1
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Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. Annu Rev Phytopathol 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, California, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, California, USA
- Department of Plant Sciences; Department of Molecular and Cellular Biology; Department of Medical Microbiology and Immunology, University of California, Davis, California, USA;
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2
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Fondevilla S, Arias-Giraldo LF, García-León FJ, Landa BB. Molecular Characterization of Peronospora variabilis Isolates Infecting Chenopodium quinoa and Chenopodium album in Spain. Plant Dis 2023; 107:999-1004. [PMID: 36190302 DOI: 10.1094/pdis-05-22-1198-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Quinoa is an expanding crop in southern Spain. Downy mildew, caused by Peronospora variabilis, is the most important quinoa disease in Spain and worldwide. In Spain, this disease has also been observed on the weed Chenopodium album. The objectives of this study were to unravel the origin of the P. variabilis isolates currently infecting quinoa in southern Spain and to study their genetic diversity. We hypothesized that P. variabilis isolates infecting quinoa in Spain could have been introduced through the seeds of the quinoa varieties currently grown in the country or, alternatively, that these isolates are endemic isolates, originally infecting C. album, that jumped to quinoa. In order to test these hypotheses, we sequenced the internal transcribed spacer (ITS), cytochrome c oxidase subunit 1 (cox1), and cox2 regions of 33 P. variabilis isolates infecting C. quinoa and C. album in southern Spain and analyzed their phylogenetic relationship with isolates present in other countries infecting Chenopodium spp. cox1 gene sequences from all of the Spanish P. variabilis isolates were identical and exhibited nine single-nucleotide polymorphisms (SNPs) compared with a single P. variabilis cox1 sequence found at GenBank. Phylogenetic analyses based on the ITS ribosomal DNA region were not suitable to differentiate isolates according to their geographical origin or host. The cox2 sequences from P. variabilis Spanish isolates collected from C. quinoa and C. album were all identical and had a distinctive SNP in the last of four polymorphic sites that distinguished Spanish isolates from isolates from other countries. These results suggest that P. variabilis infecting quinoa in southern Spain could be native isolates that originally infected C. album.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Sara Fondevilla
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | - Luis F Arias-Giraldo
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
| | | | - Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Av. Menendez Pidal s/n, Córdoba 14004, Spain
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Xue Z, Wang B, Li C, Yang H, Gao X, Sun M, Huang Z, Miao J, Liu X. Resistance Risk Assessment for the New OSBP Inhibitor Y18501 in Pseudoperonospora cubensis and Point Mutations (G705V, L798W, and I812F) in PscORP1 that Confer Resistance. J Agric Food Chem 2023; 71:4510-4520. [PMID: 36898018 DOI: 10.1021/acs.jafc.3c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Y18501 is a new oxysterol-binding protein inhibitor (OSBPI) that shows strong inhibitory activity against Pseudoperonospora cubensis. In this study, the sensitivities of 159 Ps. cubensis isolates to Y18501 were determined, with EC50 values ranging from 0.001 to 11.785 μg/mL, indicating that a Y18501-resistant subpopulation has appeared in the field. Ten Y18501-resistant mutants were obtained by fungicide adaptation and displayed fitness equal to or stronger than their parental isolates, which suggests that the resistance risk of Ps. cubensis to Y18501 is high. The consecutive applications of Y18501 in the field resulted in the rapid resistance of Ps. cubensis and decreased control efficacy of cucumber downy mildew (CDM), which could be alleviated by compounding with mancozeb. A positive cross-resistance was detected between Y18501 and oxathiapiprolin. The amino acid substitutions G705V, L798W, and I812F in PscORP1 conferred resistance to Y18501 in Ps. cubensis, which was validated by molecular docking and molecular dynamics simulations.
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Affiliation(s)
- Zhaolin Xue
- China Agricultural University, Beijing 100193, China
| | - Bin Wang
- China Agricultural University, Beijing 100193, China
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Sinochem Agrochemicals R&D Co. Ltd, Shenyang 110021, China
| | - Chengcheng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712110, China
| | - Huixin Yang
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Sinochem Agrochemicals R&D Co. Ltd, Shenyang 110021, China
| | - Xuheng Gao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712110, China
| | - Mingyou Sun
- State Key Laboratory of the Discovery and Development of Novel Pesticide, Shenyang Sinochem Agrochemicals R&D Co. Ltd, Shenyang 110021, China
| | | | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712110, China
| | - Xili Liu
- China Agricultural University, Beijing 100193, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712110, China
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4
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Fletcher K, Martin F, Isakeit T, Cavanaugh K, Magill C, Michelmore R. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3 (Bethesda) 2023; 13:jkac340. [PMID: 36592124 PMCID: PMC9997571 DOI: 10.1093/g3journal/jkac340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Frank Martin
- U.S. Department of Agriculture–Agriculture Research Service, Salinas, CA, 93905, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Keri Cavanaugh
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, CA 95616, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616, USA
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Mouafo-Tchinda RA, Fall ML, Beaulieu C, Carisse O. Competition Between Plasmopara viticola Clade riparia and Clade aestivalis: A Race to Lead Grape Downy Mildew Epidemics. Plant Dis 2022; 106:2866-2875. [PMID: 35536207 DOI: 10.1094/pdis-11-21-2465-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
There is evidence of five clades of Plasmopara viticola in the world. Only two clades, riparia and aestivalis, have been identified as responsible for downy mildew epidemics in Quebec, Canada. It was reported in 2021 that epidemics caused by clade riparia start 2 or 3 weeks before those caused by clade aestivalis and that clade aestivalis was more aggressive than clade riparia. The objective of this work was to study the competition between P. viticola clade riparia (A) and clade aestivalis (B) and to compare the aggressiveness of both clades in mono- and coinfection situations. Suspensions of sporangia from both clades with six percentage combinations (AB 100-0; AB 89-11; AB 74-26; AB 46-54; AB 23-77; and AB 0-100) were inoculated on leaf discs (cultivar Vidal), and three other combinations (AB 88-12; AB 68-32; and AB 47-53) were inoculated on living leaves of grape plants (cultivar Vidal). Then, sporangium production, expressed as the percentage of sporangia produced by each clade, was estimated on leaf discs after eight cycles of infection-sporulation and then validated on living grape leaves after five cycles. The aggressiveness of clades in monoinfection situations on leaf discs was compared with that in coinfection situations. The results show that the percentage of sporangia produced by clade aestivalis increases with the infection-sporulation cycle while that produced by clade riparia decreases. The area under the sporangium production progress curve (AUSPPC) of clade aestivalis was significantly higher than that of clade riparia. The aggressiveness of P. viticola clades riparia and aestivalis in coinfection situations was different from that in monoinfection situations and was strongly influenced by the percentage of each clade in competition. These results suggest that, on the grapevine cultivar Vidal, P. viticola clade aestivalis is more competitive than clade riparia and that the percentage of each clade present in the vineyard should be considered for management of downy mildew.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Romaric A Mouafo-Tchinda
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, 2500 de l'Université Boulevard, Sherbrooke, QC, J1K 2R1, Canada
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
| | - Mamadou L Fall
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
| | - Carole Beaulieu
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, 2500 de l'Université Boulevard, Sherbrooke, QC, J1K 2R1, Canada
| | - Odile Carisse
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, 430 Gouin Boulevard, Saint-Jean-sur-Richelieu, QC, J3B 3E6, Canada
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Paineau M, Mazet ID, Wiedemann-Merdinoglu S, Fabre F, Delmotte F. The Characterization of Pathotypes in Grapevine Downy Mildew Provides Insights into the Breakdown of Rpv3, Rpv10, and Rpv12 Factors in Grapevines. Phytopathology 2022; 112:2329-2340. [PMID: 35657702 DOI: 10.1094/phyto-11-21-0458-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We describe a standard method for characterizing the virulence profile of Plasmopara viticola, the causal agent of grapevine downy mildew. We used 33 European strains to inoculate six grapevine varieties carrying the principal factors for resistance to downy mildew (Rpv1, Rpv3.1, Rpv3.2, Rpv5, Rpv6, Rpv10, and Rpv12) and the susceptible Vitis vinifera 'Chardonnay'. For each interaction, we characterized the level of sporulation by image analysis and the intensity of the grapevine hypersensitive response by visual score. We propose a definition for the breakdown of grapevine quantitative resistances combining these two traits. Among the 33 strains analyzed, 28 are virulent on at least one resistance factor. We identified five different pathotypes across the 33 strains analyzed: two pathotypes overcoming a single resistance factor (vir3.1 and vir3.2) and three complex pathotypes overcoming multiple resistance factors (vir3.1,3.2; vir3.2,12; vir3.1,3.2,10). Our findings confirm the widespread occurrence of P. viticola strains overcoming the Rpv3 haplotypes (28 strains). We also detected the first breakdown of resistance to the Rpv10 by a strain from Germany and the breakdown of Rpv12 factors by a strain from Hungary. The pathotyping method proposed here and the associated differential host range lay the groundwork for the early detection of resistance breakdown in grapevines. This approach will also facilitate the monitoring of the evolution of P. viticola populations at large spatial scales. This is an essential step forward to promoting durable management of the resistant grapevine varieties currently available.
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Affiliation(s)
- Manon Paineau
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, Villenave d'Ornon, F-33140, France
| | - Isabelle D Mazet
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, Villenave d'Ornon, F-33140, France
| | | | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, Villenave d'Ornon, F-33140, France
| | - François Delmotte
- INRAE, Bordeaux Sciences Agro, SAVE, ISVV, Villenave d'Ornon, F-33140, France
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7
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Bello JC, Higgins DS, Sakalidis ML, Quesada-Ocampo LM, Martin F, Hausbeck MK. Clade-Specific Monitoring of Airborne Pseudoperonospora spp. Sporangia Using Mitochondrial DNA Markers for Disease Management of Cucurbit Downy Mildew. Phytopathology 2022; 112:2110-2125. [PMID: 35585721 DOI: 10.1094/phyto-12-21-0500-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Management of cucurbit downy mildew (CDM) caused by Pseudoperonospora cubensis, relies on an intensive fungicide program. In Michigan, CDM occurs annually due to an influx of airborne sporangia and timely alerts of airborne inoculum can assist growers in assessing the need to initiate fungicide sprays. This research aimed to improve the specific detection of airborne P. cubensis sporangia by adapting quantitative real-time polymerase chain reaction (qPCR) assays to distinguish among P. cubensis clades I and II and P. humuli in spore trap samples from commercial production sites and research plots. We also evaluated the suitability of impaction spore traps compared with Burkard traps for detection of airborne sporangia. A multiplex qPCR assay improved the specificity of P. cubensis clade II detection accelerating the assessment of field spore trap samples. After 2 years of monitoring, P. cubensis clade II DNA was detected in spore trap samples before CDM symptoms were first observed in cucumber fields (July and August), while P. cubensis clade I DNA was not detected in air samples before or after the disease onset. In some commercial cucumber fields, P. humuli DNA was detected throughout the growing season. The Burkard spore trap appeared to be better suited for recovery of sporangia at low concentrations than the impaction spore trap. This improved methodology for the monitoring of airborne Pseudoperonospora spp. sporangia could be used as part of a CDM risk advisory system to time fungicide applications that protect cucurbit crops in Michigan.
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Affiliation(s)
- Julian C Bello
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Douglas S Higgins
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
| | - Monique L Sakalidis
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
- Department of Forestry, Michigan State University, East Lansing, MI 48824
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613
| | - Frank Martin
- U.S. Department of Agriculture-Agriculture Research Service, Salinas, CA 93905
| | - Mary K Hausbeck
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
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Standish JR, Góngora-Castillo E, Bowman MJ, Childs KL, Tian M, Quesada-Ocampo LM. Development, Validation, and Utility of Species-Specific Diagnostic Markers for Detection of Peronospora belbahrii. Phytopathology 2022; 112:1667-1675. [PMID: 35196067 DOI: 10.1094/phyto-09-21-0393-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peronospora belbahrii is an oomycete and the cause of basil downy mildew, one of the most destructive diseases affecting basil production worldwide. Disease management is challenging due to wind-dispersed sporangia and contaminated seed; therefore, identifying P. belbahrii in seed lots before sale or planting or in the field before symptoms develop could allow for timely deployment of disease management strategies. In this study, a draft genome assembly and next-generation sequencing reads for P. belbahrii, as well as publicly available DNA-seq and RNA-seq reads of several other downy mildew pathogens, were incorporated into a bioinformatics pipeline to predict P. belbahrii-specific diagnostic markers. The specificity of each candidate marker was validated against a diverse DNA collection of P. belbahrii, host tissue, and related oomycetes using PCR. Two species-specific markers were identified and used as templates to develop a highly sensitive probe-based real-time quantitative PCR (qPCR) assay that could detect P. belbahrii in leaf tissue and seed samples. Both markers were capable of reliably detecting as low as 500 fg/µl of P. belbahrii genomic DNA and as few as 10 sporangia. The qPCR assay was then validated with seed samples collected from a basil cultivar experiment. In total, 48 seed samples were collected and tested; P. belbahrii was detected in samples of all cultivars at estimated concentrations of 600 fg/µl up to 250 pg/µl and at as few as 10 sporangia up to >1,000 sporangia. The markers and assays are valuable for diagnostics and identifying P. belbahrii-contaminated seed lots to mitigate the effects of future basil downy mildew epidemics.
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Affiliation(s)
- J R Standish
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
| | - E Góngora-Castillo
- Department of Biotechnology, Yucatan Center for Scientific Research, Chuburná de Hidalgo, 97205 Mérida, Yucatán, México
| | - M J Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
- Ball Horticultural Company, West Chicago, IL 60185, U.S.A
| | - K L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - M Tian
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, U.S.A
| | - L M Quesada-Ocampo
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695-7613, U.S.A
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Clark KJ, Anchieta AG, da Silva MB, Kandel SL, Choi YJ, Martin FN, Correll JC, Van Denyze A, Brummer EC, Klosterman SJ. Early Detection of the Spinach Downy Mildew Pathogen in Leaves by Recombinase Polymerase Amplification. Plant Dis 2022; 106:1793-1802. [PMID: 35253491 DOI: 10.1094/pdis-11-21-2398-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Downy mildew of spinach, caused by Peronospora effusa, is a major economic threat to both organic and conventional spinach production. Symptomatic spinach leaves are unmarketable and spinach with latent infections are problematic because symptoms can develop postharvest. Therefore, early detection methods for P. effusa could help producers identify infection before visible symptoms appear. Recombinase polymerase amplification (RPA) provides sensitive and specific detection of pathogen DNA and is a rapid, field-applicable method that does not require advanced technical knowledge or equipment-heavy DNA extraction. Here, we used comparative genomics to identify a unique region of the P. effusa mitochondrial genome to develop an RPA assay for the early detection of P. effusa in spinach leaves. In tandem, we established a TaqMan quantitative PCR (qPCR) assay and used this assay to validate the P. effusa specificity of the locus across Peronospora spp. and to compare assay performance. Neither the TaqMan qPCR nor the RPA showed cross reactivity with the closely related beet downy mildew pathogen, P. schachtii. TaqMan qPCR and RPA have detection thresholds of 100 and 900 fg of DNA, respectively. Both assays could detect P. effusa in presymptomatic leaves, with RPA-based detection occurring as early as 5 days before the appearance of symptoms and TaqMan qPCR-based detection occurring after 24 h of plant exposure to airborne spores. Implementation of the RPA detection method could provide real-time information for point-of-care management strategies at field sites.
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Affiliation(s)
- Kelley J Clark
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Amy G Anchieta
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Mychele B da Silva
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Shyam L Kandel
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - Young-Joon Choi
- Department of Biology, Kunsan National University, Gunsan, 54150, Korea
| | - Frank N Martin
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
| | - James C Correll
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701, U.S.A
| | - Allen Van Denyze
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - E Charles Brummer
- Department of Plant Sciences, University of California, Davis, CA 95616, U.S.A
| | - Steven J Klosterman
- United States Department of Agriculture-Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA 93905, U.S.A
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10
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Fletcher K, Shin OH, Clark KJ, Feng C, Putman AI, Correll JC, Klosterman SJ, Van Deynze A, Michelmore RW. Ancestral Chromosomes for Family Peronosporaceae Inferred from a Telomere-to-Telomere Genome Assembly of Peronospora effusa. Mol Plant Microbe Interact 2022; 35:450-463. [PMID: 35226812 DOI: 10.1094/mpmi-09-21-0227-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae; high levels of synteny were also detected with Phytophthora sojae. Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, CA, U.S.A
| | - Oon-Ha Shin
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, U.S.A
| | - Kelley J Clark
- United States Department of Agriculture-Agricultural Research Station, 1636 East Alisal Street, Salinas, CA, U.S.A
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Chunda Feng
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Alexander I Putman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, U.S.A
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AR, U.S.A
| | - Steven J Klosterman
- United States Department of Agriculture-Agricultural Research Station, 1636 East Alisal Street, Salinas, CA, U.S.A
| | - Allen Van Deynze
- Seed Biotechnology Center, Department of Plant Sciences, University of California, Davis, CA, U.S.A
| | - Richard W Michelmore
- The Genome Center, University of California, Davis, CA, U.S.A
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
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11
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Nowicki M, Hadziabdic D, Trigiano RN, Runge F, Thines M, Boggess SL, Ristaino J, Spring O. Microsatellite Markers from Peronospora tabacina, the Cause of Blue Mold of Tobacco, Reveal Species Origin, Population Structure, and High Gene Flow. Phytopathology 2022; 112:422-434. [PMID: 34058860 DOI: 10.1094/phyto-03-21-0092-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily by sporangia, whereas the sexual oospores are rarely observed. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from central, southern, and western Europe; the Middle East; Central America; North America; and Australia. Genetic variations among the six subpopulations accounted for ∼8% of the total variation, including moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P < 0.001). Evidence of linkage disequilibrium (P < 0.001) showed that populations contained partially clonal subpopulations but that subpopulations from Australia and Mediterranean Europe did not. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection and allowed conclusions regarding the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intracontinental and intercontinental migration patterns of this important pathogen.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Marcin Nowicki
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Denita Hadziabdic
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Fabian Runge
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
| | - Marco Thines
- Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany
- Department of Life Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, D-60323 Frankfurt am Main, Germany
| | - Sarah L Boggess
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996-4560, U.S.A
| | - Jean Ristaino
- Department of Entomology and Plant Pathology, Emerging Plant Disease and Global Food Security Cluster, North Carolina State University, Raleigh 27650, U.S.A
| | - Otmar Spring
- Institute of Botany 210, University of Hohenheim, D-70593 Stuttgart, Germany
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12
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Fujiwara K, Inoue H, Sonoda R, Iwamoto Y, Kusaba M, Tashiro N, Miyasaka A. Real-Time PCR Detection of the Onion Downy Mildew Pathogen Peronospora destructor From Symptomless Onion Seedlings and Soils. Plant Dis 2021; 105:643-649. [PMID: 33467897 DOI: 10.1094/pdis-05-20-1095-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An outbreak of downy mildew disease of onion, caused by Peronospora destructor, in Japan in 2016 necessitated a reevaluation of the primary inoculum sources to optimize disease management. Detection of the P. destructor pathogen in plants with asymptomatic infection and in soil would guide the application of fungicides according to the extent of infection before disease development. Here, we detected P. destructor in both plants and soil using newly developed primer sets (Pd ITS and Pd ITS 614) by both conventional and real-time PCR. Validation by real-time PCR with Pd ITS 614 showed that P. destructor DNA was amplified from symptomless seedlings at 3.7 × 102 to 1.0 × 100 conidium cells/50 mg leaf tissue, suggesting the detection of asymptomatic infection. Real-time PCR with Pd ITS amplified pathogen DNA from field soils at 1.6 × 103 to 8.3 × 101 oospore cells/g of soil. This real-time PCR assay provides a useful tool for identifying and quantifying inoculum sources, which may be the foundation of the design of integrated disease management strategies.
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Affiliation(s)
- Kazuki Fujiwara
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Hiroyoshi Inoue
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Ryoichi Sonoda
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
| | - Yutaka Iwamoto
- Hyogo Prefectural Technology Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan
| | - Motoaki Kusaba
- Faculty of Agriculture, Saga University, Saga City, Saga 840-8502, Japan
| | - Nobuya Tashiro
- Saga Prefectural Upland Farming Research and Extension Center, Karatsu, Saga 847-0326, Japan
| | - Atsushi Miyasaka
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Koshi, Kumamoto 861-1192, Japan
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13
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Klein J, Neilen M, van Verk M, Dutilh BE, Van den Ackerveken G. Genome reconstruction of the non-culturable spinach downy mildew Peronospora effusa by metagenome filtering. PLoS One 2020; 15:e0225808. [PMID: 32396560 PMCID: PMC7217449 DOI: 10.1371/journal.pone.0225808] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/24/2020] [Indexed: 01/27/2023] Open
Abstract
Peronospora effusa (previously known as P. farinosa f. sp. spinaciae, and here referred to as Pfs) is an obligate biotrophic oomycete that causes downy mildew on spinach (Spinacia oleracea). To combat this destructive many disease resistant cultivars have been bred and used. However, new Pfs races rapidly break the employed resistance genes. To get insight into the gene repertoire of Pfs and identify infection-related genes, the genome of the first reference race, Pfs1, was sequenced, assembled, and annotated. Due to the obligate biotrophic nature of this pathogen, material for DNA isolation can only be collected from infected spinach leaves that, however, also contain many other microorganisms. The obtained sequences can, therefore, be considered a metagenome. To filter and obtain Pfs sequences we utilized the CAT tool to taxonomically annotate ORFs residing on long sequences of a genome pre-assembly. This study is the first to show that CAT filtering performs well on eukaryotic contigs. Based on the taxonomy, determined on multiple ORFs, contaminating long sequences and corresponding reads were removed from the metagenome. Filtered reads were re-assembled to provide a clean and improved Pfs genome sequence of 32.4 Mbp consisting of 8,635 scaffolds. Transcript sequencing of a range of infection time points aided the prediction of a total of 13,277 gene models, including 99 RxLR(-like) effector, and 14 putative Crinkler genes. Comparative analysis identified common features in the predicted secretomes of different obligate biotrophic oomycetes, regardless of their phylogenetic distance. Their secretomes are generally smaller, compared to hemi-biotrophic and necrotrophic oomycete species. We observe a reduction in proteins involved in cell wall degradation, in Nep1-like proteins (NLPs), proteins with PAN/apple domains, and host translocated effectors. The genome of Pfs1 will be instrumental in studying downy mildew virulence and for understanding the molecular adaptations by which new isolates break spinach resistance.
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Affiliation(s)
- Joël Klein
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Manon Neilen
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Marcel van Verk
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
- Crop Data Science, KeyGene, Wageningen, The Netherlands
| | - Bas E. Dutilh
- Department of Biology, Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Guido Van den Ackerveken
- Department of Biology, Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
- * E-mail:
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14
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Natesan K, Park JY, Kim CW, Park DS, Kwon YS, Back CG, Cho H. High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew. Mol Plant Microbe Interact 2020; 33:718-720. [PMID: 32237963 DOI: 10.1094/mpmi-10-19-0280-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.
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Affiliation(s)
- Karthi Natesan
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ji Yeon Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Cheol-Woo Kim
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Dong Suk Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Young-Seok Kwon
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Chang-Gi Back
- National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Heejung Cho
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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15
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Thines M, Sharma R, Rodenburg SYA, Gogleva A, Judelson HS, Xia X, van den Hoogen J, Kitner M, Klein J, Neilen M, de Ridder D, Seidl MF, van den Ackerveken G, Govers F, Schornack S, Studholme DJ. The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. Mol Plant Microbe Interact 2020; 33:742-753. [PMID: 32237964 DOI: 10.1094/mpmi-07-19-0211-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Along with Plasmopara destructor, Peronosopora belbahrii has arguably been the economically most important newly emerging downy mildew pathogen of the past two decades. Originating from Africa, it has started devastating basil production throughout the world, most likely due to the distribution of infested seed material. Here, we present the genome of this pathogen and results from comparisons of its genomic features to other oomycetes. The assembly of the nuclear genome was around 35.4 Mbp in length, with an N50 scaffold length of around 248 kbp and an L50 scaffold count of 46. The circular mitochondrial genome consisted of around 40.1 kbp. From the repeat-masked genome, 9,049 protein-coding genes were predicted, out of which 335 were predicted to have extracellular functions, representing the smallest secretome so far found in peronosporalean oomycetes. About 16% of the genome consists of repetitive sequences, and, based on simple sequence repeat regions, we provide a set of microsatellites that could be used for population genetic studies of P. belbahrii. P. belbahrii has undergone a high degree of convergent evolution with other obligate parasitic pathogen groups, reflecting its obligate biotrophic lifestyle. Features of its secretome, signaling networks, and promoters are presented, and some patterns are hypothesized to reflect the high degree of host specificity in Peronospora species. In addition, we suggest the presence of additional virulence factors apart from classical effector classes that are promising candidates for future functional studies.
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Affiliation(s)
- Marco Thines
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Rahul Sharma
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
- Integrative Fungal Research (IPF) and Translational Biodiversity Genomics (TBG), Georg-Voigt-Str. 14-16, 60325 Frankfurt (Main), Germany
| | - Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Anna Gogleva
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521 U.S.A
| | - Xiaojuan Xia
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 9, 60323 Frankfurt (Main), Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Johan van den Hoogen
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Miloslav Kitner
- Department of Botany, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Joël Klein
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manon Neilen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Guido van den Ackerveken
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sebastian Schornack
- University of Cambridge, Sainsbury Laboratory, 47 Bateman Street, Cambridge, CB2 1LR, U.K
| | - David J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
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16
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Duduk B, Duduk N, Vico I, Stepanović J, Marković T, Rekanović E, Kube M, Radanović D. Chamomile Floricolous Downy Mildew Caused by Peronospora radii. Phytopathology 2019; 109:1900-1907. [PMID: 31369362 DOI: 10.1094/phyto-04-19-0138-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Floricolous downy mildews (Peronospora, oomycetes) are a small, monophyletic group of mostly inconspicuous plant pathogens that induce symptoms exclusively on flowers. Characterization of this group of pathogens, and information about their biology, is particularly sparse. The recurrent presence of a disease causing flower malformation which, in turn, leads to high production losses of the medicinal herb Matricaria chamomilla in Serbia has enabled continuous experiments focusing on the pathogen and its biology. Peronospora radii was identified as the causal agent of the disease, and morphologically and molecularly characterized. Diseased chamomile flowers showed severe malformations of the disc and ray florets, including phyllody and secondary inflorescence formation, followed by the onset of downy mildew. Phylogeny, based on internal transcribed spacer and cox2, indicates clustering of the Serbian P. radii with other P. radii from chamomile although, in cox2 analyses, they formed a separate subcluster. Evidence pointing to systemic infection was provided through histological and molecular analyses, with related experiments validating the impact of soilborne and blossom infections. This study provides new findings in the biology of P. radii on chamomile, thus enabling the reconstruction of this floricolous Peronospora species' life cycle.
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Affiliation(s)
- Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Nataša Duduk
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Ivana Vico
- University of Belgrade, Faculty of Agriculture, Belgrade, Serbia
| | - Jelena Stepanović
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Tatjana Marković
- Institute for Medicinal Plant Research "Dr Josif Pančić", Belgrade, Serbia
| | - Emil Rekanović
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Michael Kube
- University of Hohenheim, Integrative Infection Biology Crops-Livestock, Stuttgart, Germany
| | - Dragoja Radanović
- Institute for Medicinal Plant Research "Dr Josif Pančić", Belgrade, Serbia
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17
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Gent DH, Adair N, Knaus BJ, Grünwald NJ. Genotyping-by-Sequencing Reveals Fine-Scale Differentiation in Populations of Pseudoperonospora humuli. Phytopathology 2019; 109:1801-1810. [PMID: 31199202 DOI: 10.1094/phyto-12-18-0485-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pseudoperonospora humuli is the causal agent of downy mildew of hop, one of the most important diseases of this plant and a limiting factor for production of susceptible cultivars in certain environments. The degree of genetic diversity and population differentiation within and among P. humuli populations at multiple spatial scales was quantified using genotyping-by-sequencing to test the hypothesis that populations of P. humuli have limited genetic diversity but are differentiated at the scale of individual hop yards. Hierarchical sampling was conducted to collect isolates from three hop yards in Oregon, plants within these yards, and infected shoots within heavily diseased plants. Additional isolates also were collected broadly from other geographic regions and from the two previously described clades of the sister species, P. cubensis. Genotyping of these 240 isolates produced a final quality-filtered data set of 216 isolates possessing 25,227 variants. Plots of G'ST values indicated that the majority of variants had G'ST values near 0 and were scattered randomly across contig positions. However, there was a subset of variants that were highly differentiated (G'ST > 0.3) and reproducible when genotyped independently. Within P. humuli, there was evidence of genetic differentiation at the level of hop yards and plants within yards; 19.8% of the genetic variance was associated with differences among yards and 20.3% of the variance was associated with plants within the yard. Isolates of P. humuli were well differentiated from two isolates of P. cubensis representative of the two clades of this organism. There was strong evidence of linkage disequilibrium in variant loci, consistent with nonrandom assortment of alleles expected from inbreeding and/or asexual recombination. Mantel tests found evidence that the genetic distance between isolates collected from heavily diseased plants within a hop yard was associated with the physical distance of the plants from which the isolates were collected. The sum of the data presented here indicates that populations of P. humuli are consistent with a clonal or highly inbred genetic structure with a small, yet significant differentiation of populations among yards and plants within yards. Fine-scale genetic differentiation at the yard and plant scales may point to persistence of founder genotypes associated with planting material, and chronic, systemic infection of hop plants by P. humuli. More broadly, genotyping-by-sequencing appears to have sufficient resolution to identify rare variants that differentiate subpopulations within organisms with limited genetic variability.
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Affiliation(s)
- David H Gent
- Forage Seed and Cereal Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97331
| | - Nanci Adair
- Forage Seed and Cereal Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97331
| | - Brian J Knaus
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Unit, Corvallis, OR 97330
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18
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Lenarčič T, Pirc K, Hodnik V, Albert I, Borišek J, Magistrato A, Nürnberger T, Podobnik M, Anderluh G. Molecular basis for functional diversity among microbial Nep1-like proteins. PLoS Pathog 2019; 15:e1007951. [PMID: 31479498 PMCID: PMC6743777 DOI: 10.1371/journal.ppat.1007951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/13/2019] [Accepted: 06/29/2019] [Indexed: 11/18/2022] Open
Abstract
Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by several phytopathogenic microorganisms. They trigger necrosis in various eudicot plants upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Interestingly, HaNLP3 from the obligate biotroph oomycete Hyaloperonospora arabidopsidis does not induce necrosis. We determined the crystal structure of HaNLP3 and showed that it adopts the NLP fold. However, the conformations of the loops surrounding the GIPC headgroup-binding cavity differ from those of cytotoxic Pythium aphanidermatum NLPPya. Essential dynamics extracted from μs-long molecular dynamics (MD) simulations reveals a limited conformational plasticity of the GIPC-binding cavity in HaNLP3 relative to toxic NLPs. This likely precludes HaNLP3 binding to GIPCs, which is the underlying reason for the lack of toxicity. This study reveals that mutations at key protein regions cause a switch between non-toxic and toxic phenotypes within the same protein scaffold. Altogether, these data provide evidence that protein flexibility is a distinguishing trait of toxic NLPs and highlight structural determinants for a potential functional diversification of non-toxic NLPs utilized by biotrophic plant pathogens.
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Affiliation(s)
- Tea Lenarčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
| | - Katja Pirc
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
| | - Vesna Hodnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva, Ljubljana, Slovenia
| | - Isabell Albert
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle, Tübingen, Germany
| | - Jure Borišek
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos at International School for Advanced Studies (SISSA), Trieste, Italy
| | - Thorsten Nürnberger
- Center of Plant Molecular Biology (ZMBP), Eberhard-Karls-University Tübingen, Auf der Morgenstelle, Tübingen, Germany
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- * E-mail: (MP); (GA)
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova, Ljubljana, Slovenia
- * E-mail: (MP); (GA)
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Feng C, Lamour KH, Bluhm BH, Sharma S, Shrestha S, Dhillon BDS, Correll JC. Genome Sequences of Three Races of Peronospora effusa: A Resource for Studying the Evolution of the Spinach Downy Mildew Pathogen. Mol Plant Microbe Interact 2018; 31:1230-1231. [PMID: 29944056 DOI: 10.1094/mpmi-04-18-0085-a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Downy mildew disease, caused by the obligate oomycete pathogen Peronospora effusa, is the most important economic constraint for spinach production. Three races (races 12, 13, and 14) of P. effusa have been sequenced and assembled. The draft genomes of these three races have been deposited to GenBank and provide useful resources for dissecting the interaction between the host and the pathogen and may provide a framework for determining the mechanism by which new races of the pathogen are rapidly emerging.
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Affiliation(s)
- Chunda Feng
- 1 Department of Plant Pathology, University of Arkansas, Fayetteville 72701; and
| | - Kurt H Lamour
- 2 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996
| | - Burt H Bluhm
- 1 Department of Plant Pathology, University of Arkansas, Fayetteville 72701; and
| | - Sandeep Sharma
- 1 Department of Plant Pathology, University of Arkansas, Fayetteville 72701; and
| | - Sandesh Shrestha
- 2 Department of Entomology and Plant Pathology, University of Tennessee, Knoxville 37996
| | | | - James C Correll
- 1 Department of Plant Pathology, University of Arkansas, Fayetteville 72701; and
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Salgado-Salazar C, LeBlanc N, Ismaiel A, Rivera Y, Warfield CY, Crouch JA. Genetic Variation of the Pathogen Causing Impatiens Downy Mildew Predating and Including Twenty-first Century Epidemics on Impatiens walleriana. Plant Dis 2018; 102:2411-2420. [PMID: 30253113 DOI: 10.1094/pdis-01-18-0077-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Impatiens downy mildew (IDM) of cultivated Impatiens walleriana has had a significant economic impact on the ornamental horticulture industry in the United States and globally. Although recent IDM outbreaks started in 2003, downy mildews on noncultivated Impatiens species have been documented since the 1880s. To understand the relationship between the pathogen causing recent epidemics and the pathogen historically present in the United States, this work characterized genetic variation among a collection of 1,000 samples on 18 plant hosts. Samples included collections during recent IDM epidemics and historical herbarium specimens. Ten major genotypes were identified from cloned rDNA amplicon sequencing and endpoint SNP genotyping. Three genotypes accounted for >95% of the samples, with only one of these three genotypes found on samples predating recent IDM outbreaks. Based on phylogenetic analysis integrating data from three markers and the presence of individual genotypes on multiple Impatiens species, there was some evidence of pathogen-specific infection of I. noli-tangere, but the distinction between genotypes infecting I. walleriana and I. balsamina was not upheld. Overall, this work provides evidence that the majority of rDNA genotypes recovered from recent IDM epidemics are different from historical U.S. genotypes, and that these genotypes can infect Impatiens spp. other than I. walleriana.
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Affiliation(s)
- Catalina Salgado-Salazar
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN 37831; and Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | - Nicholas LeBlanc
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; and Oak Ridge Institute for Science and Education, ARS Research Participation Program, MC-100-44, Oak Ridge, TN 37831
| | - Adnan Ismaiel
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
| | - Yazmín Rivera
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705; and Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901
| | | | - Jo Anne Crouch
- USDA-ARS, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
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21
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Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lida Derevnina
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Frank Martin
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lien D. Bertier
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven Koike
- UC Davis Cooperative Extension Monterey County, Salinas, CA 93901 USA
- Present Address: TriCal Diagnostics, Hollister, CA 95023 USA
| | - Sebastian Reyes-Chin-Wo
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Beiquan Mou
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616 USA
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22
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Thangavel T, Jones S, Scott JB, Livermore M, Wilson CR. Detection of Two Peronospora spp., Responsible for Downy Mildew, in Opium Poppy Seed. Plant Dis 2018; 102:2277-2284. [PMID: 30211657 DOI: 10.1094/pdis-03-18-0503-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Downy mildew is a serious threat to opium poppy production globally. In recent years, two pathogen species, Peronospora somniferi and Peronospora meconopsidis, which induce distinct symptoms, have been confirmed in Australia. In order to manage the spread of these pathogens, identifying the sources of inoculum is essential. In this study, we assessed pathogen presence associated with poppy seed. We developed PCR and qPCR assays targeting the coxI and coxII gene regions, for the detection, differentiation, and quantification of P. somniferi and P. meconopsidis in poppy seed. These results were complemented and compared with direct seed histological examination and a seed washing combined with viability staining for oospore detection. The majority of seed lots from all harvest years contained detectable P. meconopsidis, the earliest (1987) predating the first official record of the disease in Tasmania (1996). In contrast, only seed lots harvested in 2012 or later contained P. somniferi, evidence of its more recent introduction. P. meconopsidis contamination was estimated to be as high as 33.04 pg DNA/g of seed and P. somniferi as high as 35.17 pg DNA/g of seed. Incidence of pathogen contamination of seeds, estimated via a group testing protocol, ranged from 0 to 9% (P. meconopsidis) or 0 to 11% (P. somniferi). Mycelia were predominately found external to the seed coat. Seed washing and viability staining demonstrated that putatively viable oospores were present in the majority of seed lots. Transmission testing confirmed both pathogens can be successfully transmitted from infested seed to infected seedling. PCR and qPCR pathogen assays were found to be reliable and offer a routine test for determining pathogen inoculum in poppy seeds.
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Affiliation(s)
- Tamilarasan Thangavel
- Tasmanian Institute of Agriculture (TIA), University of Tasmania, New Town, Tasmania 7008, Australia
| | - Suzanne Jones
- TIA, University of Tasmania, Burnie TAS 7320, Australia
| | - Jason B Scott
- TIA, University of Tasmania, Burnie TAS 7320, Australia
| | - Mark Livermore
- Tasmanian Alkaloids Pty Ltd, P.O. Box 130, Westbury, TAS 7303, Australia
| | - Calum R Wilson
- TIA, University of Tasmania, New Town, Tasmania 7008, Australia
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23
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Abstract
Peronospora sparsa is a downy mildew-causing oomycete that can infect roses, blackberries, and other members of the rose family. During the last 70 years, this disease has become a serious problem for rose growers in the U.S. and worldwide. While much is known about the disease and its treatment, including significant research on molecular identification methods, as well as environmental conditions conducive to disease and the fungicides used to prevent it, significant knowledge gaps remain in our basic comprehension of the pathogen's biology. For example, the degree of genetic relatedness of pathogen isolates collected from rose, caneberries, and cherry laurel has never been examined, and the natural movement of genotypes from host to host is not known. Further work could be done to determine the differences in pathogen population structure over time (using herbarium specimens and fresh collections) or differences in pathogen population structure and pathogen environmental adaptation for specimens from different geographic regions. The oospore stage of the organism is poorly understood, both as to how it forms and whether it serves as an overwintering structure in nurseries and landscapes. In production greenhouses, the detection of the pathogen using infrared thermographic imaging and possible inhibition by ultraviolet light needs to be explored. Further work needs to be done on breeding using wild roses as new sources for resistance and using new methods such as marker assisted selection and RNAi technologies. As roses are one of the most economically important ornamental crops worldwide, a proper understanding of the disease cycle could allow for better use of cultural and chemical controls to manage rose downy mildew in landscapes and in greenhouse and nursery production areas.
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Affiliation(s)
- Catalina Salgado-Salazar
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD; Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN; and The IR4 Project, Rutgers University, Princeton, NJ
| | - Nina Shiskoff
- Foreign Disease/Weed Science Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Frederick, MD
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Long Island, NY
| | | | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD
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24
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Subbarao CS, Anchieta A, Ochoa L, Dhar N, Kunjeti SG, Subbarao KV, Klosterman SJ. Detection of Latent Peronospora effusa Infections in Spinach. Plant Dis 2018; 102:1766-1771. [PMID: 30125212 DOI: 10.1094/pdis-12-17-1956-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Downy mildew disease of spinach, caused by Peronospora effusa, is managed in conventional fields by a combination of host resistance and scheduled fungicide applications. Fungicides are currently applied to prevent downy mildew epidemics regardless of the infection status of spinach crops. A more streamlined approach would be to develop methods to target either latent infections for fungicide application in conventional production systems or to hasten harvest in organic production. In this study, conventional polymerase chain reaction (PCR) was applied to detect P. effusa DNA in symptomless spinach leaves in three spatially and temporally separated field plots, each containing four 2-m beds, 35 m in length. Spinach leaves were sampled weekly at 3-m intervals at 48 locations throughout each plot. Initial samples were asymptomatic and yet PCR enabled detection of P. effusa DNA extracted from sampled spinach leaves. Detection of latent downy mildew infection in spinach leaves was confirmed by PCR as early as 7 days prior to symptom development. The limit of pathogen DNA detection in spinach leaves was calculated at 10 pg using the conventional PCR approach. Quantitative PCR with TaqMan methodology revealed the presence of inhibitors from spinach leaf DNA extracts and affected amplification efficiencies, but not when diluted, enabling detection of P. effusa DNA at a concentration of <0.1 pg. In conclusion, detection of latent infections may enable management decisions for earlier-than-normal harvest of infected, symptomless organic crops, and for timing fungicide applications on symptomless plants in conventional production.
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Affiliation(s)
| | - Amy Anchieta
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, CA 93905
| | - Lorena Ochoa
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Salinas, CA 93905
| | - Nikhilesh Dhar
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas 93905
| | - Sridhara G Kunjeti
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas 93905
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas 93905
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25
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Miao J, Dong X, Chi Y, Lin D, Chen F, Du Y, Liu P, Liu X. Pseudoperonospora cubensis in China: Its sensitivity to and control by oxathiapiprolin. Pestic Biochem Physiol 2018; 147:96-101. [PMID: 29933999 DOI: 10.1016/j.pestbp.2018.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/29/2018] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
The novel fungicide oxathiapiprolin has potential for the control of downy mildew of cucumber, which is caused by Pseudoperonospora cubensis. In this study, an in vitro bioassay with detached leaves was used to determine the baseline sensitivity to oxathiapiprolin for 77 Ps. cubensis isolates from 11 provinces in China. The baseline sensitivity curve was continuous, and the average EC50 value was 2.23 × 10-4 μg ml-1. In field trials, the control of downy mildew of cucumber was greater with oxathiapiprolin at 20 or 30 g a.i. ha-1 than with dimethomorph at 262.5 g a.i. ha-1. Oxathiapiprolin was taken up by cucumber roots and transported upwards to stems and leaves. The full length of PscORP1, the gene that encodes the target protein of oxathiapiprolin in Ps. cubensis, was sequenced for the first time. Our results suggested that oxathiapiprolin will be an excellent alternative fungicide for control of cucumber downy mildew. However, as Ps. cubensis is a high-risk pathogen, resistance development to oxathiapiprolin should be monitored and managed.
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Affiliation(s)
- Jianqiang Miao
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China
| | - Xue Dong
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China
| | - Yuandong Chi
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China
| | - Dong Lin
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China
| | - Furu Chen
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fujian 350003, PR China
| | - Yixin Du
- Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fujian 350003, PR China
| | - Pengfei Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China.
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing 100193, PR China.
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26
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Abstract
Phylogenetic relationships between thirteen species of downy mildew and 103 species of Phytophthora (plant-pathogenic oomycetes) were investigated with two nuclear and four mitochondrial loci, using several likelihood-based approaches. Three Phytophthora taxa and all downy mildew taxa were excluded from the previously recognized subgeneric clades of Phytophthora, though all were strongly supported within the paraphyletic genus. Downy mildews appear to be polyphyletic, with graminicolous downy mildews (GDM), brassicolous downy mildews (BDM) and downy mildews with colored conidia (DMCC) forming a clade with the previously unplaced Phytophthora taxon totara; downy mildews with pyriform haustoria (DMPH) were placed in their own clade with affinities to the obligate biotrophic P. cyperi. Results suggest the recognition of four additional clades within Phytophthora, but few relationships between clades could be resolved. Trees containing all twenty extant downy mildew genera were produced by adding partial coverage of seventeen additional downy mildew taxa; these trees supported the monophyly of the BDMs, DMCCs and DMPHs but suggested that the GDMs are paraphyletic in respect to the BDMs or polyphyletic. Incongruence between nuclear-only and mitochondrial-only trees suggests introgression may have occurred between several clades, particularly those containing biotrophs, questioning whether obligate biotrophic parasitism and other traits with polyphyletic distributions arose independently or were horizontally transferred. Phylogenetic approaches may be limited in their ability to resolve some of the complex relationships between the "subgeneric" clades of Phytophthora, which include twenty downy mildew genera and hundreds of species.
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Affiliation(s)
- Tyler B. Bourret
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
- * E-mail:
| | - Robin A. Choudhury
- Plant Pathology Department, University of Florida, Gainesville, Florida, United States of America
| | - Heather K. Mehl
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - Cheryl L. Blomquist
- California Department of Food and Agriculture, Sacramento, California, United States of America
| | - Neil McRoberts
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
| | - David M. Rizzo
- Department of Plant Pathology, University of California, Davis, Davis, California, United States of America
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27
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Feng C, Saito K, Liu B, Manley A, Kammeijer K, Mauzey SJ, Koike S, Correll JC. New Races and Novel Strains of the Spinach Downy Mildew Pathogen Peronospora effusa. Plant Dis 2018; 102:613-618. [PMID: 30673485 DOI: 10.1094/pdis-05-17-0781-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildew disease, caused by Peronospora effusa (=P. farinosa f. sp. spinaciae [Pfs]), is the most economically important disease of spinach. Current high-density fresh-market spinach production provides conducive conditions for disease development, and downy mildew frequently forces growers to harvest early owing to disease development, to cull symptomatic leaves prior to harvest, or to abandon the field if the disease is too severe. The use of resistant cultivars to manage downy mildew, particularly on increasing acreages of organic spinach production, applies strong selection pressure on the pathogen, and many new races of Pfs have been identified in recent years in spinach production areas worldwide. To monitor the virulence diversity in the Pfs population, downy mildew samples were collected from spinach production areas and tested for race identification based on the disease reactions of a standard set of international spinach differentials. Two new races (designated races 15 and 16) and eight novel strains were identified between 2013 and 2017. The disease reaction of Pfs 15 was similar to race 4, except race 4 could not overcome the resistance imparted by the RPF9 locus. Several resistance loci (RPF1, 2, 4, and 6) were effective in preventing disease caused by Pfs 15. The race Pfs 16 could overcome several resistance loci (RPF2, 4, 5, 9, and 10) but not others (RPF1, 3, 6, and 7). One novel strain (UA1014) could overcome the resistance of spinach resistant loci RPF1 to RPF7 but only infected the cotyledons and not the true leaves of certain cultivars. A new set of near-isogenic lines has been developed and evaluated for disease reactions to the new races and novel strains as differentials. None of the 360 U.S. Department of Agriculture spinach germplasm accessions tested were resistant to Pfs 16 or UA1014. A survey of isolates over several years highlighted the dynamic nature of the virulence diversity of the Pfs population. Identification of virulence diversity and evaluation of the genetics of resistance to Pfs will continue to allow for a more effective disease management strategy through resistance gene deployment.
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Affiliation(s)
| | | | - Bo Liu
- University of Arkansas, Fayetteville, 72701
| | | | | | - Stacy J Mauzey
- University of California Cooperative Extension, Salinas, 93901
| | - Steven Koike
- University of California Cooperative Extension, Salinas, 93901
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28
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Crandall SG, Rahman A, Quesada-Ocampo LM, Martin FN, Bilodeau GJ, Miles TD. Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges. Plant Dis 2018; 102:265-275. [PMID: 30673522 DOI: 10.1094/pdis-09-17-1455-fe] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States' economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
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Affiliation(s)
- Sharifa G Crandall
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
| | - Alamgir Rahman
- North Carolina State University, Department of Plant Pathology, Raleigh, NC, 27695
| | | | - Frank N Martin
- USDA-ARS, Crop Improvement and Protection Research Unit, Salinas, CA, 93905
| | | | - Timothy D Miles
- California State University Monterey Bay, School of Natural Sciences, Seaside, CA, 93955
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29
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Li DH, Shen FJ, Li HY, Li W. Kale BoRACK1 is involved in the plant response to salt stress and Peronospora brassicae Gaumann. J Plant Physiol 2017; 213:188-198. [PMID: 28411489 DOI: 10.1016/j.jplph.2017.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 06/07/2023]
Abstract
The receptor for activated C kinase 1 (RACK1) belongs to a protein subfamily containing a tryptophan-aspartic acid-domain (WD) repeat structure. Compelling evidence indicates that RACK1 can interact with many signal molecules and affect different signal transduction pathways. In this study, a kale (Brassica oleracea var. acephala f.tricolor) RACK1 gene (BoRACK1) was cloned by RT-PCR. The amino acid sequence of BoRACK1 had seven WD repeats in which there were typical GH (glycine-histidine) and WD dipeptides. Comparison with AtRACK1 from Arabidopsis revealed 87.1% identity at the amino acid level. Expression pattern analysis by RT-PCR showed that BoRACK1 was expressed in all analyzed tissues of kale and that its transcription in leaves was down-regulated by salt, abscisic acid, and H2O2 at a high concentration. Overexpression of BoRACK1 in kale led to a reduction in symptoms caused by Peronospora brassicae Gaumann on kale leaves. The expression levels of the pathogenesis-related protein genes, PR-1 and PRB-1, increased 2.5-4-fold in transgenic kale, and reactive oxygen species production was more active than in the wild-type. They also exhibited increased tolerance to salt stress in seed germination. H2O2 may also be involved in the regulation of BoRACK1 during seed germination under salt stress. Quantitative real-time PCR analyses showed that the transcript levels of BoRbohs genes were significantly higher in overexpression of BoRACK1 transgenic lines. Yeast two-hybrid assays showed that BoRACK1 could interact with WNK8, eIF6, RAR1, and SGT1. This study and previous work lead us to believe that BoRACK1 may form a complex with regulators of plant salt and disease resistance to coordinate kale reactions to pathogens.
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Affiliation(s)
- Da-Hong Li
- Department of Biological Engineering, Huanghuai University, Zhumadian, China
| | - Fu-Jia Shen
- Department of Biological Engineering, Huanghuai University, Zhumadian, China
| | - Hong-Yan Li
- Department of Biological Engineering, Huanghuai University, Zhumadian, China.
| | - Wei Li
- Department of Biological Engineering, Huanghuai University, Zhumadian, China
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30
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Choudhury RA, Koike ST, Fox AD, Anchieta A, Subbarao KV, Klosterman SJ, McRoberts N. Spatiotemporal Patterns in the Airborne Dispersal of Spinach Downy Mildew. Phytopathology 2017; 107:50-58. [PMID: 27482627 DOI: 10.1094/phyto-04-16-0162-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Downy mildew is the most devastating disease threatening sustainable spinach production, particularly in the organic sector. The disease is caused by the biotrophic oomycete pathogen Peronospora effusa, and the disease results in yellow lesions that render the crop unmarketable. In this study, the levels of DNA from airborne spores of P. effusa were assessed near a field of susceptible plants in Salinas, CA during the winter months of 2013-14 and 2014/15 using rotating-arm impaction spore-trap samplers that were assessed with a species-specific quantitative polymerase chain reaction (qPCR) assay. Low levels of P. effusa DNA were detectable from December through February in both winters but increased during January in both years, in correlation with observed disease incidence; sharp peaks in P. effusa DNA detection were associated with the onset of disease incidence. The incidence of downy mildew in the susceptible field displayed logistic-like dynamics but with considerable interseason variation. Analysis of the area under the disease progress curves suggested that the 2013-14 epidemic was significantly more severe than the 2014-15 epidemic. Spatial analyses indicated that disease incidence was dependent within an average range of 5.6 m, approximately equivalent to the width of three planted beds in a typical production field. The spatial distribution of spores captured during an active epidemic most closely fit a power-law distribution but could also be fit with an exponential distribution. These studies revealed two important results in the epidemiology of spinach downy mildew in California. First, they demonstrated the potential of impaction spore-trap samplers linked with a qPCR assay for indicating periods of high disease risk, as well as the detection of long-distance dispersal of P. effusa spores. Second, at the scale of individual crops, a high degree of spatial aggregation in disease incidence was revealed.
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Affiliation(s)
- R A Choudhury
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - S T Koike
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - A D Fox
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - A Anchieta
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - K V Subbarao
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - S J Klosterman
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
| | - N McRoberts
- First, fifth, and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E. Alisal St., Salinas, CA 93905
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Choudhury RA, Koike ST, Fox AD, Anchieta A, Subbarao KV, Klosterman SJ, McRoberts N. Season-Long Dynamics of Spinach Downy Mildew Determined by Spore Trapping and Disease Incidence. Phytopathology 2016; 106:1311-1318. [PMID: 27442537 DOI: 10.1094/phyto-12-15-0333-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Peronospora effusa is an obligate oomycete that causes downy mildew of spinach. Downy mildew threatens sustainable production of fresh market organic spinach in California, and routine fungicide sprays are often necessary for conventional production. In this study, airborne P. effusa spores were collected using rotating arm impaction spore trap samplers at four sites in the Salinas Valley between late January and early June in 2013 and 2014. Levels of P. effusa DNA were determined by a species-specific quantitative polymerase chain reaction assay. Peronospora effusa was detected prior to and during the growing season in both years. Nonlinear time series analyses on the data suggested that the within-season dynamics of P. effusa airborne inoculum are characterized by a mixture of chaotic, deterministic, and stochastic features, with successive data points somewhat predictable from the previous values in the series. Analyses of concentrations of airborne P. effusa suggest both an exponential increase in concentration over the course of the season and oscillations around the increasing average value that had season-specific periodicity around 30, 45, and 75 days, values that are close to whole multiples of the combined pathogen latent and infectious periods. Each unit increase in temperature was correlated with 1.7 to 6% increased odds of an increase in DNA copy numbers, while each unit decrease in wind speed was correlated with 4 to 12.7% increased odds of an increase in DNA copy numbers. Disease incidence was correlated with airborne P. effusa levels and weather variables, and a receiver operating characteristic curve analysis suggested that P. effusa DNA copy numbers determined from the spore traps nine days prior to disease rating could predict disease incidence.
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Affiliation(s)
- R A Choudhury
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - S T Koike
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - A D Fox
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - A Anchieta
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - K V Subbarao
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - S J Klosterman
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
| | - N McRoberts
- First, fifth and seventh authors: Department of Plant Pathology, University of California, Davis 95616; second author: University of California Cooperative Extension, 1432 Abbott St., Salinas 93901; third author: Fox Weather, LLC, Fortuna, CA 95540; and fourth and sixth authors: United States Department of Agriculture-Agricultural Research Service, 1636 E Alisal St., Salinas, CA 93905
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Lyon R, Correll J, Feng C, Bluhm B, Shrestha S, Shi A, Lamour K. Population Structure of Peronospora effusa in the Southwestern United States. PLoS One 2016; 11:e0148385. [PMID: 26828428 PMCID: PMC4734700 DOI: 10.1371/journal.pone.0148385] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/18/2016] [Indexed: 11/18/2022] Open
Abstract
Peronospora effusa is an obligate pathogen that causes downy mildew on spinach and is considered the most economically important disease of spinach. The objective of the current research was to assess genetic diversity of known historical races and isolates collected in 2014 from production fields in Yuma, Arizona and Salinas Valley, California. Candidate neutral single nucleotide polymorphisms (SNPs) were identified by comparing sequence data from reference isolates of known races of the pathogen collected in 2009 and 2010. Genotypes were assessed using targeted sequencing on genomic DNA extracted directly from infected plant tissue. Genotyping 26 historical and 167 contemporary samples at 46 SNP loci revealed 82 unique multi-locus genotypes. The unique genotypes clustered into five groups and the majority of isolates collected in 2014 were genetically closely related, regardless of source location. The historical samples, representing several races, showed greater genetic differentiation. Overall, the SNP data indicate much of the genotypic variation found within fields was produced during asexual development, whereas overall genetic diversity may be influenced by sexual recombination on broader geographical and temporal scales.
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Affiliation(s)
- Rebecca Lyon
- Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - James Correll
- Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Chunda Feng
- Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Burt Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Sandesh Shrestha
- Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Kurt Lamour
- Department of Entomology & Plant Pathology, University of Tennessee, Knoxville, Tennessee, United States of America
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Abstract
Downy mildews are a notorious group of oomycete plant pathogens, causing high economic losses in various crops and ornamentals. The most species-rich genus of oomycetes is the genus Peronospora. This review provides a wide overview of these pathogens, ranging from macro- and micro-evolutionary patterns, their biodiversity and ecology to short overviews for the currently economically most important pathogens and potential emerging diseases. In this overview, the taxonomy of economically relevant species is also discussed, as the application of the correct names and species concepts is a prerequisite for effective quarantine regulations and phytosanitary measures.
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Affiliation(s)
- Marco Thines
- First and second authors: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; and Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; and first author: Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; and second author: Kunsan National University, Department of Biology, Gunsan 54150, Korea
| | - Young-Joon Choi
- First and second authors: Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany; and Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60438 Frankfurt am Main, Germany; and first author: Integrative Fungal Research Cluster (IPF), Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany; and second author: Kunsan National University, Department of Biology, Gunsan 54150, Korea
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Derevnina L, Chin-Wo-Reyes S, Martin F, Wood K, Froenicke L, Spring O, Michelmore R. Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina. Mol Plant Microbe Interact 2015; 28:1198-215. [PMID: 26196322 DOI: 10.1094/mpmi-05-15-0112-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain-containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.
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Affiliation(s)
- Lida Derevnina
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | | | - Frank Martin
- 2 United States Department of Agriculture-Agricultural Research Service, Salinas, CA U.S.A
| | - Kelsey Wood
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Lutz Froenicke
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Otmar Spring
- 3 Institute of Botany, University of Hohenheim, Germany
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Abstract
Some of the most devastating oomycete pathogens deploy effector proteins, with the signature amino acid motif RXLR, that enter plant cells to promote virulence. Research on the function and evolution of RXLR effectors has been very active over the decade that has transpired since their discovery. Comparative genomics indicate that RXLR genes play a major role in virulence for Phytophthora and downy mildew species. Importantly, gene-for-gene resistance against these oomycete lineages is based on recognition of RXLR proteins. Comparative genomics have revealed several mechanisms through which this resistance can be broken, most notably involving epigenetic control of RXLR gene expression. Structural studies have revealed a core fold that is present in the majority of RXLR proteins, providing a foundation for detailed mechanistic understanding of virulence and avirulence functions. Finally, functional studies have demonstrated that suppression of host immunity is a major function for RXLR proteins. Host protein targets are being identified in a variety of plant cell compartments. Some targets comprise hubs that are also manipulated by bacteria and fungi, thereby revealing key points of vulnerability in the plant immune network.
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Affiliation(s)
- Ryan G Anderson
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Devdutta Deb
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - Kevin Fedkenheuer
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, U.S.A
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Choi YJ, Thines M. Host Jumps and Radiation, Not Co-Divergence Drives Diversification of Obligate Pathogens. A Case Study in Downy Mildews and Asteraceae. PLoS One 2015; 10:e0133655. [PMID: 26230508 PMCID: PMC4521919 DOI: 10.1371/journal.pone.0133655] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 06/26/2015] [Indexed: 12/15/2022] Open
Abstract
Even though the microevolution of plant hosts and pathogens has been intensely studied, knowledge regarding macro-evolutionary patterns is limited. Having the highest species diversity and host-specificity among Oomycetes, downy mildews are a useful a model for investigating long-term host-pathogen coevolution. We show that phylogenies of Bremia and Asteraceae are significantly congruent. The accepted hypothesis is that pathogens have diverged contemporarily with their hosts. But maximum clade age estimation and sequence divergence comparison reveal that congruence is not due to long-term coevolution but rather due to host-shift driven speciation (pseudo-cospeciation). This pattern results from parasite radiation in related hosts, long after radiation and speciation of the hosts. As large host shifts free pathogens from hosts with effector triggered immunity subsequent radiation and diversification in related hosts with similar innate immunity may follow, resulting in a pattern mimicking true co-divergence, which is probably limited to the terminal nodes in many pathogen groups.
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Affiliation(s)
- Young-Joon Choi
- Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, D-60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), D-60325, Frankfurt am Main, Germany
| | - Marco Thines
- Faculty of Biosciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, D-60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre (BiK-F), D-60325, Frankfurt am Main, Germany
- Integrative Fungal Research Cluster (IPF), D-60325, Frankfurt am Main, Germany
- Senckenberg Gesellschaft für Naturforschung, D-60325, Frankfurt am Main, Germany
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Klosterman SJ, Anchieta A, McRoberts N, Koike ST, Subbarao KV, Voglmayr H, Choi YJ, Thines M, Martin FN. Coupling Spore Traps and Quantitative PCR Assays for Detection of the Downy Mildew Pathogens of Spinach (Peronospora effusa) and Beet (P. schachtii). Phytopathology 2014; 104:1349-59. [PMID: 24964150 PMCID: PMC4841388 DOI: 10.1094/phyto-02-14-0054-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Downy mildew of spinach (Spinacia oleracea), caused by Peronospora effusa, is a production constraint on production worldwide, including in California, where the majority of U.S. spinach is grown. The aim of this study was to develop a real-time quantitative polymerase chain reaction (qPCR) assay for detection of airborne inoculum of P. effusa in California. Among oomycete ribosomal DNA (rDNA) sequences examined for assay development, the highest nucleotide sequence identity was observed between rDNA sequences of P. effusa and P. schachtii, the cause of downy mildew on sugar beet and Swiss chard in the leaf beet group (Beta vulgaris subsp. vulgaris). Single-nucleotide polymorphisms were detected between P. effusa and P. schachtii in the 18S rDNA regions for design of P. effusa- and P. schachtii-specific TaqMan probes and reverse primers. An allele-specific probe and primer amplification method was applied to determine the frequency of both P. effusa and P. schachtii rDNA target sequences in pooled DNA samples, enabling quantification of rDNA of P. effusa from impaction spore trap samples collected from spinach production fields. The rDNA copy numbers of P. effusa were, on average, ≈3,300-fold higher from trap samples collected near an infected field compared with those levels recorded at a site without a nearby spinach field. In combination with disease-conducive weather forecasting, application of the assays may be helpful to time fungicide applications for disease management.
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Rouxel M, Mestre P, Baudoin A, Carisse O, Delière L, Ellis MA, Gadoury D, Lu J, Nita M, Richard-Cervera S, Schilder A, Wise A, Delmotte F. Geographic distribution of cryptic species of Plasmopara viticola causing downy mildew on wild and cultivated grape in eastern North America. Phytopathology 2014; 104:692-701. [PMID: 24915427 DOI: 10.1094/phyto-08-13-0225-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The putative center of origin of Plasmopara viticola, the causal agent of grape downy mildew, is eastern North America, where it has been described on several members of the family Vitaceae (e.g., Vitis spp., Parthenocissus spp., and Ampelopsis spp.). We have completed the first large-scale sampling of P. viticola isolates across a range of wild and cultivated host species distributed throughout the above region. Sequencing results of four partial genes indicated the presence of a new P. viticola species on Vitis vulpina in Virginia, adding to the four cryptic species of P. viticola recently recorded. The phylogenetic analysis also indicated that the P. viticola species found on Parthenocissus quinquefolia in North America is identical to Plasmopara muralis in Europe. The geographic distribution and host range of five pathogen species was determined through analysis of the internal transcribed spacer polymorphism of 896 isolates of P. viticola. Among three P. viticola species found on cultivated grape, one was restricted to Vitis interspecific hybrids within the northern part of eastern North America. A second species was recovered from V. vinifera and V. labrusca, and was distributed across most of the sampled region. A third species, although less abundant, was distributed across a larger geographical range, including the southern part of eastern North America. P. viticola clade aestivalis predominated (83% of isolates) in vineyards of the European winegrape V. vinifera within the sampled area, indicating that a single pathogen species may represent the primary threat to the European host species within eastern North America.
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Voglmayr H, Montes-Borrego M, Landa BB. Disentangling Peronospora on Papaver: phylogenetics, taxonomy, nomenclature and host range of downy mildew of opium poppy (Papaver somniferum) and related species. PLoS One 2014; 9:e96838. [PMID: 24806292 PMCID: PMC4013089 DOI: 10.1371/journal.pone.0096838] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/09/2014] [Indexed: 11/19/2022] Open
Abstract
Based on sequence data from ITS rDNA, cox1 and cox2, six Peronospora species are recognised as phylogenetically distinct on various Papaver species. The host ranges of the four already described species P. arborescens, P. argemones, P. cristata and P. meconopsidis are clarified. Based on sequence data and morphology, two new species, P. apula and P. somniferi, are described from Papaver apulum and P. somniferum, respectively. The second Peronospora species parasitizing Papaver somniferum, that was only recently recorded as Peronospora cristata from Tasmania, is shown to represent a distinct taxon, P. meconopsidis, originally described from Meconopsis cambrica. It is shown that P. meconopsidis on Papaver somniferum is also present and widespread in Europe and Asia, but has been overlooked due to confusion with P. somniferi and due to less prominent, localized disease symptoms. Oospores are reported for the first time for P. meconopsidis from Asian collections on Papaver somniferum. Morphological descriptions, illustrations and a key are provided for all described Peronospora species on Papaver. cox1 and cox2 sequence data are confirmed as equally good barcoding loci for reliable Peronospora species identification, whereas ITS rDNA does sometimes not resolve species boundaries. Molecular phylogenetic data reveal high host specificity of Peronospora on Papaver, which has the important phytopathological implication that wild Papaver spp. cannot play any role as primary inoculum source for downy mildew epidemics in cultivated opium poppy crops.
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Affiliation(s)
- Hermann Voglmayr
- Division of Systematic and Evolutionary Botany, Department of Botany and Biodiversity Research, University of Vienna, Wien, Austria
- Institute of Forest Entomology, Forest Pathology and Forest Protection, Department of Forest and Soil Sciences, BOKU-University of Natural Resources and Life Sciences, Wien, Austria
| | - Miguel Montes-Borrego
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
| | - Blanca B. Landa
- Department of Crop Protection, Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Córdoba, Spain
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Testen AL, del Mar Jiménez-Gasco M, Ochoa JB, Backman PA. Molecular detection of Peronospora variabilis in quinoa seed and phylogeny of the quinoa downy mildew pathogen in South America and the United States. Phytopathology 2014; 104:379-386. [PMID: 24224871 DOI: 10.1094/phyto-07-13-0198-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Quinoa (Chenopodium quinoa) is an important export of the Andean region, and its key disease is quinoa downy mildew, caused by Peronospora variabilis. P. variabilis oospores can be seedborne and rapid methods to detect seedborne P. variabilis have not been developed. In this research, a polymerase chain reaction (PCR)-based detection method was developed to detect seedborne P. variabilis and a sequencing-based method was used to validate the PCR-based method. P. variabilis was detected in 31 of 33 quinoa seed lots using the PCR-based method and in 32 of 33 quinoa seed lots using the sequencing-based method. Thirty-one of the quinoa seed lots tested in this study were sold for human consumption, with seed originating from six different countries. Internal transcribed spacer (ITS) and cytochrome c oxidase subunit 2 (COX2) phylogenies were examined to determine whether geographical differences occurred in P. variabilis populations originating from Ecuador, Bolivia, and the United States. No geographical differences were observed in the ITS-derived phylogeny but the COX2 phylogeny indicated that geographical differences existed between U.S. and South American samples. Both ITS and COX2 phylogenies supported the existence of a Peronospora sp., distinct from P. variabilis, that causes systemic-like downy mildew symptoms on quinoa in Ecuador. The results of these studies allow for a better understanding of P. variabilis populations in South America and identified a new causal agent for quinoa downy mildew. The PCR-based seed detection method allows for the development of P. variabilis-free quinoa seed, which may prove important for management of quinoa downy mildew.
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Stassen JHM, Seidl MF, Vergeer PWJ, Nijman IJ, Snel B, Cuppen E, Van den Ackerveken G. Effector identification in the lettuce downy mildew Bremia lactucae by massively parallel transcriptome sequencing. Mol Plant Pathol 2012; 13:719-31. [PMID: 22293108 PMCID: PMC6638827 DOI: 10.1111/j.1364-3703.2011.00780.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Lettuce downy mildew (Bremia lactucae) is a rapidly adapting oomycete pathogen affecting commercial lettuce cultivation. Oomycetes are known to use a diverse arsenal of secreted proteins (effectors) to manipulate their hosts. Two classes of effector are known to be translocated by the host: the RXLRs and Crinklers. To gain insight into the repertoire of effectors used by B. lactucae to manipulate its host, we performed massively parallel sequencing of cDNA derived from B. lactucae spores and infected lettuce (Lactuca sativa) seedlings. From over 2.3 million 454 GS FLX reads, 59 618 contigs were assembled representing both plant and pathogen transcripts. Of these, 19 663 contigs were determined to be of B. lactucae origin as they matched pathogen genome sequences (SOLiD) that were obtained from >270 million reads of spore-derived genomic DNA. After correction of cDNA sequencing errors with SOLiD data, translation into protein models and filtering, 16 372 protein models remained, 1023 of which were predicted to be secreted. This secretome included elicitins, necrosis and ethylene-inducing peptide 1-like proteins, glucanase inhibitors and lectins, and was enriched in cysteine-rich proteins. Candidate host-translocated effectors included 78 protein models with RXLR effector features. In addition, we found indications for an unknown number of Crinkler-like sequences. Similarity clustering of secreted proteins revealed additional effector candidates. We provide a first look at the transcriptome of B. lactucae and its encoded effector arsenal.
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Affiliation(s)
- Joost H M Stassen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3508 CH Utrecht, the Netherlands
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Trigiano RN, Wadl PA, Dean D, Hadziabdic D, Scheffler BE, Runge F, Telle S, Thines M, Ristaino J, Spring O. Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. Mycologia 2012; 104:633-40. [PMID: 22241615 DOI: 10.3852/11-288] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ten polymorphic microsatellite loci for the obligate biotrophic, oomycete pathogen of tobacco, Peronospora tabacina, were identified from a small insert genomic library enriched for GT motifs. Eighty-five percent of the 162 loci identified were composed of dinucleotide repeats, whereas only 4% and 11% were tri-and tetra-nucleotide repeats respectively. About 82% of all the microsatellites were perfect and within the library; only about 7% of the loci were duplicated. Primers were designed for 63 loci; 10 loci were polymorphic, 19 were monomorphic and 34 either failed to amplify or produced ambiguous/inconsistent results. The 10 polymorphic loci were characterized with 44 isolates of P. tabacina collected from tobacco plants growing in Europe, the Near East and North and South America. The number of alleles per locus was either three or four with a mean of 3.2, and the mean number of genotypes per locus was 3.6. Observed heterozygosity was 0.32-0.95, whereas expected heterozygosity was 0.44-0.69 for these loci. All loci except PT054 did not conform to the Hardy-Weinberg distribution. Polymorphic information content (PIC) for the loci was 0.35-0.69 with a mean of 0.50. These microsatellite loci provide a set of markers sufficient to perform genetic diversity and population studies of P. tabacina, and possibly other species of Peronospora.
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Affiliation(s)
- Robert N Trigiano
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560, USA.
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Savory EA, Zou C, Adhikari BN, Hamilton JP, Buell CR, Shiu SH, Day B. Alternative splicing of a multi-drug transporter from Pseudoperonospora cubensis generates an RXLR effector protein that elicits a rapid cell death. PLoS One 2012; 7:e34701. [PMID: 22496844 PMCID: PMC3320632 DOI: 10.1371/journal.pone.0034701] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 03/05/2012] [Indexed: 12/31/2022] Open
Abstract
Pseudoperonospora cubensis, an obligate oomycete pathogen, is the causal agent of cucurbit downy mildew, a foliar disease of global economic importance. Similar to other oomycete plant pathogens, Ps. cubensis has a suite of RXLR and RXLR-like effector proteins, which likely function as virulence or avirulence determinants during the course of host infection. Using in silico analyses, we identified 271 candidate effector proteins within the Ps. cubensis genome with variable RXLR motifs. In extending this analysis, we present the functional characterization of one Ps. cubensis effector protein, RXLR protein 1 (PscRXLR1), and its closest Phytophthora infestans ortholog, PITG_17484, a member of the Drug/Metabolite Transporter (DMT) superfamily. To assess if such effector-non-effector pairs are common among oomycete plant pathogens, we examined the relationship(s) among putative ortholog pairs in Ps. cubensis and P. infestans. Of 271 predicted Ps. cubensis effector proteins, only 109 (41%) had a putative ortholog in P. infestans and evolutionary rate analysis of these orthologs shows that they are evolving significantly faster than most other genes. We found that PscRXLR1 was up-regulated during the early stages of infection of plants, and, moreover, that heterologous expression of PscRXLR1 in Nicotiana benthamiana elicits a rapid necrosis. More interestingly, we also demonstrate that PscRXLR1 arises as a product of alternative splicing, making this the first example of an alternative splicing event in plant pathogenic oomycetes transforming a non-effector gene to a functional effector protein. Taken together, these data suggest a role for PscRXLR1 in pathogenicity, and, in total, our data provide a basis for comparative analysis of candidate effector proteins and their non-effector orthologs as a means of understanding function and evolutionary history of pathogen effectors.
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Affiliation(s)
- Elizabeth A. Savory
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
| | - Cheng Zou
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Bishwo N. Adhikari
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - John P. Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Shin-Han Shiu
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Brad Day
- Department of Plant Pathology, Michigan State University, East Lansing, Michigan, United States of America
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Choi YJ, Shin HD, Thines M. Two novel Peronospora species are associated with recent reports of downy mildew on sages. ACTA ACUST UNITED AC 2009; 113:1340-50. [PMID: 19699301 DOI: 10.1016/j.mycres.2009.08.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Revised: 08/11/2009] [Accepted: 08/14/2009] [Indexed: 11/20/2022]
Affiliation(s)
- Young-Joon Choi
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea
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Göker M, García-Blázquez G, Voglmayr H, Tellería MT, Martín MP. Molecular taxonomy of phytopathogenic fungi: a case study in Peronospora. PLoS One 2009; 4:e6319. [PMID: 19641601 PMCID: PMC2712678 DOI: 10.1371/journal.pone.0006319] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 06/01/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms. METHODOLOGY Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews. CONCLUSIONS A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.
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Affiliation(s)
- Markus Göker
- Organismic Botany, Eberhard Karls University of Tübingen, Tübingen, Germany.
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Montes-Borrego M, Muñoz Ledesma FJ, Jiménez-Díaz RM, Landa BB. A nested-polymerase chain reaction protocol for detection and population biology studies of Peronospora arborescens, the downy mildew pathogen of opium poppy, using herbarium specimens and asymptomatic, fresh plant tissues. Phytopathology 2009; 99:73-81. [PMID: 19055437 DOI: 10.1094/phyto-99-1-0073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A sensitive nested-polymerase chain reaction (PCR) protocol was developed using either of two primer pairs that improves the in planta detection of Peronospora arborescens DNA. The new protocol represented an increase in sensitivity of 100- to 1,000-fold of detection of the oomycete in opium poppy tissue compared with the detection limit of single PCR using the same primer pairs. The new protocol allowed amplification of 5 to 0.5 fg of Peronospora arborescens DNA mixed with Papaver somniferum DNA. The protocol proved useful for amplifying Peronospora arborescens DNA from 96-year-old herbarium specimens of Papaver spp. and to demonstrate that asymptomatic, systemic infections by Peronospora arborescens can occur in wild Papaver spp. as well as in cultivated opium poppy. Also, the increase in sensitivity of the protocol made possible the detection of seedborne Peronospora arborescens in commercial opium poppy seed stocks in Spain with a high frequency, which poses a threat for pathogen spread. Direct sequencing of purified amplicons allowed alignment of a Peronospora arborescens internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequence up to 730-bp long when combining the sequences obtained with the two primer sets. Maximum parsimony analysis of amplified Peronospora arborescens ITS rDNA sequences from specimens of Papaver dubium, P. hybridum, P. rhoeas, and P. somniferum from different countries indicated for the first time that a degree of host specificity may exist within populations of Peronospora arborescens. The reported protocol will be useful for epidemiological and biogeographical studies of downy mildew diseases as well as to unravel misclassification of Peronospora arborescens and Peronospora cristata, the reported causal agents of the opium poppy downy mildew disease.
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Thines M, Göker M, Telle S, Ryley M, Mathur K, Narayana YD, Spring O, Thakur RP. Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data. ACTA ACUST UNITED AC 2007; 112:345-51. [PMID: 18308532 DOI: 10.1016/j.mycres.2007.10.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 09/03/2007] [Accepted: 10/23/2007] [Indexed: 11/17/2022]
Abstract
Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.
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Affiliation(s)
- Marco Thines
- Universität Hohenheim, Institut für Botanik, Garbenstr. 30, 70599 Stuttgart, Germany.
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Chen X, Hou X, Zhang J, Zheng J. Molecular characterization of two important antifungal proteins isolated by downy mildew infection in non-heading Chinese cabbage. Mol Biol Rep 2007; 35:621-9. [PMID: 17762976 DOI: 10.1007/s11033-007-9132-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 08/14/2007] [Indexed: 10/22/2022]
Abstract
Two cDNA clones for a pathogen induced genes in non-heading Chinese cabbage (Brassica rapa ssp. chinensis L. cv. Suzhouqing) were isolated and characterized. The two full-length cDNA clones, designated Bcchi and BcAF were isolated during the resistance response to Peronospora parasitica. Sequence analysis of corresponding cDNA clones confirmed the translation products of both genes showed high degree of homology to other plant chitinases and plant defensins, respectively. Genomic DNA Southern blot analysis indicated that each gene represented a small multi-gene family. Upon inoculation with P. parasitica, both genes transcripts were rapid accumulated in the infected leaves. Tissue-specific expression of both genes showed that 24 h post-inoculation the highest expression tissue of Bcchi mRNA was leaves, and 12 h post-inoculation the highest expression tissue of BcAF mRNA was leaves. These data revealed that both genes may be involved in plant resistance against fungal pathogen infection.
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Affiliation(s)
- Xiaofeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, 6 Tongwei Road, Nanjing, 210095, PR China
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Chen WJ, Delmotte F, Richard-Cervera S, Douence L, Greif C, Corio-Costet MF. At least two origins of fungicide resistance in grapevine downy mildew populations. Appl Environ Microbiol 2007; 73:5162-72. [PMID: 17586672 PMCID: PMC1950979 DOI: 10.1128/aem.00507-07] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 06/09/2007] [Indexed: 11/20/2022] Open
Abstract
Quinone outside inhibiting (QoI) fungicides represent one of the most widely used groups of fungicides used to control agriculturally important fungal pathogens. They inhibit the cytochrome bc1 complex of mitochondrial respiration. Soon after their introduction onto the market in 1996, QoI fungicide-resistant isolates were detected in field plant pathogen populations of a large range of species. However, there is still little understanding of the processes driving the development of QoI fungicide resistance in plant pathogens. In particular, it is unknown whether fungicide resistance occurs independently in isolated populations or if it appears once and then spreads globally by migration. Here, we provide the first case study of the evolutionary processes that lead to the emergence of QoI fungicide resistance in the plant pathogen Plasmopara viticola. Sequence analysis of the complete cytochrome b gene showed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Phylogenetic analysis of a large mitochondrial DNA fragment including the cytochrome b gene (2,281 bp) across a wide range of European P. viticola isolates allowed the detection of four major haplotypes belonging to two distinct clades, each of which contains a different QoI fungicide resistance allele. This is the first demonstration that a selected substitution conferring resistance to a fungicide has occurred several times in a plant-pathogen system. Finally, a high population structure was found when the frequency of QoI fungicide resistance haplotypes was assessed in 17 French vineyards, indicating that pathogen populations might be under strong directional selection for local adaptation to fungicide pressure.
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Affiliation(s)
- Wei-Jen Chen
- Institut National de la Recherche Agronomique, UMR Santé Végétale (INRA-ENITAB), Institut des Sciences de la Vigne et du Vin, BP 81, 33883 Villenave d'Ornon Cedex, France
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Choi YJ, Hong SB, Shin HD. Re-consideration of Peronospora farinosa infecting Spinacia oleracea as distinct species, Peronospora effusa. ACTA ACUST UNITED AC 2007; 111:381-91. [PMID: 17509849 DOI: 10.1016/j.mycres.2007.02.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 01/06/2007] [Accepted: 02/05/2007] [Indexed: 11/28/2022]
Abstract
Downy mildew is probably the most widespread and potentially destructive global disease of spinach (Spinacia oleracea). The causal agent of downy mildew disease on various plants of Chenopodiaceae, including spinach, is regarded as a single species, Peronospora farinosa. In the present study, the ITS rDNA sequence and morphological data demonstrated that P. farinosa from S. oleracea is distinct from downy mildew of other chenopodiaceous hosts. Fifty-eight spinach specimens were collected or loaned from 17 countries of Asia, Europe, Oceania, North and South America, which all formed a distinct monophyletic group. No intercontinental genetic variation of the ITS rDNA within Peronospora accessions causing spinach downy mildew disease was found. Phylogenetic trees supported recognition of Peronospora from spinach as a separate species. Microscopic examination also revealed morphological differences between Peronospora specimens from Spinacia and P. farinosa s. lat. specimens from Atriplex, Bassia, Beta, and Chenopodium. Consequently, the name Peronospora effusa should be reinstated for the downy mildew fungus found on spinach. Here, a specimen of the original collections of Peronospora effusa is designated as lectotype.
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Affiliation(s)
- Young-Joon Choi
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
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