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Comparative genomics‐guided loop‐mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola
Author(s) -
Li X.,
Nie J.,
Ward L.,
Madani M.,
Hsiang T.,
Zhao Y.,
De Boer S.H.
Publication year - 2009
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/j.1365-2672.2009.04262.x
Subject(s) - pseudomonas syringae , biology , pathovar , microbiology and biotechnology , comparative genomics , pathogenic bacteria , pseudomonas fluorescens , pseudomonas , genomics , genome , bacteria , pseudomonadaceae , genetics , pathogen , gene
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.