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Osdaghi E, van der Wolf JM, Abachi H, Li X, De Boer S, Ishimaru CA. Bacterial ring rot of potato caused by Clavibacter sepedonicus: A successful example of defeating the enemy under international regulations. MOLECULAR PLANT PATHOLOGY 2022; 23:911-932. [PMID: 35142424 PMCID: PMC9190974 DOI: 10.1111/mpp.13191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Bacterial ring rot of potato (Solanum tuberosum) caused by the gram-positive coryneform bacterium Clavibacter sepedonicus is an important quarantine disease threatening the potato industry around the globe. Since its original description in 1906 in Germany, management of ring rot has been a major problem due to the seedborne nature (via seed tubers not true seeds) of the pathogen allowing the bacterium to be transmitted long distances via infected tubers. DISEASE SYMPTOMS On growing potato plants: interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. On infected tubers: vascular tissues become yellowish brown with a cheesy texture due to bacterial colonization and decay. HOST RANGE Potato is the main host of the pathogen, but natural infection also occurs on eggplant, tomato, and sugar beet. TAXONOMIC STATUS OF THE PATHOGEN Class: Actinobacteria; Order: Actinomycetales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES) Aplanobacter sepedonicus; Bacterium sepedonicum; Corynebacterium sepedonicum; Corynebacterium michiganense pv. sepedonicum; Clavibacter michiganensis subsp. sepedonicus. MICROBIOLOGICAL PROPERTIES Gram-positive, club-shaped cells with creamy to yellowish-cream colonies for which the optimal growth temperature is 20-23°C. DISTRIBUTION Asia (China, Japan, Kazakhstan, Nepal, North Korea, Pakistan, South Korea, Uzbekistan, the Asian part of Russia), Europe (Belarus, Bulgaria, Czech Republic, Estonia, Finland, Georgia, Germany, Greece, Hungary, Latvia, Lithuania, Norway, Poland, Romania, European part of Russia, Slovakia, Spain, Sweden, Turkey, Ukraine), and North America (Canada, Mexico, USA). PHYTOSANITARY CATEGORIZATION CORBSE: EPPO A2 list no. 51. EU; Annex designation I/A2.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Jan M. van der Wolf
- Business Unit Biointeractions and Plant HealthWageningen University and ResearchWageningenNetherlands
| | - Hamid Abachi
- Department of Plant ProtectionCollege of AgricultureUniversity of TehranKarajIran
| | - Xiang Li
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
| | - Solke H. De Boer
- Canadian Food Inspection Agency, Charlottetown LaboratoryCharlottetownPECanada
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Motyka A, Zoledowska S, Sledz W, Lojkowska E. Molecular methods as tools to control plant diseases caused by Dickeya and Pectobacterium spp: A minireview. N Biotechnol 2017; 39:181-189. [PMID: 28847714 DOI: 10.1016/j.nbt.2017.08.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022]
Abstract
Dickeya spp. and Pectobacterium spp. are etiological agents of soft rot on crops, vegetables, and ornamentals. They also cause blackleg on potato. These pectinolytic phytopathogens are responsible for significant economic losses, mostly within the potato production sector. Importantly, there are no methods to eradicate these microorganisms once they have infected plant material. Solely preventive measures remain, including early detection and identification of the pathogens, monitoring of their spread in addition to planting certified seed material tested for latent infections. As proper identification of the causative agent allows for efficient limitation of disease spread, numerous detection and differentiation methods have been developed. Most commonly followed procedures involve: isolation of viable bacterial cells (alternatively post-enrichment) on semi-selective media, identification to species level by PCR (single, multiplex, Real time), serology or fatty acids profiling. Differentiation of the isolates is often accomplished by sequencing the housekeeping genes or molecular fingerprinting. In view of lowering total costs of next-generation sequencing (NGS), a huge amount of generated data reveals subtle differences between strains that have proven to be potentially useful for the establishment of specific novel detection pipelines. Successful implementation of molecular diagnostic methods is exemplified by 20-year studies on the populations of pectinolytic bacteria on potatoes in Poland. The presented work aims to gather the characteristics of Dickeya spp. and Pectobacterium spp. important for the identification process in addition to providing an overview of modern and newly developed specific, rapid, high-throughput and cost-effective screening methods for the detection and identification of these phytopathogens.
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Affiliation(s)
- Agata Motyka
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Sabina Zoledowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Wojciech Sledz
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Ewa Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland.
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Cellier G, Arribat S, Chiroleu F, Prior P, Robène I. Tube-Wise Diagnostic Microarray for the Multiplex Characterization of the Complex Plant Pathogen Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2017; 8:821. [PMID: 28596774 PMCID: PMC5442206 DOI: 10.3389/fpls.2017.00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Ralstonia solanacearum is a well-known agricultural and ecological threat worldwide. The complexity of the R. solanacearum species complex (Rssc) represents a challenge for the accurate characterization of epidemiological strains by official services and research laboratories. The majority of protocols only focus on a narrow range of strains; however, this species complex includes strains that represent major constraints and are under strict regulation. The main drawback associated with the current methods of detecting and characterizing Rssc strains is their reliance on combining different protocols to properly characterize the strains at the ecotype level, which require time and money. Therefore, we used microarray technology (ArrayTube) to develop a standard protocol, which characterizes 17 major groups of interest in the Rssc, in a single multiplex reaction. These 17 majors groups are linked with a phylogenetic assignation (phylotypes, sequevars), but also with an ecotype assignation associated with a range of hosts (e.g., brown rot, Moko). Probes were designed with a 50-mer length constraint and thoroughly evaluated for any flaws or secondary structures. The strains are characterized based on a DNA extraction from pure culture. Validation data showed strong intra-repeatability, inter-repeatability, and reproducibility as well as good specificity. A hierarchical analysis of the probe groups is suitable for an accurate characterization. Compared with single marker detection tests, the method described in this paper addresses efficiently the issue of combining several tests by testing a large number of phylogenetic markers in a single reaction assay. This custom microarray (RsscAT) represents a significant improvement in the epidemiological monitoring of Rssc strains worldwide, and it has the potential to provide insights for phylogenetic incongruence of Rssc strains based on the host of isolation and may be used to indicate potentially emergent strains.
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Affiliation(s)
- Gilles Cellier
- Tropical Pests and Diseases Unit, Plant Health Laboratory, ANSESSaint-Pierre, France
| | - Sandrine Arribat
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRADSaint-Pierre, France
| | - Frédéric Chiroleu
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRADSaint-Pierre, France
| | - Philippe Prior
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRADSaint-Pierre, France
- Département Santé des Plantes et Environnement, Institut National de la Recherche AgronomiqueSaint-Pierre, France
| | - Isabelle Robène
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRADSaint-Pierre, France
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Hamilton JP, Neeno-Eckwall EC, Adhikari BN, Perna NT, Tisserat N, Leach JE, Lévesque CA, Buell CR. The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. Database (Oxford) 2011; 2011:bar053. [PMID: 22120664 PMCID: PMC3225079 DOI: 10.1093/database/bar053] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera. Database URL: http://cpgr.plantbiology.msu.edu.
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Affiliation(s)
- John P. Hamilton
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - Eric C. Neeno-Eckwall
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - Bishwo N. Adhikari
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - Nicole T. Perna
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - Ned Tisserat
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - Jan E. Leach
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - C. André Lévesque
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
| | - C. Robin Buell
- Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI, 48824, USA, Department of Genetics, 4434 Genetics-Biotech Center BLDG, 425 Henry Mall, University of Wisconsin, Madison, WI, 53706, USA, Department of Bioagricultural Sciences and Pest Management, Plant Science C129, Colorado State University, Fort Collins, CO, 80523–1177, USA, Agriculture and Agri-Food Canada, 960 Carling Ave., ON, K1A 0C6 and Department of Biology, Carleton University, ON, K1S 5B6, Ottawa, Canada
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Pritchard L, Liu H, Booth C, Douglas E, François P, Schrenzel J, Hedley PE, Birch PRJ, Toth IK. Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens. PLoS Comput Biol 2009; 5:e1000473. [PMID: 19696881 PMCID: PMC2718846 DOI: 10.1371/journal.pcbi.1000473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Accepted: 07/16/2009] [Indexed: 11/18/2022] Open
Abstract
Microarray comparative genomic hybridisation (aCGH) provides an estimate of the relative abundance of genomic DNA (gDNA) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. The experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desirable in each problem domain.We present a method for analysis of bacterial aCGH data that encodes spatial information from the reference genome in a hidden Markov model. This technique is the first such method to be validated in comparisons of sequenced bacteria that diverge at the strain and at the genus level: Pectobacterium atrosepticum SCRI1043 (Pba1043) and Dickeya dadantii 3937 (Dda3937); and Lactococcus lactis subsp. lactis IL1403 and L. lactis subsp. cremoris MG1363. In all cases our method is found to outperform common and widely used aCGH analysis methods that do not incorporate spatial information. This analysis is applied to comparisons between commercially important plant pathogenic soft-rotting enterobacteria (SRE) Pba1043, P. atrosepticum SCRI1039, P. carotovorum 193, and Dda3937.Our analysis indicates that it should not be assumed that hybridisation strength is a reliable proxy for sequence identity in aCGH experiments, and robustly extends the applicability of aCGH to bacterial comparisons at the genus level. Our results in the SRE further provide evidence for a dynamic, plastic 'accessory' genome, revealing major genomic islands encoding gene products that provide insight into, and may play a direct role in determining, variation amongst the SRE in terms of their environmental survival, host range and aetiology, such as phytotoxin synthesis, multidrug resistance, and nitrogen fixation.
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Affiliation(s)
- Leighton Pritchard
- Plant Pathology Programme, SCRI, Dundee, Scotland, United Kingdom
- * E-mail: (LP); (IKT)
| | - Hui Liu
- Plant Pathology Programme, SCRI, Dundee, Scotland, United Kingdom
| | - Clare Booth
- Genetics Programme, SCRI, Dundee, Scotland, United Kingdom
| | - Emma Douglas
- Plant Pathology Programme, SCRI, Dundee, Scotland, United Kingdom
| | - Patrice François
- Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals and the University of Geneva, Geneva, Switzerland
| | - Jacques Schrenzel
- Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals and the University of Geneva, Geneva, Switzerland
| | | | - Paul R. J. Birch
- Plant Pathology Programme, SCRI, Dundee, Scotland, United Kingdom
- Division of Plant Science, College of Life Sciences, University of Dundee at SCRI, Dundee, Scotland, United Kingdom
| | - Ian K. Toth
- Plant Pathology Programme, SCRI, Dundee, Scotland, United Kingdom
- * E-mail: (LP); (IKT)
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