Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola |
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Authors: | X Li J Nie L Ward M Madani T Hsiang Y Zhao SH De Boer |
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Institution: | Canadian Food Inspection Agency, Charlottetown Laboratory, Charlottetown, PE, Canada; Department of Environmental Biology, University of Guelph, Guelph, ON, Canada; Department of Crop Sciences, University of Illinois, Urbana, IL, USA |
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Abstract: | Aims: To design and evaluate a loop-mediated isothermal amplification (LAMP) protocol by combining comparative genomics and bioinformatics for characterization of Pseudomonas syringae pv. phaseolicola (PSP), the causal agent of halo blight disease of bean ( Phaseolus vulgaris L.). Methods and Results: Genomic sequences of Pseudomonas syringae pathovars, P. fluorescens and P. aeruginosa were analysed using multiple sequence alignment. A pathovar-specific region encoding pathogenicity-related secondary metabolites in the PSP genome was targeted for developing a LAMP assay. The final assay targeted a polyketide synthase gene, and readily differentiated PSP strains from other Pseudomonas syringae pathovars and other Pseudomonas species, as well as other plant pathogenic bacteria, e.g. species of Pectobacterium , Erwinia and Pantoea . Conclusion: A LAMP assay has been developed for rapid and specific characterization and identification of PSP from other pathovars of P. syringae and other plant-associated bacteria . Significance and Impact of the Study: This paper describes an approach combining a bioinformatic data mining strategy and comparative genomics with the LAMP technology for characterization and identification of a plant pathogenic bacterium. The LAMP assay could serve as a rapid protocol for microbial identification and detection with significant applications in agriculture and environmental sciences. |
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Keywords: | characterization comparative genomics detection loop-mediated isothermal amplification Pseudomonas syringae pv phaseolicola |
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