Phytopathology (2016) 106, 1473-1485

James T. Tambong, Renlin Xu, Fouad Daayf, Stephan Brière, Guillaume J. Bilodeau, Raymond Tropiano, Allison Hartke, Lana M. Reid, Morgan Cott, Tammy Cote and Irina Agarkova (2016)
Genome analysis and development of a multiplex TaqMan real-time PCR for specific identification and detection of Clavibacter michiganensis subsp. nebraskensis
Phytopathology 106 (12), 1473-1485
Abstract: The reemergence of the Goss's bacterial wilt and blight disease in corn in the United States and Canada has prompted investigative research to better understand the genome organization. In this study, we generated a draft genome sequence of Clavibacter michiganensis subsp. nebraskensis strain DOAB 395 and performed genome and proteome analysis of C. michiganensis subsp. nebraskensis strains isolated in 2014 (DOAB 397 and DOAB 395) compared with the type strain, NCPPB 2581 (isolated over 40 years ago). The proteomes of strains DOAB 395 and DOAB 397 exhibited a 99.2% homology but had 92.1 and 91.8% homology, respectively, with strain NCPPB 2581. The majority (99.9%) of the protein sequences had a 99.6 to 100% homology between C. michiganensis subsp. nebraskensis strains DOAB 395 and DOAB 397, with only four protein sequences (0.1%) exhibiting a similarity <70%. In contrast, 3.0% of the protein sequences of strain DOAB 395 or DOAB 397 showed low homologies (<70%) with the type strain NCPPB 2581. The genome data were exploited for the development of a multiplex TaqMan real-time polymerase chain reaction (PCR) tool for rapid detection of C. michiganensis subsp. nebraskensis. The specificity of the assay was validated using 122 strains of Clavibacter and non-Clavibacter spp. A blind test and naturally infected leaf samples were used to confirm specificity. The sensitivity (0.1 to 1.0 pg) compared favorably with previously reported real-time PCR assays. This tool should fill the current gap for a reliable diagnostic technique.
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Link to article at publishers website
Database assignments for author(s): James T. Tambong, Fouad Daayf, Guillaume J. Bilodeau

Research topic(s) for pests/diseases/weeds:
molecular biology - genes
surveys/sampling/distribution

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Pest and/or beneficial records:

Beneficial	Pest/Disease/Weed	Crop/Product	Country	Quarant.
	Clavibacter nebraskensis	Maize/corn (Zea mays)