulated in the resistant genotypes relative to susceptible. We identified 7 transcripts with homology in other plants but yet unclear functional characterization which are an interesting pool for further analyses and 3 transcripts where no significant similarity was found. This is the first microarray study addressing an evaluation of transcriptional changes in response to P. parasitica in Citrus.
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Affiliation(s)
- Leonardo P Boava
- Centro APTA Citros Sylvio Moreira, CP4, 13490-970, Cordeirópolis-SP, Brazil.
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