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Osdaghi E, Taghavi SM, Aliabadi AA, Khojasteh M, Abachi H, Moallem M, Mohammadikhah S, Shah SMA, Chen G, Liu Z. Detection and Diagnosis of Bacterial Leaf Streak on Small Grain Cereals: From Laboratory to Field. Phytopathology 2023; 113:2024-2036. [PMID: 37069135 DOI: 10.1094/phyto-09-22-0343-sa] [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: 06/19/2023]
Abstract
Bacterial leaf streak of small-grain cereals is an economically important disease of wheat and barley crops. The disease occurs in many countries across the globe, with particular importance in regions characterized by high precipitation or areas in which sprinkler irrigation is used. Three genetically distinct lineages of the Gram-negative bacterium Xanthomonas translucens (X. translucens pv. undulosa, X. translucens pv. translucens, and X. translucens pv. cerealis) are responsible for most of the bacterial leaf streak infections on wheat and barley crops. Considering the seedborne nature of the pathogens, they are included in the A2 (high-risk) list of quarantine organisms for some European countries; hence, they are under strict quarantine control and zero tolerance. Due to the taxonomic complexities within X. translucens, the exact geographic distribution of each pathovar has not yet been determined. In this mini review, we provide an updated overview of the detection and diagnosis of the bacterial leaf streak pathogens. First, a short history of the leaf streak pathogens is provided, followed by the symptomology and host range of the causal agents. Then, the utility of conventional methods and high-throughput molecular approaches in the precise detection and identification of the pathogens is explained. Finally, we highlight the role of quarantine inspections and early detection of the pathogen in combating the risk of bacterial leaf streak in the 21st century's small-grains cereals' industry.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Alizadeh Aliabadi
- Plant Pathology Research Department, Iranian Research Institute of Plant Protection (IRIPP), Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Moein Khojasteh
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Hamid Abachi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Mahsa Moallem
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Sedighe Mohammadikhah
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Syed Mashab Ali Shah
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
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Alvandi H, Taghavi SM, Khojasteh M, Rahimi T, Dutrieux C, Taghouti G, Jacques MA, Portier P, Osdaghi E. Pathovar-Specific PCR Method for Detection and Identification of Xanthomonas translucens pv. undulosa. Plant Dis 2023; 107:2279-2287. [PMID: 36611242 DOI: 10.1094/pdis-11-22-2677-sr] [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: 06/17/2023]
Abstract
Bacterial leaf streak disease caused by Xanthomonas translucens pv. undulosa is an economically important disease threatening wheat and barley crops around the globe. Thus far, specific PCR-based detection and identification tests for X. translucens pathovars are not available. In this study, we used comparative genomics approach to design a pathovar-specific primer pair for detection of X. translucens pv. undulosa in naturally infected seeds and its differentiation from other pathovars of the species. For this aim, complete genome sequences of strains of different X. translucens pathovars were compared and the specific PCR primer pair XtuF/XtuR was designed. These primers were strictly specific to X. translucens pv. undulosa because the expected 229-bp DNA fragment was not amplified in the closely related pathovars or in other xanthomonads, wheat-pathogenic bacteria, and other plant-pathogenic bacteria. High sensitivity of the primer pair XtuF/XtuR allowed detection of pure DNA of the pathogen in a concentration as low as 4.5 pg/μl. The pathogen was also detected in water suspension at a concentration of 8.6 × 102 CFU/ml. The PCR test was capable of detecting the pathogen in extracts of naturally infected wheat seeds at a concentration of 3.5 × 104 CFU/g while a culture-plate method was able to detect the pathogen at a concentration of 50 × 105 CFU/g of the same seeds. The PCR test developed in this study is a step forward for precise detection and identification of X. translucens pv. undulosa to prevent outbreaks of the bacterial leaf streak disease.
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Affiliation(s)
- Hosna Alvandi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Moein Khojasteh
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Touraj Rahimi
- Department of Plant Production and Genetics, Agriculture Faculty, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Cecile Dutrieux
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Geraldine Taghouti
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institute of Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
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Osdaghi E, Robertson AE, Jackson-Ziems TA, Abachi H, Li X, Harveson RM. Clavibacter nebraskensis causing Goss's wilt of maize: Five decades of detaining the enemy in the New World. Mol Plant Pathol 2023; 24:675-692. [PMID: 36116105 DOI: 10.1111/mpp.13268] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 06/11/2023]
Abstract
Goss's bacterial wilt and leaf blight of maize (Zea mays) caused by the gram-positive coryneform bacterium Clavibacter nebraskensis is an economically important disease in North America. C. nebraskensis is included within the high-risk list of quarantine pathogens by several plant protection organizations (EPPO code: CORBMI), hence it is under strict quarantine control around the world. The causal agent was reported for the first time on maize in Nebraska (USA) in 1969. After an outbreak during the 1970s, prevalence of the disease decreased in the 1980s to the early 2000s, before the disease resurged causing a serious threat to maize production in North America. The re-emergence of Goss's wilt in the corn belt of the United States led to several novel achievements in understanding the pathogen biology and disease control. In this review, we provide an updated overview of the pathogen taxonomy, biology, and epidemiology as well as management strategies of Goss's wilt disease. First, a taxonomic history of the pathogen is provided followed by symptomology and host range, genetic diversity, and pathogenicity mechanisms of the bacterium. Then, utility of high-throughput molecular approaches in the precise detection and identification of the pathogen and the management strategies of the disease are explained. Finally, we highlight the role of integrated pest management strategies to combat the risk of Goss's wilt in the 21st century maize industry. DISEASE SYMPTOMS Large (2-15 cm) tan to grey elongated oval lesions with wavy, irregular water-soaked margins on the leaves. The lesions often start at the leaf tip or are associated with wounding caused by hail or wind damage. Small (1 mm in diameter), dark, discontinuous water-soaked spots, known as "freckles", can be observed in the periphery of lesions. When backlit, the freckles appear translucent. Early infection (prior to growth stage V6) may become systemic and cause seedlings to wilt, wither, and die. Coalescence of lesions results in leaf blighting. HOST RANGE Maize (Zea mays) is the only economic host of the pathogen. A number of Poaceae species are reported to act as secondary hosts for C. nebraskensis. TAXONOMIC STATUS OF THE PATHOGEN Class: Actinobacteria; Order: Micrococcales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter nebraskensis. SYNONYMS Corynebacterium nebraskense (Schuster, 1970) Vidaver & Mandel 1974; Corynebacterium michiganense pv. nebraskense (Vidaver & Mandel 1974) Dye & Kemp 1977; Corynebacterium michiganense subsp. nebraskense (Vidaver & Mandel 1974) Carlson & Vidaver 1982; Clavibacter michiganense subsp. nebraskense (Vidaver & Mandel 1974) Davis et al. 1984; Clavibacter michiganensis subsp. nebraskensis (Vidaver & Mandel 1974) Davis et al. 1984. TYPE MATERIALS ATCC 27794T ; CFBP 2405T ; ICMP 3298T ; LMG 3700T ; NCPPB 2581T . MICROBIOLOGICAL PROPERTIES Cells are gram-positive, orange-pigmented, pleomorphic club- or rod-shaped, nonspore-forming, nonmotile, and without flagella, approximately 0.5 × 1-2.0 μm. DISTRIBUTION The pathogen is restricted to Canada and the United States. PHYTOSANITARY CATEGORIZATION EPPO code CORBNE.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Alison E Robertson
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Tamra A Jackson-Ziems
- Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Hamid Abachi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj, Iran
| | - Xiang Li
- Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, Prince Edward Island, Canada
| | - Robert M Harveson
- Panhandle Research & Extension Center, University of Nebraska, Scottsbluff, Nebraska, USA
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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. Mol Plant Pathol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Osdaghi E, Taghouti G, Dutrieux C, Taghavi SM, Fazliarab A, Briand M, Le Saux MF, Portier P, Jacques MA. Whole Genome Resources of 17 Curtobacterium flaccumfaciens Strains Including Pathotypes of C. flaccumfaciens pv. betae, C. flaccumfaciens pv. oortii, and C. flaccumfaciens pv. poinsettiae. Mol Plant Microbe Interact 2022; 35:352-356. [PMID: 35021852 DOI: 10.1094/mpmi-11-21-0282-a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Geraldine Taghouti
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Cecile Dutrieux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - S Mohsen Taghavi
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Martial Briand
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marion Fischer Le Saux
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Marie-Agnes Jacques
- University of Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
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Chen G, Khojasteh M, Taheri-Dehkordi A, Taghavi SM, Rahimi T, Osdaghi E. Complete Genome Sequencing Provides Novel Insight Into the Virulence Repertories and Phylogenetic Position of Dry Beans Pathogen Curtobacterium flaccumfaciens pv. flaccumfaciens. Phytopathology 2021; 111:268-280. [PMID: 32716255 DOI: 10.1094/phyto-06-20-0243-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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
Bacterial wilt of dry beans (family Fabaceae) caused by the actinobacterial agent Curtobacterium flaccumfaciens pv. flaccumfaciens is one of the most important diseases threatening edible legume production around the globe. Despite the economic losses due to the bacterial wilt disease, the pathogen has not so far been investigated for its genomic features, pathogenicity determinants, and virulence strategies. Here we present the first complete genome sequence of a highly virulent bacteriocin-producing C. flaccumfaciens pv. flaccumfaciens strain P990. The bacterium has a circular chromosome consisting of 3,736 kbp with the G+C% content of 71.0%. Furthermore, a 147-kbp circular plasmid (pCff1) with 66.1% G+C% content as well as two circular plasmid-like DNAs with sizes of 25 and 22 kbp were detected within the genomic contents of C. flaccumfaciens pv. flaccumfaciens. Phylogenetic analyses revealed that only a few number of Curtobacterium sp. strains deposited in the public databases could be classified within the species C. flaccumfaciens. Comparative genomics of C. flaccumfaciens pv. flaccumfaciens using the genome sequences of actinobacterial plant pathogens revealed the presence of a set of unique low G+C% content genomic islands in the C. flaccumfaciens pv. flaccumfaciens genome. Homologs of pathogenicity-determinant loci capable of producing 1,4-beta-xylanase (xysA), pectate lyase (pelA1 and pelA2), serine protease (chpC, chpG, and pat-1), and sortase (srtA) were detected in C. flaccumfaciens pv. flaccumfaciens genome. The genomic data presented here extend our understanding of the C. flaccumfaciens pv. flaccumfaciens genomic features and pave the ways of research on functional and interaction genetics to combat the risk of bacterial wilt disease in the 21st century's dry bean industry.
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Affiliation(s)
- Gongyou Chen
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Moein Khojasteh
- School of Agriculture and Biology/State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ayat Taheri-Dehkordi
- Department of Horticultural Science, College of Agriculture & Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - S Mohsen Taghavi
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Touraj Rahimi
- Department of Agronomy and Plant Breeding, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Ebrahim Osdaghi
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
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Osdaghi E, Young AJ, Harveson RM. Bacterial wilt of dry beans caused by Curtobacterium flaccumfaciens pv. flaccumfaciens: A new threat from an old enemy. Mol Plant Pathol 2020; 21:605-621. [PMID: 32097989 PMCID: PMC7170776 DOI: 10.1111/mpp.12926] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 05/20/2023]
Abstract
Bacterial wilt and tan spot of dry beans (family Fabaceae), caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is an important emerging disease threatening the edible legume industry around the globe. The management of bacterial wilt has been a major problem since its original description in 1922. This is in part due to the seedborne nature of the pathogen allowing the bacterium to be transmitted long distances via infected seeds, as well as a lack of detailed molecular information concerning the pathogenicity repertoires and virulence determinates of the pathogen. Identification can also be difficult owing to the presence of five different colony colour variants (i.e., yellow, orange, pink, purple, and red) on culture media. In this review, we provide an overview of the aetiology, epidemiology, and management strategies of bacterial wilt disease. First, a comprehensive and comparative symptomology of the disease on different dry bean species is described. Then, the taxonomic history of the causal agent and utility of high-throughput sequencing-based approaches in the precise characterization of the pathogen is explained. Furthermore, we provide an updated outline on the global distribution of the pathogen, highlighting expansion of the causal agent into the areas with no history of the disease until the beginning of the current century. Finally, because there are limited options for use of conventional pesticides against the pathogen, we highlight the use of integrated pest management strategies, for example quarantine inspections, resistant cultivars, and crop sanitation, to combat the risk of bacterial wilt disease in the dry bean industry. DISEASE SYMPTOMS Interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. Seed discolouration to yellow, orange, pink, or purple is seen in white-seeded cultivars. HOST RANGE Causes bacterial wilt and tan spot disease on edible dry beans in the Fabaceae family, including common bean (Phaseolus vulgaris), cowpea (Vigna unguiculata), mungbean (Vigna radiata), soybean (Glycine max), as well as a number of weed species. TAXONOMIC STATUS OF THE PATHOGEN Bacteria; phylum Actinobacteria; order Actinomycetales; suborder: Micrococcineae; family Microbacteriaceae; genus Curtobacterium; species Curtobacterium flaccumfaciens. SYNONYMS Corynebacterium flaccumfaciens subsp. flaccumfaciens; Corynebacterium flaccumfaciens pv. flaccumfaciens, Corynebacterium flaccumfaciens, Phytomonas flaccumfaciens, Bacterium flaccumfaciens. MICROBIOLOGICAL PROPERTIES Multicoloured (yellow, orange, pink, purple, and red), gram-positive, aerobic, curved rod, nonspore-forming, polar flagellated, motile cells. DISTRIBUTION Widespread in America (Brazil, Canada, and the USA), Australia, and Iran. Restricted occurrence in Africa and Europe. PHYTOSANITARY CATEGORIZATION EPPO A2 list no. 48, EU Annex II⁄B.
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Affiliation(s)
- Ebrahim Osdaghi
- Department of Plant ProtectionCollege of AgricultureShiraz UniversityShirazIran
| | - Anthony J. Young
- School of Agriculture and Food SciencesThe University of QueenslandGattonQueenslandAustralia
| | - Robert M. Harveson
- University of NebraskaPanhandle Research & Extension CenterScottsbluffUSA
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Osdaghi E, Rahimi T, Taghavi SM, Ansari M, Zarei S, Portier P, Briand M, Jacques MA. Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains. Appl Environ Microbiol 2020; 86:e02873-19. [PMID: 31924620 DOI: 10.1128/AEM.02873-19] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023] Open
Abstract
Members of the genus Clavibacter are economically important bacterial plant pathogens infecting a set of diverse agricultural crops (e.g., alfalfa, corn, potato, tomato, and wheat). Tomato-associated Clavibacter sp. strains account for a great portion of the genetic diversity of the genus, and C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis), causing bacterial canker disease, is considered one of the most destructive seed-borne agents for the crop worldwide. However, current taxonomic descriptions of the genus do not reflect the existing diversity of the strains, resulting in unsatisfactory results in quarantine surveys for the pathogens. In this study, we used all the available genome sequences of Clavibacter sp. strains, including the type strains of newly described subspecies, to provide precise insight into the diversity of tomato-associated members of the genus and further clarify the taxonomic status of the strains using genotypic and phenotypic features. The results of phylogenetic analyses revealed the existence of nine hypothetical new species among the investigated strains. None of the three new subspecies (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) is included within the tomato-pathogenic C. michiganensis sensu stricto lineage. Although comparative genomics revealed the lack of chp and tomA pathogenicity determinant gene clusters in the nonpathogenic strains, a number of pathogenicity-related genes were noted to be present in all the strains regardless of their pathogenicity characteristics. Altogether, our results indicate a need for a formal taxonomic reconsideration of tomato-associated Clavibacter sp. strains to facilitate differentiation of the lineages in quarantine inspections.IMPORTANCE Clavibacter spp. are economically important bacterial plant pathogens infecting a set of diverse agricultural crops, such as alfalfa, corn, pepper, potato, tomato, and wheat. A number of plant-pathogenic members of the genus (e.g., C. michiganensis sensu stricto and C. sepedonicus, infecting tomato and potato plants, respectively) are included in the A2 (high-risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Although tomato-associated members of Clavibacter spp. account for a significant portion of the genetic diversity in the genus, only the strains belonging to C. michiganensis sensu stricto (formerly C. michiganensis subsp. michiganensis) cause bacterial canker disease of tomato and are subjected to the quarantine inspections. Hence, discrimination between the pathogenic and nonpathogenic Clavibacter sp. strains associated with tomato seeds and transplants plays a pivotal role in the accurate detection and cost-efficient management of the disease. On the other hand, detailed information on the genetic contents of different lineages of the genus would lead to the development of genome-informed specific detection techniques. In this study, we have provided an overview of the phylogenetic and genomic differences between the pathogenic and nonpathogenic tomato-associated Clavibacter sp. strains. We also noted that the taxonomic status of newly introduced subspecies of C. michiganensis (i.e., C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis, and C. michiganensis subsp. phaseoli) should be reconsidered.
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Cho HJ, Hong SW, Kim HJ, Kwak YS. Development of a Multiplex PCR Method to Detect Fungal Pathogens for Quarantine on Exported Cacti. Plant Pathol J 2016; 32:53-7. [PMID: 26889115 PMCID: PMC4755675 DOI: 10.5423/ppj.nt.09.2015.0184] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 05/22/2023]
Abstract
Major diseases in grafted cacti have been reported and Fusarium oxysporum, Bipolaris cactivora, Phytophthora spp. and Collectotrichum spp. are known as causal pathogens. These pathogens can lead to plant death after infection. Therefore, some European countries have quarantined imported cacti that are infected with specific fungal pathogens. Consequently, we developed PCR detection methods to identify four quarantined fungal pathogens and reduce export rejection rates of Korean grafted cacti. The pathogen specific primer sets F.oF-F.oR, B.CF-B.CR, P.nF-P.nR, and P.cF-P.CR were tested for F. oxysporum, B. cactivora, P. nicotinae, and P. cactorum, respectively. The F.oF-F.oR primer set was designed from the Fusarium ITS region; the B.CF-B.CR and P.nF-P.nR primers respectively from Bipolaris and Phytophthora ITS1; and the P.cF-P.CR primer set from the Ypt1protein gene region. The quarantine fungal pathogen primer pairs were amplified to the specific number of base pairs in each of the following fungal pathogens: 210-bp (F. oxysporum), 510-bp (B. cactivora), 313-bp (P. nicotinae), and 447-bp (P. cactorum). The detection limit for the mono- and multiplex PCR primer sets was 0.1 ng of template DNA under in vitro conditions. Therefore, each primer set successfully diagnosed contamination of quarantine pathogens in export grafted cacti. Consequently, our methodology is a viable tool to screen contamination of the fungal pathogen in exported grafted cacti.
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Affiliation(s)
- Hyun ji Cho
- Division of Applied Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Seong Won Hong
- Department of Plant Medicine and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701,
Korea
| | - Hyun-ju Kim
- Plant Quarantine Technology Center, Animal and Plant Quarantine Agency, Suwon 443-400,
Korea
| | - Youn-Sig Kwak
- Department of Plant Medicine and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701,
Korea
- Corresponding author. Phone) +82-55-772-1922, FAX) +82-55-772-1929, E-mail)
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