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Brochu AS, Dumonceaux TJ, Valenzuela M, Bélanger R, Pérez-López E. A New Multiplex TaqMan qPCR for Precise Detection and Quantification of Clavibacter michiganensis in Seeds and Plant Tissue. PLANT DISEASE 2024:PDIS06231194SR. [PMID: 38381965 DOI: 10.1094/pdis-06-23-1194-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Bacterial canker of tomato caused by Clavibacter michiganensis (Cm) is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of Cm colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, what makes Cm an even more dangerous pathogen is its ability to infect seeds and plants without causing symptoms. Unfortunately, there are no resistant cultivars or effective chemical or biological control methods available to growers against Cm. Its control relies heavily on prevention. The implementation of a rapid and accurate detection tool is imperative to monitor the presence of Cm and prevent its spread. In this study, we developed a specific and sensitive multiplex TaqMan qPCR assay to detect Cm and distinguish it from related bacterial species that affect tomato plants. Two Cm chromosomal virulence-related genes, rhuM and tomA, were used as specific targets. The plant internal control tubulin alpha-3 was included in each of the multiplexes to improve the reliability of the assay. Specificity was evaluated with 37 bacterial strains including other Clavibacter spp. and related and unrelated bacterial pathogens from different geographic locations affecting a wide variety of hosts. Results showed that the assay is able to discriminate Cm strains from other related bacteria. The assay was validated on tissue and seed samples following artificial infection, and all tested samples accurately detected the presence of Cm. The tool described here is highly specific, sensitive, and reliable for the detection of Cm and allows the quantification of Cm in seeds, roots, stems, and leaves. The diagnostic assay can also be adapted for multiple purposes such as seed certification programs, surveillance, biosafety, the effectiveness of control methods, border protection, and epidemiological studies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Anne-Sophie Brochu
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
- L'Institute EDS, Université Laval, Québec City, Canada
| | - Tim J Dumonceaux
- Agriculture and Agri-Food Canada Saskatoon Research and Development Centre, Saskatoon, SK, Canada
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry & Center of Biotechnology Dr. Daniel Alkalay Lowitt, Universidad Tecnica Federico Santa Maria, Valparaiso 2390123, Chile
| | - Richard Bélanger
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
| | - Edel Pérez-López
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Québec City, Canada
- Centre de Recherche et d'Innovation sur les Végétaux (CRIV), Université Laval, Québec City, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Canada
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2
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Verma RK, Roman-Reyna V, Raanan H, Coaker G, Jacobs JM, Teper D. Allelic variations in the chpG effector gene within Clavibacter michiganensis populations determine pathogen host range. PLoS Pathog 2024; 20:e1012380. [PMID: 39028765 PMCID: PMC11290698 DOI: 10.1371/journal.ppat.1012380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 07/31/2024] [Accepted: 06/27/2024] [Indexed: 07/21/2024] Open
Abstract
Plant pathogenic bacteria often have a narrow host range, which can vary among different isolates within a population. Here, we investigated the host range of the tomato pathogen Clavibacter michiganensis (Cm). We determined the genome sequences of 40 tomato Cm isolates and screened them for pathogenicity on tomato and eggplant. Our screen revealed that out of the tested isolates, five were unable to cause disease on any of the hosts, 33 were exclusively pathogenic on tomato, and two were capable of infecting both tomato and eggplant. Through comparative genomic analyses, we identified that the five non-pathogenic isolates lacked the chp/tomA pathogenicity island, which has previously been associated with virulence in tomato. In addition, we found that the two eggplant-pathogenic isolates encode a unique allelic variant of the putative serine hydrolase chpG (chpGC), an effector that is recognized in eggplant. Introduction of chpGC into a chpG inactivation mutant in the eggplant-non-pathogenic strain Cm101, failed to complement the mutant, which retained its ability to cause disease in eggplant and failed to elicit hypersensitive response (HR). Conversely, introduction of the chpG variant from Cm101 into an eggplant pathogenic Cm isolate (C48), eliminated its pathogenicity on eggplant, and enabled C48 to elicit HR. Our study demonstrates that allelic variation in the chpG effector gene is a key determinant of host range plasticity within Cm populations.
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Affiliation(s)
- Raj Kumar Verma
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
| | - Veronica Roman-Reyna
- Dept. Of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Hagai Raanan
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Gilat Research Center, Negev, Israel
| | - Gitta Coaker
- Dept. of Plant Pathology, University of California Davis, Davis, California, United States of America
| | - Jonathan M. Jacobs
- Dept. of Plant Pathology, The Ohio State University, Columbus, Ohio, United States of America
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Doron Teper
- Dept. of Plant Pathology and Weed Research, Agricultural Research Organization—Volcani Institute, Rishon LeZion, Israel
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3
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Osdaghi E, Taghavi SM, Hamidizade M, Fazliarab A, Hajian Maleki H, Li X, Jacques MA, Portier P. Clavibacter lycopersici sp. nov.: a peach-colored actinobacterium isolated from symptomless tomato plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737062 DOI: 10.1099/ijsem.0.006022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
In 2015, Gram-positive peach-coloured actinobacterial strains were isolated from symptomless tomato phyllosphere in Iran. Biochemical and physiological characteristics, as well as 16S rRNA phylogeny showed that the strains belong to Clavibacter sp., while they were non-pathogenic on the host of isolation, and morphologically distinct from the tomato pathogen C. michiganensis and other plant-associated bacteria. Multilocus sequence analysis of five housekeeping genes showed that the two peach-coloured strains CFBP 8615T (Tom532T) and CFBP 8616 (Tom495) were phylogenetically distinct from all validly described Clavibacter species. Whole genome sequence-based indices, i.e. average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH), showed that the two peach-colored strains share nearly 100 % orthoANI value with one another, while they differ from all validly described Clavibacter species with the orthoANI/dDDH values <93 % and <50 %, respectively. Thus, based on both phenotypic features and orthoANI/dDDH indices the peach-coloured strains could belong to a new species within Clavibacter. In this study, we provide a formal species description for the peach-coloured tomato-associated Clavibacter strains. Clavibacter lycopersici sp. nov. is proposed for the new species with Tom532T = CFBP 8615T = ICMP 22100T as type strain.
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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
| | - Mozhde Hamidizade
- 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
| | - Amal Fazliarab
- Iranian Sugarcane Research and Training Institute (ISCRTI), Ahvaz, Khuzestan, Iran
| | - Habibeh Hajian Maleki
- Department of Plant Protection, College of Agriculture, University of Tehran, Karaj 31587-77871, Iran
| | - Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Marie-Agnes Jacques
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
| | - Perrine Portier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, CIRM-CFBP, F-49000 Angers, France
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4
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Arizala D, Dobhal S, Alvarez AM, Arif M. Elevation of Clavibacter michiganensis subsp. californiensis to species level as Clavibacter californiensis sp. nov., merging and re-classification of Clavibacter michiganensis subsp. chilensis and Clavibacter michiganensis subsp. phaseoli as Clavibacter phaseoli sp. nov. based on complete genome in silico analyses. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Gram-positive genus
Clavibacter
is currently divided into seven species (
Clavibacter michiganensis
,
Clavibacter nebraskensis
,
Clavibacter capsici
,
Clavibacter sepedonicus
,
Clavibacter tessellarius
,
Clavibacter insidiosus
and
Clavibacter zhangzhiyongii
) and three subspecies (
C. michiganensis
subsp.
californiensis
,
C. michiganensis
subsp.
chilensis
and
C. michiganensis
subsp.
phaseoli
). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three
C. michiganensis
subspecies and clarified the taxonomic nomenclature of other 75
Clavibacter
strains. The complete genomes of the type strains of the three
Clavibacter
subspecies, the type strain of
C. tessellarius
and
C. nebraskensis
A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA–DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising
C. michiganensis
subsp.
californiensis
to the species level. These results led us to propose the establishment of Clavibacter californiensis sp. nov. as a species with its type strain C55T (=CFBP 8216T=ATCC BAA-2691T). Moreover, the orthologous and in silico dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between
C. michiganensis
subsp.
chilensis
and
C. michiganensis
subsp.
phaseoli
. Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as Clavibacter phaseoli sp. nov., with LPPA 982T (= CECT 8144T= LMG 27667T) as the type strain.
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Affiliation(s)
- Dario Arizala
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Shefali Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawai'i at Manoa, Honolulu, HI 96822, USA
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Oh EJ, Hwang IS, Park IW, Oh CS. Comparative Genome Analyses of Clavibacter michiganensis Type Strain LMG7333 T Reveal Distinct Gene Contents in Plasmids From Other Clavibacter Species. Front Microbiol 2022; 12:793345. [PMID: 35178040 PMCID: PMC8844524 DOI: 10.3389/fmicb.2021.793345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Clavibacter michiganensis, a Gram-positive, plant-pathogenic bacterium belonging to Actinobacteria, is a causal agent of bacterial canker in tomatoes. Although LMG7333T is the type strain of C. michiganensis, it has not been used in many studies, probably because of a lack of the complete genome sequence being available. Therefore, in this study, the complete genome sequence of this type strain was obtained, and comparative genome analysis was conducted with the genome sequences of two other C. michiganensis strains and type strains of Clavibacter species, of which their complete genome sequences are available. C. michiganensis LMG7333T carries one chromosome and two plasmids, pCM1 and pCM2, like two other C. michiganensis strains. All three chromosomal DNA sequences were almost identical. However, the DNA sequences of two plasmids of LMG7333T are similar to those of UF1, but different from those of NCPPB382, indicating that both plasmids carry distinct gene content among C. michiganensis strains. Moreover, 216 protein-coding sequences (CDSs) were only present in the LMG7333T genome compared with type strains of other Clavibacter species. Among these 216 CDSs, approximately 83% were in the chromosome, whereas others were in both plasmids (more than 6% in pCM1 and 11% in pCM2). However, the ratio of unique CDSs of the total CDSs in both plasmids were approximately 38% in pCM1 and 30% in pCM2, indicating that the high gene content percentage in both plasmids of C. michiganensis are different from those of other Clavibacter species, and plasmid DNAs might be derived from different origins. A virulence assay with C. michiganensis LMG7333T using three different inoculation methods, root-dipping, leaf-clipping, and stem injection, resulted in typical disease symptoms, including wilting and canker in tomato. Altogether, our results indicate that two plasmids of C. michiganensis carry distinct gene content, and the genome information of the type strain LMG7333T will help to understand the genetic diversity of the two plasmids of Clavibacter species, including C. michiganensis.
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Affiliation(s)
- Eom-Ji Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Sun Hwang
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - In Woong Park
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea
| | - Chang-Sik Oh
- Department of Horticultural Biotechnology, College of Life Science, Kyung Hee University, Yongin, South Korea.,Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
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6
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Wang L, Tian Q, Zhou P, Zhao W, Sun X. Evaluation of Droplet Digital PCR for the Detection of Black Canker Disease in Tomato. PLANT DISEASE 2022; 106:395-405. [PMID: 34569829 DOI: 10.1094/pdis-02-21-0317-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis, the cause of bacterial canker disease, is one of the most destructive pathogens in greenhouse and field tomato. The pathogen is now present in all main production areas of tomato and is widely distributed in the European and Mediterranean Plant Protection Organization region. The inspection and quarantine of the plant pathogens relies heavily on accurate detection tools. Primers and probes reported in previous studies do not distinguish the C. michiganensis subsp. michiganensis pathogen from other closely related subspecies of C. michiganensis, especially the nonpathogenic subspecies that were identified from tomato seeds recently. Here, we have developed a droplet digital PCR (ddPCR) method for the identification of this specific bacterium with primers/TaqMan probe set designed based on the pat-1 gene of C. michiganensis subsp. michiganensis. This new primers/probe set has been evaluated by real-time PCR (qPCR) and ddPCR. The detection results suggest that the ddPCR method established in this study was highly specific for the target strains. The result showed the positive amplification for all five C. michiganensis subsp. michiganensis strains, and no amplification was observed for the other 43 tested bacteria, including the closely related C. michiganensis strains. The detection threshold of ddPCR was 10.8 CFU/ml for both pure C. michiganensis subsp. michiganensis cell suspensions and infected tomato seed, which was 100-fold more sensitive than qPCR performed using the same primers and probe. The data obtained suggest that our established ddPCR could detect C. michiganensis subsp. michiganensis even with low bacterial load, which could facilitate both C. michiganensis subsp. michiganensis inspection for pathogen quarantine and the routine pathogen detection for disease control of black canker in tomato.
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Affiliation(s)
- Li Wang
- Laboratory of Plant Immunity and Plant Disease Ecological Control, College of Plant Protection, Southwest University, Chongqing 400716, China
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Guizhou Academy of Forestry, Guiyang 550011, China
| | - Qian Tian
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Pei Zhou
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wenjun Zhao
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xianchao Sun
- Laboratory of Plant Immunity and Plant Disease Ecological Control, College of Plant Protection, Southwest University, Chongqing 400716, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing 400716, China
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Valenzuela M, González M, Velásquez A, Dorta F, Montenegro I, Besoain X, Salvà-Serra F, Jaén-Luchoro D, Moore ERB, Seeger M. Analyses of Virulence Genes of Clavibacter michiganensis subsp. michiganensis Strains Reveal Heterogeneity and Deletions That Correlate with Pathogenicity. Microorganisms 2021; 9:microorganisms9071530. [PMID: 34361965 PMCID: PMC8305413 DOI: 10.3390/microorganisms9071530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/07/2021] [Accepted: 07/15/2021] [Indexed: 12/04/2022] Open
Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is the causal agent of bacterial canker of tomato. Differences in virulence between Cmm strains have been reported. The aim of this study was the characterization of nine Cmm strains isolated in Chile to reveal the causes of their differences in virulence. The virulence assays in tomato seedlings revealed different levels of severity associated with the strains, with two highly virulent strains and one causing only mild symptoms. The two most virulent showed increased cellulase activity, and no cellulase activity was observed in the strain causing mild symptoms. In three strains, including the two most virulent strains, PCR amplification of the 10 virulence genes analyzed was observed. In the strain causing mild symptoms, no amplification was observed for five genes, including celA. Sequence and cluster analyses of six virulence genes grouped the strains, as has been previously reported, except for gene pelA1. Gene sequence analysis from the genomes of five Chilean strains revealed the presence of deletions in the virulence genes, celB, xysA, pat-1, and phpA. The results of this study allow us to establish correlations between the differences observed in disease severity and the presence/absence of genes and deletions not previously reported.
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Affiliation(s)
- Miryam Valenzuela
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
- Centro de Biotecnología “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, Valparaíso 2390136, Chile;
- Correspondence: (M.V.); (M.S.)
| | - Marianela González
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile;
| | - Alexis Velásquez
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
- Centro de Biotecnología “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, Valparaíso 2390136, Chile;
| | - Fernando Dorta
- Centro de Biotecnología “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, Valparaíso 2390136, Chile;
| | - Iván Montenegro
- Escuela de Obstetricia y Puericultura, Facultad de Medicina, Universidad de Valparaíso, Valparaíso 2540064, Chile;
| | - Ximena Besoain
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile;
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, 071 22 Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, SE-41346 Gothenburg, Sweden
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
- Centro de Biotecnología “Dr. Daniel Alkalay Lowitt”, Universidad Técnica Federico Santa María, Valparaíso 2390136, Chile;
- Correspondence: (M.V.); (M.S.)
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8
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Multiplex recombinase polymerase amplification assay developed using unique genomic regions for rapid on-site detection of genus Clavibacter and C. nebraskensis. Sci Rep 2021; 11:12017. [PMID: 34103568 PMCID: PMC8187419 DOI: 10.1038/s41598-021-91336-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 05/19/2021] [Indexed: 11/08/2022] Open
Abstract
Clavibacter is an agriculturally important bacterial genus comprising nine host-specific species/subspecies including C. nebraskensis (Cn), which causes Goss's wilt and blight of maize. A robust, simple, and field-deployable method is required to specifically detect Cn in infected plants and distinguish it from other Clavibacter species for quarantine purposes and timely disease management. A multiplex Recombinase Polymerase Amplification (RPA) coupled with a Lateral Flow Device (LFD) was developed for sensitive and rapid detection of Clavibacter and Cn directly from infected host. Unique and conserved genomic regions, the ABC transporter ATP-binding protein CDS/ABC-transporter permease and the MFS transporter gene, were used to design primers/probes for specific detection of genus Clavibacter and Cn, respectively. The assay was evaluated using 52 strains, representing all nine species/subspecies of Clavibacter, other closely related bacterial species, and naturally- and artificially-infected plant samples; no false positives or negatives were detected. The RPA reactions were also incubated in a closed hand at body temperature; results were again specific. The assay does not require DNA isolation and can be directly performed using host sap. The detection limit of 10 pg (~ 3000 copies) and 100 fg (~ 30 copies) was determined for Clavibacter- and Cn-specific primers/probes, respectively. The detection limit for Cn-specific primer/probe set was decreased to 1 pg (~ 300 copies) when 1 µL of host sap was added into the RPA reaction containing tenfold serially diluted genomic DNA; though no effect was observed on Clavibacter-specific primer/probe set. The assay is accurate and has applications at point-of-need diagnostics. This is the first multiplex RPA assay for any plant pathogen.
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9
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Tian Q, Chuan J, Sun X, Zhou A, Wang L, Zou J, Zhao W, Li X. Description of Clavibacter zhangzhiyongii sp. nov., a phytopathogenic actinobacterium isolated from barley seeds, causing leaf brown spot and decline. Int J Syst Evol Microbiol 2021; 71:004786. [PMID: 33983875 PMCID: PMC8289203 DOI: 10.1099/ijsem.0.004786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/21/2021] [Indexed: 11/18/2022] Open
Abstract
Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies, five of which have been redefined as different species on the basis of their genome sequence data. On the basis of the results of phylogenetic analysis of dnaA gene sequences, strains of members of the genus Clavibacter isolated from barley have been grouped in a separate clade from other species and subspecies of the genus Clavibacter. In this study, the biochemical, physiological, fatty acids and genetic characteristics of strains DM1T and DM3, which represented the barley isolates, were examined. On the basis of results from multi-locus sequence typing and other biochemical and physiological features, including colony colour, carbon source utilisation and enzyme activities, DM1T and DM3 are categorically differentiated from the aforementioned eight species and subspecies of the genus Clavibacter. Moreover, the results of genomic analysis reveal that the DNA G+C contents of DM1T and DM3 are 73.7 and 73.5 %, respectively, and the average nucleotide identity (ANI) values between DM1T and DM3 and other species and subspecies range from 90.4 to 92.0 %. The ANI value between DM1T and DM3 is 98.0 %. These results indicate that DM1T and DM3 are distinct from other known species and subspecies of the genus Clavibacter. Therefore, we propose a novel species, C. zhangzhiyongii, with DM1T (=CFCC 16553 T=LMG 31970T) as the type strain.
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Affiliation(s)
- Qian Tian
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Jiacheng Chuan
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, Charlottetown, PE C1A 5T1, Canada
| | - Xianchao Sun
- College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Aiguo Zhou
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, Charlottetown, PE C1A 5T1, Canada
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Li Wang
- College of Plant Protection, Southwest University, Chongqing 400715, PR China
| | - Jixing Zou
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, PR China
| | - Wenjun Zhao
- Institute of Plant Quarantine Research, Chinese Academy of Inspection and Quarantine, Beijing 100176, PR China
| | - Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, Charlottetown, PE C1A 5T1, Canada
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10
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Ramachandran S, Dobhal S, Alvarez AM, Arif M. Improved multiplex TaqMan qPCR assay with universal internal control offers reliable and accurate detection of Clavibacter michiganensis. J Appl Microbiol 2021; 131:1405-1416. [PMID: 33484618 DOI: 10.1111/jam.15017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/16/2020] [Accepted: 01/21/2021] [Indexed: 11/27/2022]
Abstract
AIM Clavibacter michiganensis (Cm) is a seed-borne plant pathogen that significantly reduces tomato production worldwide. Due to repeated outbreaks and rapid spread of the disease, seeds/transplants need to be certified free of the pathogen before planting. To this end, we developed a multiplex TaqMan qPCR assay that can accurately detect Cm in infected samples. METHODS AND RESULTS A specific region of Cm (clvG gene) was selected for primer design using comparative genomics approach. A fully synthetic universal internal control (UIC) was also designed to detect PCR inhibitors and false-negative results in qPCRs. The Cm primers can be used alone or in a triplex TaqMan qPCR assay with UIC and previously described Clavibacter primers. The assay was specific for Cm and detected up to 10 fg of Cm DNA in sensitivity and spiked assays. Addition of the UIC did not change the specificity or sensitivity of the multiplex TaqMan qPCR assay. CONCLUSION The triplex TaqMan qPCR provides a specific and sensitive diagnostic assay for Cm. SIGNIFICANCE AND IMPACT OF THE STUDY This assay can be used for biosecurity surveillance, routine diagnostics, estimating bacterial titres in infected material and for epidemiological studies. The UIC is fully synthetic, efficiently amplified and multiplex compatible with any other qPCR assay.
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Affiliation(s)
- S Ramachandran
- Foreign Disease and Weed Science Research Unit, USDA-ARS, Fort Detrick, MD, USA.,ARS Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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11
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Méndez V, Valenzuela M, Salvà-Serra F, Jaén-Luchoro D, Besoain X, Moore ERB, Seeger M. Comparative Genomics of Pathogenic Clavibacter michiganensis subsp. michiganensis Strains from Chile Reveals Potential Virulence Features for Tomato Plants. Microorganisms 2020; 8:microorganisms8111679. [PMID: 33137950 PMCID: PMC7692107 DOI: 10.3390/microorganisms8111679] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
The genus Clavibacter has been associated largely with plant diseases. The aims of this study were to characterize the genomes and the virulence factors of Chilean C. michiganensis subsp. michiganensis strains VL527, MSF322 and OP3, and to define their phylogenomic positions within the species, Clavibacter michiganensis. VL527 and MSF322 genomes possess 3,396,632 and 3,399,199 bp, respectively, with a pCM2-like plasmid in strain VL527, with pCM1- and pCM2-like plasmids in strain MSF322. OP3 genome is composed of a chromosome and three plasmids (including pCM1- and pCM2-like plasmids) of 3,466,104 bp. Genomic analyses confirmed the phylogenetic relationships of the Chilean strains among C.michiganensis subsp. michiganensis and showed their low genomic diversity. Different virulence levels in tomato plants were observable. Phylogenetic analyses of the virulence factors revealed that the pelA1 gene (chp/tomA region)—that grouped Chilean strains in three distinct clusters—and proteases and hydrolases encoding genes, exclusive for each of the Chilean strains, may be involved in these observed virulence levels. Based on genomic similarity (ANIm) analyses, a proposal to combine and reclassify C. michiganensis subsp. phaseoli and subsp. chilensis at the species level, as C. phaseoli sp. nov., as well as to reclassify C. michiganensis subsp. californiensis as the species C. californiensis sp. nov. may be justified.
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Affiliation(s)
- Valentina Méndez
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
- Correspondence: (V.M.); (M.S.)
| | - Miryam Valenzuela
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
| | - Francisco Salvà-Serra
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden
- Microbiology, Department of Biology, University of the Balearic Islands, 07122 Palma de Mallorca, Spain
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Ximena Besoain
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile;
| | - Edward R. B. Moore
- Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden; (F.S.-S.); (D.J.-L.); (E.R.B.M.)
- Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, 413 46 Gothenburg, Sweden
| | - Michael Seeger
- Molecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2390123, Chile;
- Correspondence: (V.M.); (M.S.)
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12
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The endosphere bacteriome of diseased and healthy tomato plants. Arch Microbiol 2020; 202:2629-2642. [PMID: 32710156 DOI: 10.1007/s00203-020-01987-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 06/29/2020] [Accepted: 07/14/2020] [Indexed: 12/16/2022]
Abstract
Here we analyze the microbial community of healthy and diseased tomato plants to evaluate its impact on plant health. The organisms found in all samples mainly belonged to 4 phyla: Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. The Proteobacteria were the highest relative abundant within the endophytic communities of different plant organs of diseased tomato. Among endophytic bacteria of tomato, only a few taxa could be cultured. Here we showed that only a few taxa of bacteria inhabiting tomato plants could be cultured and that all plant organs have a highly diverse endophytic bacterial, whose activity might affect plant growth and development as well as health. The roots seem to be an important barrier for microbes and leaves appear to be the organs with the higher diversity which is incidentally related to plant health. Fruits also contain a complex bacterial community that appeared to be unaffected by foliar diseases such as gray leaf spot at least under the conditions studied.
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13
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Yasuhara-Bell J, Arif M, Busot GY, Mann R, Rodoni B, Stack JP. Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. Microorganisms 2020; 8:E366. [PMID: 32150860 PMCID: PMC7143919 DOI: 10.3390/microorganisms8030366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/24/2020] [Accepted: 03/03/2020] [Indexed: 02/01/2023] Open
Abstract
Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.
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Affiliation(s)
- Jarred Yasuhara-Bell
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
| | - Mohammad Arif
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Plant and Environmental Protection Sciences, University of Hawai`i at Mānoa, Honolulu, HI 96822, USA
| | - Grethel Y. Busot
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
| | - Rachel Mann
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Jobs, Precincts and Regions, Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - Brendan Rodoni
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
- Department of Jobs, Precincts and Regions, Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio Centre, La Trobe University, 5 Ring Rd, Bundoora, Victoria 3083, Australia
| | - James P. Stack
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, 4024 Throckmorton Plant Science Center, Manhattan, KS 66506, USA; (J.Y.-B.); (G.Y.B.)
- Plant Biosecurity Cooperative Research Centre, CRC for National Plant Biosecurity, Level 2, Building 22, Innovation Centre, University Drive, University of Canberra, Bruce, Australian Capital Territory, Canberra 2617, Australia; (M.A.); (R.M.); (B.R.)
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14
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Comparative Genomics and Phylogenetic Analyses Suggest Several Novel Species within the Genus Clavibacter, Including Nonpathogenic Tomato-Associated Strains. Appl Environ Microbiol 2020; 86:AEM.02873-19. [PMID: 31924620 DOI: 10.1128/aem.02873-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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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15
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Thapa SP, O'Leary M, Jacques MA, Gilbertson RL, Coaker G. Comparative Genomics to Develop a Specific Multiplex PCR Assay for Detection of Clavibacter michiganensis. PHYTOPATHOLOGY 2020; 110:556-566. [PMID: 31799900 DOI: 10.1094/phyto-10-19-0405-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Clavibacter michiganensis is a Gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial wilt and canker symptoms. Accurate detection is a crucial step in confirming outbreaks of bacterial canker and developing management strategies. A major problem with existing detection methods are false-positive and -negative results. Here, we report the use of comparative genomics of 37 diverse Clavibacter strains, including 21 strains sequenced in this study, to identify specific sequences that are C. michiganensis detection targets. Genome-wide phylogenic analyses revealed additional diversity within the genus Clavibacter. Pathogenic C. michiganensis strains varied in plasmid composition, highlighting the need for detection methods based on chromosomal targets. We utilized sequences of C. michiganensis-specific loci to develop a multiplex PCR-based diagnostic platform using two C. michiganensis chromosomal genes (rhuM and tomA) and an internal control amplifying both bacterial and plant DNA (16s ribosomal RNA). The multiplex PCR assay specifically detected C. michiganensis strains from a panel of 110 additional bacteria, including other Clavibacter spp. and bacterial pathogens of tomato. The assay was adapted to detect the presence of C. michiganensis in seed and tomato plant materials with high sensitivity and specificity. In conclusion, the described method represents a robust, specific tool for detection of C. michiganensis in tomato seed and infected plants.
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Affiliation(s)
- Shree P Thapa
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | - Michael O'Leary
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | - Marie-Agnès Jacques
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 Quasav, Beaucouzé, France
| | | | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, U.S.A
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16
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Multiple Introductions of Tomato Pathogen Clavibacter michiganensis subsp. michiganensis into Iran as Revealed by a Global-Scale Phylogeographic Analysis. Appl Environ Microbiol 2019; 85:AEM.02098-19. [PMID: 31604763 DOI: 10.1128/aem.02098-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 09/25/2019] [Indexed: 11/20/2022] Open
Abstract
Tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most important seed-borne tomato diseases around the globe. The disease was initially reported in 1993 in Iran, and it became a rising threat for the multibillion dollar tomato industry of the country during the last decade. In this study, using phylogeographic analyses, we determined genetic diversity and geographic distribution of C. michiganensis subsp. michiganensis in Iran. Our field surveys showed that the pathogen is expanding into the southern and eastern areas of the country. Furthermore, multilocus sequence analysis and typing (MLSA/MLST) using the sequences of five housekeeping genes (atpD, gyrB, ppk, recA, and rpoB) revealed that 37 C. michiganensis subsp. michiganensis strains isolated in Iran had high genetic diversity and placed in 15 sequence types (STs), while all the available 184 worldwide C. michiganensis subsp. michiganensis sequences were placed in 43 STs. MLSA divided the worldwide C. michiganensis subsp. michiganensis strains into two phylogroups (I and II). Among the 37 strains isolated in Iran, 30 strains clustered in phylogroup I, while 7 strains clustered in phylogroup II. Phylogeographic data inferred from the allelic profile of the five housekeeping genes suggested multiple introductions of C. michiganensis subsp. michiganensis inoculum into Iran, while the geographic origin of the Iranian C. michiganensis subsp. michiganensis strains remains undetermined. Further analyses using higher numbers of strains are warranted to decipher the evolutionary history of C. michiganensis subsp. michiganensis in Iran. Additionally, stricter seed/transplant inspections are recommended to reduce the risk of pathogen expansion to areas with no history of the disease.IMPORTANCE Clavibacter michiganensis subsp. michiganensis, the causal agent of tomato bacterial canker disease, is one of the economically important pathogens of solanaceous crops (e.g., eggplant, pepper, and tomato) around the world. The disease occurs in many countries, with a particular importance in regions characterized by high precipitation and humid environmental conditions. As a seed-borne pathogen, C. michiganensis subsp. michiganensis is included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Bacterial canker disease was reported for the first time in 1993 in Iran, while the geographic distribution, genetic diversity, and phylogenetic position of the causal agent remain undetermined. In this study, using the multilocus sequence analysis and typing (MLSA/MLST) approach, we provided a phylogeographic scheme for the C. michiganensis subsp. michiganensis strains isolated in Iran. Furthermore, global-scale phylogenetic analyses led to determination of phylogenetic position of Iranian C. michiganensis subsp. michiganensis strains among worldwide population of the pathogen. Based on diversity parameters and population structure, we suggest relatively higher genetic diversity of the bacterial canker pathogen in Iran than has so far been observed in the other areas of the world. Results obtained in this study provide a novel insight into the genetic diversity and population structure of the bacterial canker pathogen on a global scale.
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Larrea-Sarmiento A, Alvarez AM, Stack JP, Arif M. Synergetic effect of non-complementary 5' AT-rich sequences on the development of a multiplex TaqMan real-time PCR for specific and robust detection of Clavibacter michiganensis and C. michiganensis subsp. nebraskensis. PLoS One 2019; 14:e0218530. [PMID: 31295263 PMCID: PMC6622472 DOI: 10.1371/journal.pone.0218530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/22/2019] [Indexed: 11/25/2022] Open
Abstract
Clavibacter is an agriculturally important genus comprising a single species, Clavibacter michiganensis, and multiple subspecies, including, C. michiganensis subsp. nebraskensis which causes Goss's wilt/blight of corn, accounts for high yield losses and is listed among the five most significant diseases of corn in the United States of America. Our research objective was to develop a robust and rapid multiplex TaqMan real-time PCR (qPCR) to detect C. michiganensis in general and C. michiganensis subsp. nebraskensis with enhanced reliability and accuracy by adding non-complementary AT sequences to the 5’ end of the forward and reverse primers. Comparative genomic analyses were performed to identify unique and conserved gene regions for primer and probe design. The unique genomic regions, ABC transporter ATP-binding protein CDS/ABC-transporter permease and MFS transporter were determined for specific detection of C. michiganensis and C. m. subsp. nebraskensis, respectively. The AT-rich sequences at the 5’ position of the primers enhanced the reaction efficiency and sensitivity of rapid qPCR cycling; the reliability, accuracy and high efficiency of the developed assay was confirmed after testing with 59 strains from inclusivity and exclusivity panels–no false positives or false negatives were detected. The assays were also validated through naturally and artificially infected corn plant samples; all samples were detected for C. michiganensis and C. m. subsp. nebraskensis with 100% accuracy. The assay with 5’ AT-rich sequences detected up to 10- and 100-fg of C. michiganensis and C. michiganensis subsp. nebraskensis genome targets, respectively. No adverse effect was observed when sensitivity assays were spiked with host genomic DNA. Addition of 5’ AT-rich sequences enhanced the qPCR reaction efficiency from 0.82 (M = -3.83) and 0.91 (M = -3.54) to 1.04 (with optimum slope value; M = -3.23) for both C. michiganensis and C. michiganensis subsp. nebraskensis, respectively; an increase of 10-fold sensitivity was also obtained with C. michiganensis primer set. The methodology proposed here can be used to optimize reaction efficiency and to harmonize diagnostic protocols which have prodigious applications in routine diagnostics, biosecurity and microbial forensics.
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Affiliation(s)
- Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - James P. Stack
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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Liu SW, Li FN, Zheng HY, Qi X, Huang DL, Xie YY, Sun CH. Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert. Int J Syst Evol Microbiol 2018; 69:616-624. [PMID: 30387709 DOI: 10.1099/ijsem.0.003095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-staining-positive, aerobic, irregular coccoid- to ovoid-shaped, non-spore-forming and motile bacterium, designated strain 13S1-3T, was isolated from a soil sample from the rhizosphere of Tamarix collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China. The strain was examined by a polyphasic approach to clarify its taxonomic position. Strain 13S1-3T grew optimally at 28-30 °C, pH 7.0 and with 0-1 % (w/v) NaCl. The cell-wall peptidoglycan was of the B2γ type and contained d-alanine, d-glutamic acid, glycine, d-2,4-diaminobutyric acid and l-2,4-diaminobutyric acid. Ribose, xylose, glucose and galactose were detected as cell-wall sugars. The acyl type of the muramic acid was acetyl. The predominant menaquinones were MK-12, MK-11, MK-13 and MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids and one unidentified phospholipid. The major whole-cell fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 70.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 13S1-3T represented a member of the family Microbacteriaceae and showed the highest level of 16S rRNA gene sequence similarity with Frondihabitans australicus E1HC-02T (97.11 %). Phylogenetic trees revealed that 13S1-3T formed a distinct lineage with respect to closely related genera within the family Microbacteriaceae. On the basis of the results of phylogenetic, phenotypic and chemotaxonomic analyses, 13S1-3T is distinguishable from phylogenetically related genera in the family Microbacteriaceae, and represents a novel species of a new genus, for which the name Planctomonas deserti gen. nov., sp. nov. is proposed. The type strain is 13S1-3T (=KCTC 49115T=CGMCC 1.16554T).
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Affiliation(s)
- Shao-Wei Liu
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Fei-Na Li
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yun Zheng
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China.,2College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, PR China
| | - Xin Qi
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Da-Lin Huang
- 2College of Basic Medical Sciences, Guilin Medical University, Guilin 541004, PR China
| | - Yun-Ying Xie
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Cheng-Hang Sun
- 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
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Dobhal S, Larrea-Sarmiento A, Alvarez AM, Arif M. Development of a loop-mediated isothermal amplification assay for specific detection of all known subspecies of Clavibacter michiganensis. J Appl Microbiol 2018; 126:388-401. [PMID: 30307676 DOI: 10.1111/jam.14128] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/02/2023]
Abstract
AIMS Clavibacter michiganensis is an important bacterial plant pathogen that causes vast destruction to agriculturally important crops worldwide. Early detection is critical to evaluate disease progression and to implement efficient control measures to avoid serious epidemics. In this study, we developed a sensitive, specific and robust loop-mediated isothermal amplification (LAMP) assay for detection of all known subspecies of C. michiganensis. METHODS AND RESULTS Whole genome comparative genomics approach was taken to identify a unique and conserved region within all known subspecies of C. michiganensis. Primer specificity was evaluated in silico and with 64 bacterial strains included in inclusivity and exclusivity panels; no false positives or false negatives were detected. Both the sensitivity and spiked assay of the developed LAMP assay was 1 fg of the pathogen DNA per reaction. A 100% accuracy was observed when tested with infected plant samples. CONCLUSIONS The developed LAMP assay is simple, sensitive, robust and easy to perform using different detection platforms and chemistries. SIGNIFICANCE AND IMPACT OF THE STUDY The developed LAMP assay can detect all known subspecies of C. michiganensis. The LAMP process can be performed isothermally at 65°C and results can be visually assessed, which makes this technology a promising tool for monitoring the disease progression and for accurate pathogen detection at point-of-care.
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Affiliation(s)
- S Dobhal
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - A M Alvarez
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - M Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
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Draft Genome Sequences of the Type Strains of Three Clavibacter Subspecies and Atypical Peach-Colored Strains Isolated from Tomato. Microbiol Resour Announc 2018; 7:MRA01357-18. [PMID: 30533783 PMCID: PMC6256548 DOI: 10.1128/mra.01357-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus. Here, we present the draft genome sequences of 10 Clavibacter sp. strains, including the type strains of different subspecies of Clavibacter michiganensis and a potentially novel species within the genus. Genome lengths of the strains varied between 2,982,864 and 3,288,331 bp, with G+C contents of 72.23 to 73.50%.
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21
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Osdaghi E, Taghavi SM, Calamai S, Biancalani C, Cerboneschi M, Tegli S, Harveson RM. Phenotypic and Molecular-Phylogenetic Analysis Provide Novel Insights into the Diversity of Curtobacterium flaccumfaciens. PHYTOPATHOLOGY 2018; 108:1154-1164. [PMID: 29714091 DOI: 10.1094/phyto-12-17-0420-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A multiphasic approach was used to decipher the phenotypic features, genetic diversity, and phylogenetic position of 46 Curtobacterium spp. strains isolated from dry beans and other annual crops in Iran and Spain. Pathogenicity tests, resistance to arsenic compounds, plasmid profiling and BOX-PCR were performed on the strains. Multilocus sequence analysis (MLSA) was also performed on five housekeeping genes (i.e., atpD, gyrB, ppk, recA, and rpoB) of all the strains, as well as five pathotype strains of the species. Pathogenicity test showed that six out of 42 strains isolated in Iran were nonpathogenic on common bean. Despite no differences found between pathogenic and nonpathogenic strains in their plasmid profiling, the former were resistant to different concentrations of arsenic, while the latter were sensitive to the same concentrations. Strains pathogenic on common bean were polyphyletic with at least two evolutionary lineages (i.e., yellow-pigmented strains versus red/orange-pigmented strains). Nonpathogenic strains isolated from solanaceous vegetables were clustered within either the strains of C. flaccumfaciens pv. flaccumfaciens or different pathovars of the species. The results of MLSA and BOX-PCR analysis were similar to each other and both methods were able to discriminate the yellow-pigmented strains from the red/orange-pigmented strains. A comprehensive study of a worldwide collection representing all five pathovars as well as nonpathogenic strains of C. flaccumfaciens is warranted for a better understanding of the diversity within this phytopathogenic bacterium.
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Affiliation(s)
- Ebrahim Osdaghi
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - S Mohsen Taghavi
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - Silvia Calamai
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - Carola Biancalani
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - Matteo Cerboneschi
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - Stefania Tegli
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
| | - Robert M Harveson
- First and second authors: Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz 71441-65186, Iran; third, fourth, fifth, and sixth authors: Dipartimento di Scienze delle Produzioni Agroalimentari e dell'Ambiente, Laboratorio di Patologia Vegetale Molecolare, Università degli Studi di Firenze, Via della Lastruccia 10, 50019 Sesto Fiorentino, Firenze, Italy; and seventh author: University of Nebraska, Panhandle Research & Extension Center, 4502 Ave. I., Scottsbluff 69361
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Nandi M, Macdonald J, Liu P, Weselowski B, Yuan Z. Clavibacter michiganensis ssp. michiganensis: bacterial canker of tomato, molecular interactions and disease management. MOLECULAR PLANT PATHOLOGY 2018; 19:2036-2050. [PMID: 29528201 PMCID: PMC6638088 DOI: 10.1111/mpp.12678] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/06/2018] [Accepted: 03/07/2018] [Indexed: 05/11/2023]
Abstract
Bacterial canker disease is considered to be one of the most destructive diseases of tomato (Solanum lycopersicum), and is caused by the seed-borne Gram-positive bacterium Clavibacter michiganensis ssp. michiganensis (Cmm). This vascular pathogen generally invades and proliferates in the xylem through natural openings or wounds, causing wilt and canker symptoms. The incidence of symptomless latent infections and the invasion of tomato seeds by Cmm are widespread. Pathogenicity is mediated by virulence factors and transcriptional regulators encoded by the chromosome and two natural plasmids. The virulence factors include serine proteases, cell wall-degrading enzymes (cellulases, xylanases, pectinases) and others. Mutational analyses of these genes and gene expression profiling (via quantitative reverse transcription-polymerase chain reaction, transcriptomics and proteomics) have begun to shed light on their roles in colonization and virulence, whereas the expression of tomato genes in response to Cmm infection suggests plant factors involved in the defence response. These findings may aid in the generation of target-specific bactericides or new resistant varieties of tomato. Meanwhile, various chemical and biological controls have been researched to control Cmm. This review presents a detailed investigation regarding the pathogen Cmm, bacterial canker infection, molecular interactions between Cmm and tomato, and current perspectives on improved disease management.
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Affiliation(s)
- Munmun Nandi
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Jacqueline Macdonald
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Peng Liu
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
| | - Brian Weselowski
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
| | - Ze‐Chun Yuan
- Department of Microbiology & Immunology, Schulich School of Medicine & DentistryUniversity of Western OntarioLondonONCanada, N6A 5C1
- London Research and Development Centre, Agriculture & Agri‐Food CanadaLondonONCanada, N5V 4T3
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23
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Lu Y, Ishimaru CA, Glazebrook J, Samac DA. Comparative Genomic Analyses of Clavibacter michiganensis subsp. insidiosus and Pathogenicity on Medicago truncatula. PHYTOPATHOLOGY 2018; 108:172-185. [PMID: 28952422 DOI: 10.1094/phyto-05-17-0171-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clavibacter michiganensis is the most economically important gram-positive bacterial plant pathogen, with subspecies that cause serious diseases of maize, wheat, tomato, potato, and alfalfa. Much less is known about pathogenesis involving gram-positive plant pathogens than is known for gram-negative bacteria. Comparative genome analyses of C. michiganensis subspecies affecting tomato, potato, and maize have provided insights on pathogenicity. In this study, we identified strains of C. michiganensis subsp. insidiosus with contrasting pathogenicity on three accessions of the model legume Medicago truncatula. We generated complete genome sequences for two strains and compared these to a previously sequenced strain and genome sequences of four other subspecies. The three C. michiganensis subsp. insidiosus strains varied in gene content due to genome rearrangements, most likely facilitated by insertion elements, and plasmid number, which varied from one to three depending on strain. The core C. michiganensis genome consisted of 1,917 genes, with 379 genes unique to C. michiganensis subsp. insidiosus. An operon for synthesis of the extracellular blue pigment indigoidine, enzymes for pectin degradation, and an operon for inositol metabolism are among the unique features. Secreted serine proteases belonging to both the pat-1 and ppa families were present but highly diverged from those in other subspecies.
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Affiliation(s)
- You Lu
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Carol A Ishimaru
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Jane Glazebrook
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
| | - Deborah A Samac
- First and third authors: Department of Plant and Microbial Biology, second and fourth authors: Department of Plant Pathology, and first, second, third, and fourth authors: the Microbial and Plant Genomics Institute, University of Minnesota, St. Paul 55108; and fourth author: United States Department of Agriculture-Agricultural Research Service, Plant Science Research, St. Paul, MN 55108
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24
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Li X, Tambong J, Yuan KX, Chen W, Xu H, Lévesque CA, De Boer SH. Re-classification of Clavibacter michiganensis subspecies on the basis of whole-genome and multi-locus sequence analyses. Int J Syst Evol Microbiol 2017; 68:234-240. [PMID: 29160202 PMCID: PMC5882085 DOI: 10.1099/ijsem.0.002492] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2γ diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA-DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov.
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Affiliation(s)
- Xiang Li
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - James Tambong
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Kat Xiaoli Yuan
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - Wen Chen
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Huimin Xu
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
| | - C André Lévesque
- Agricultural and Agri-Food Canada (AAFC), Ottawa Laboratory, 960 Carling Ave, Ottawa K1A 0C6, Canada
| | - Solke H De Boer
- Canadian Food Inspection Agency (CFIA), Charlottetown Laboratory, 93 Mount Edward Road, Charlottetown, PE C1A 5T1, Canada
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25
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Thapa SP, Pattathil S, Hahn MG, Jacques MA, Gilbertson RL, Coaker G. Genomic Analysis of Clavibacter michiganensis Reveals Insight Into Virulence Strategies and Genetic Diversity of a Gram-Positive Bacterial Pathogen. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:786-802. [PMID: 28677494 DOI: 10.1094/mpmi-06-17-0146-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial canker disease. In this study, we sequenced and assembled genomes of 11 C. michiganensis subsp. michiganensis strains isolated from infected tomato fields in California as well as five Clavibacter strains that colonize tomato endophytically but are not pathogenic in this host. The analysis of the C. michiganensis subsp. michiganensis genomes supported the monophyletic nature of this pathogen but revealed genetic diversity among strains, consistent with multiple introduction events. Two tomato endophytes that clustered phylogenetically with C. michiganensis strains capable of infecting wheat and pepper and were also able to cause disease in these plants. Plasmid profiles of the California strains were variable and supported the essential role of the pCM1-like plasmid and the CelA cellulase in virulence, whereas the absence of the pCM2-like plasmid in some pathogenic C. michiganensis subsp. michiganensis strains revealed it is not essential. A large number of secreted C. michiganensis subsp. michiganensis proteins were carbohydrate-active enzymes (CAZymes). Glycome profiling revealed that C. michiganensis subsp. michiganensis but not endophytic Clavibacter strains is able to extensively alter tomato cell-wall composition. Two secreted CAZymes found in all C. michiganensis subsp. michiganensis strains, CelA and PelA1, enhanced pathogenicity on tomato. Collectively, these results provide a deeper understanding of C. michiganensis subsp. michiganensis diversity and virulence strategies.
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Affiliation(s)
- Shree P Thapa
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Sivakumar Pattathil
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | - Michael G Hahn
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | | | - Robert L Gilbertson
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Gitta Coaker
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
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26
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Genome Sequences for Multiple Clavibacter Strains from Different Subspecies. GENOME ANNOUNCEMENTS 2017; 5:5/38/e00721-17. [PMID: 28935724 PMCID: PMC5609403 DOI: 10.1128/genomea.00721-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Gram-positive genus Clavibacter harbors economically important plant pathogens infecting a variety of agricultural crops, such as potato, tomato, corn, barley, etc. Here, we report five new genome sequences, those of strains CFIA-Cs3N, CFIA-CsR14, LMG 3663T, LMG 7333T, and ATCC 33566T, from different subspecies of Clavibacter michiganensis All these genomic data will be used for reclassification and niche-adapted feature comparisons.
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27
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Hąc-Wydro K, Flasiński M, Broniatowski M, Sołtys M. Studies on the Behavior of Eucalyptol and Terpinen-4-ol-Natural Food Additives and Ecological Pesticides-in Model Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6916-6924. [PMID: 28654274 DOI: 10.1021/acs.langmuir.7b00774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Effective application of the essential oils requires detailed exploration of their mechanism of action and the origin of diverse activity of their components. In this work, the influence of eucalyptol and terpinen-4-ol on artificial membranes was studied to verify whether the differences in the activity of these compounds are related to their effect on membranes. The properties of monolayers formed from structurally different lipids in the presence of terpenes were examined based on the results of the surface pressure-area measurements, penetration studies, and Brewster angle microscopy experiments. Both compounds were able to incorporate into the membrane and alter lipid/lipid interactions, making the monolayer less stable and more fluid. These effects were determined by monolayer composition (but not by its condensation per se) and the resulting rheological properties and were stronger in the presence of terpinen-4-ol. These findings confirm the hypothesis that differences in the antimicrobial potency of these terpenes are membrane-related, and membrane composition may determine their selectivity.
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Affiliation(s)
- Katarzyna Hąc-Wydro
- Department of Environmental Chemistry, Faculty of Chemistry, Jagiellonian University , Gronostajowa 3, 30-387, Kraków, Poland
| | - Michał Flasiński
- Department of Environmental Chemistry, Faculty of Chemistry, Jagiellonian University , Gronostajowa 3, 30-387, Kraków, Poland
| | - Marcin Broniatowski
- Department of Environmental Chemistry, Faculty of Chemistry, Jagiellonian University , Gronostajowa 3, 30-387, Kraków, Poland
| | - Monika Sołtys
- Department of Environmental Chemistry, Faculty of Chemistry, Jagiellonian University , Gronostajowa 3, 30-387, Kraków, Poland
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Yasuhara‐Bell J, Marrero G, De Silva A, Alvarez AM. Specific detection of Pectobacterium carotovorum by loop-mediated isothermal amplification. MOLECULAR PLANT PATHOLOGY 2016; 17:1499-1505. [PMID: 26833881 PMCID: PMC6638492 DOI: 10.1111/mpp.12378] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/13/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
Potatoes are an important agroeconomic crop worldwide and maceration diseases caused by pectolytic bacterial pathogens result in significant pre- and post-harvest losses. Pectobacterium carotovorum shares a common host range with other Pectobacterium spp. and other members of the Enterobacteriaceae, such as Dickeya spp. As these pathogens cannot be clearly differentiated on the basis of the symptoms they cause, improved methods of identification are critical for the determination of sources of contamination. Current standardized methods for the differentiation of pectolytic species are time consuming and require trained personnel, as they rely on traditional bacteriological practices that do not always produce conclusive results. In this growing world market, there is a need for rapid diagnostic tests that can differentiate between pectolytic pathogens, as well as separate them from non-pectolytic enteric bacteria associated with soft rots of potato. An assay has been designed previously to detect the temperate pathogen Pectobacterium atrosepticum, but there is currently no recognized rapid assay for the detection of the tropical/subtropical counterpart, Pectobacterium carotovorum. This report describes the development of a loop-mediated isothermal amplification (LAMP) assay that detects P. carotovorum with high specificity. The assay was evaluated using all known species of Pectobacterium and only showed positive reactions for P. carotovorum. This assay was also tested against 15 non-target genera of plant-associated bacteria and did not produce any false positives. The LAMP assay described here can be used as a rapid test for the differentiation of P. carotovorum from other pectolytic pathogens, and its gene target can be the basis for the development of other molecular-based detection assays.
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Affiliation(s)
- Jarred Yasuhara‐Bell
- Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human ResourcesUniversity of Hawai‘i at Mānoa3190 Maile Way, St. John Room 315HonoluluHI96822USA
| | - Glorimar Marrero
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human ResourcesUniversity of Hawai‘i at Mānoa3190 Maile Way, St. John Room 315HonoluluHI96822USA
| | - Asoka De Silva
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human ResourcesUniversity of Hawai‘i at Mānoa3190 Maile Way, St. John Room 315HonoluluHI96822USA
| | - Anne M. Alvarez
- Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human ResourcesUniversity of Hawai‘i at Mānoa3190 Maile Way, St. John Room 315HonoluluHI96822USA
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McNally RR, Ishimaru CA, Malvick DK. PCR-Mediated Detection and Quantification of the Goss's Wilt Pathogen Clavibacter michiganensis subsp. nebraskensis Via a Novel Gene Target. PHYTOPATHOLOGY 2016; 106:1465-1472. [PMID: 27442535 DOI: 10.1094/phyto-05-16-0190-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Goss's leaf blight and wilt of maize (corn) is a significant and reemerging disease caused by the bacterium Clavibacter michiganensis subsp. nebraskensis. Despite its importance, molecular tools for diagnosing and studying this disease remain limited. We report the identification of CMN_01184 as a novel gene target and its use in conventional PCR (cPCR) and SYBR green-based quantitative PCR (qPCR) assays for specific detection and quantification of C. michiganensis subsp. nebraskensis. The cPCR and qPCR assays based on primers targeting CMN_01184 specifically amplified only C. michiganensis subsp. nebraskensis among a diverse collection of 129 bacterial and fungal isolates, including multiple maize bacterial and fungal pathogens, environmental organisms from agricultural fields, and all known subspecies of C. michiganensis. Specificity of the assays for detection of only C. michiganensis subsp. nebraskensis was also validated with field samples of C. michiganensis subsp. nebraskensis-infected and uninfected maize leaves and C. michiganensis subsp. nebraskensis-infested and uninfested soil. Detection limits were determined at 30 and 3 ng of pure C. michiganensis subsp. nebraskensis DNA, and 100 and 10 CFU of C. michiganensis subsp. nebraskensis for the cPCR and qPCR assays, respectively. Infection of maize leaves by C. michiganensis subsp. nebraskensis was quantified from infected field samples and was standardized using an internal maize DNA control. These novel, specific, and sensitive PCR assays based on CMN_01184 are effective for diagnosis of Goss's wilt and for studies of the epidemiology and host-pathogen interactions of C. michiganensis subsp. nebraskensis.
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Affiliation(s)
- R Ryan McNally
- First, second, and third authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; and second and third authors: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota
| | - Carol A Ishimaru
- First, second, and third authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; and second and third authors: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota
| | - Dean K Malvick
- First, second, and third authors: Department of Plant Pathology, University of Minnesota, St. Paul 55108; and second and third authors: Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota
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30
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Clavibacter michiganensis subsp. capsici subsp. nov., causing bacterial canker disease in pepper. Int J Syst Evol Microbiol 2016; 66:4065-4070. [DOI: 10.1099/ijsem.0.001311] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Yasuhara-Bell J, de Silva A, Heuchelin SA, Chaky JL, Alvarez AM. Detection of Goss's Wilt Pathogen Clavibacter michiganensis subsp. nebraskensis in Maize by Loop-Mediated Amplification. PHYTOPATHOLOGY 2016; 106:226-235. [PMID: 26595113 DOI: 10.1094/phyto-10-15-0249-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The Goss's wilt pathogen, Clavibacter michiganensis subsp. nebraskensis, can cause considerable losses in maize (Zea mays) production. Diagnosis of Goss's wilt currently is based on symptomology and identification of C. michiganensis subsp. nebraskensis, following isolation on a semiselective medium and/or serological testing. In an effort to provide a more efficient identification method, a loop-mediated amplification (LAMP) assay was developed to detect the tripartite ATP-independent periplasmic (TRAP)-type C4-dicarboxylate transport system large permease component and tested using strains of C. michiganensis subsp. nebraskensis, all other C. michiganensis subspecies and several genera of nontarget bacteria. Only strains of C. michiganensis subsp. nebraskensis reacted positively with the LAMP assay. The LAMP assay was then used to identify bacterial isolates from diseased maize. 16S rDNA and dnaA sequence analyses were used to confirm the identity of the maize isolates and validate assay specificity. The Cmm ImmunoStrip assay was included as a presumptive identification test of C. michiganensis subsp. nebraskensis at the species level. The Cmn-LAMP assay was further tested using symptomatic leaf tissue. The Cmn-LAMP assay was run in a hand-held real-time monitoring device (SMART-DART) and performed equally to in-lab quantitative polymerase chain reaction equipment. The Cmn-LAMP assay accurately identified C. michiganensis subsp. nebraskensis and has potential as a field test. The targeted sequence also has potential application in other molecular detection platforms.
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Affiliation(s)
- Jarred Yasuhara-Bell
- First author: Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and second and fifth authors: Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and third and fourth authors: DuPont Pioneer, Johnston, IA 50131
| | - Asoka de Silva
- First author: Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and second and fifth authors: Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and third and fourth authors: DuPont Pioneer, Johnston, IA 50131
| | - Scott A Heuchelin
- First author: Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and second and fifth authors: Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and third and fourth authors: DuPont Pioneer, Johnston, IA 50131
| | - Jennifer L Chaky
- First author: Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and second and fifth authors: Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and third and fourth authors: DuPont Pioneer, Johnston, IA 50131
| | - Anne M Alvarez
- First author: Department of Molecular Biosciences and Bioengineering, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and second and fifth authors: Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Mānoa, Honolulu 96822; and third and fourth authors: DuPont Pioneer, Johnston, IA 50131
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Bae C, Oh EJ, Lee HB, Kim BY, Oh CS. Complete genome sequence of the cellulase-producing bacterium Clavibacter michiganensis PF008. J Biotechnol 2015; 214:103-4. [DOI: 10.1016/j.jbiotec.2015.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/21/2015] [Indexed: 11/16/2022]
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