Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola
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.). Genomic sequences of Pseu...
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| Veröffentlicht in: | Journal of applied microbiology 2009-09, Vol.107 (3), p.717-726 |
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| creator | Li, X Nie, J Ward, L Madani, M Hsiang, T Zhao, Y De Boer, S.H |
| description | 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.). 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. 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. 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. |
| doi_str_mv | 10.1111/j.1365-2672.2009.04262.x |
| format | Article |
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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. 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. 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.</description><identifier>ISSN: 1364-5072</identifier><identifier>EISSN: 1365-2672</identifier><identifier>DOI: 10.1111/j.1365-2672.2009.04262.x</identifier><identifier>PMID: 19486391</identifier><language>eng</language><publisher>Oxford, UK: Oxford, UK : Blackwell Publishing Ltd</publisher><subject>Bacterial Proteins - genetics ; Biological and medical sciences ; characterization ; comparative genomics ; detection ; DNA Primers - genetics ; Erwinia ; Fundamental and applied biological sciences. Psychology ; loop-mediated isothermal amplification ; Microbiology ; Nucleic Acid Amplification Techniques - methods ; Pectobacterium ; Phaseolus - virology ; Phaseolus vulgaris ; Polyketide Synthases - genetics ; Pseudomonas aeruginosa ; Pseudomonas aeruginosa - genetics ; Pseudomonas fluorescens - genetics ; Pseudomonas syringae ; Pseudomonas syringae - genetics ; Pseudomonas syringae - isolation & purification ; Pseudomonas syringae pv. phaseolicola ; Sensitivity and Specificity ; Sequence Alignment ; Sequence Analysis, DNA</subject><ispartof>Journal of applied microbiology, 2009-09, Vol.107 (3), p.717-726</ispartof><rights>2009 The Authors. Journal compilation © 2009 The Society for Applied Microbiology</rights><rights>2009 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4532-537feeaeb26f2fde35966e7145d4ab4eb8e6b718d5d3f00f6e620f126a7fcbba3</citedby><cites>FETCH-LOGICAL-c4532-537feeaeb26f2fde35966e7145d4ab4eb8e6b718d5d3f00f6e620f126a7fcbba3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1111%2Fj.1365-2672.2009.04262.x$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2Fj.1365-2672.2009.04262.x$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>315,781,785,1418,27929,27930,45579,45580</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21834531$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/19486391$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Li, X</creatorcontrib><creatorcontrib>Nie, J</creatorcontrib><creatorcontrib>Ward, L</creatorcontrib><creatorcontrib>Madani, M</creatorcontrib><creatorcontrib>Hsiang, T</creatorcontrib><creatorcontrib>Zhao, Y</creatorcontrib><creatorcontrib>De Boer, S.H</creatorcontrib><title>Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola</title><title>Journal of applied microbiology</title><addtitle>J Appl Microbiol</addtitle><description>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.). 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. 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. 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.</description><subject>Bacterial Proteins - genetics</subject><subject>Biological and medical sciences</subject><subject>characterization</subject><subject>comparative genomics</subject><subject>detection</subject><subject>DNA Primers - genetics</subject><subject>Erwinia</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>loop-mediated isothermal amplification</subject><subject>Microbiology</subject><subject>Nucleic Acid Amplification Techniques - methods</subject><subject>Pectobacterium</subject><subject>Phaseolus - virology</subject><subject>Phaseolus vulgaris</subject><subject>Polyketide Synthases - genetics</subject><subject>Pseudomonas aeruginosa</subject><subject>Pseudomonas aeruginosa - genetics</subject><subject>Pseudomonas fluorescens - genetics</subject><subject>Pseudomonas syringae</subject><subject>Pseudomonas syringae - genetics</subject><subject>Pseudomonas syringae - isolation & purification</subject><subject>Pseudomonas syringae pv. phaseolicola</subject><subject>Sensitivity and Specificity</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, DNA</subject><issn>1364-5072</issn><issn>1365-2672</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2009</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkk1v1DAQhiMEoqXwFyAXyinBH4mTHDhUKyigIpCgZ2vijHe9cuJgJ6XLqT8dp1mVG8IXz9jPO2PN6yRJKclpXG_3OeWizJioWM4IaXJSMMHy20fJ6cPF4_u4yEpSsZPkWQh7QignpXianNCmqAVv6Glyt3H9CB4mc4PpFgfXGxWy7Ww67FLr3Jj12BmYYmaCm3boe7Ap9KM12qgoc0OqnU_VLhZRE3rzez10Ov0WcO5c7wYIaTh4M2wB0_EmT8cdBHTWKGfhefJEgw344rifJdcf3v_YfMyuvl5-2lxcZaooOctKXmlEwJYJzXSHvGyEwIoWZVdAW2Bbo2grWndlxzUhWqBgRFMmoNKqbYGfJW_WuqN3P2cMk-xNUGgtDOjmICvOOWUN4ZE8_yfJSNXUcYIRrFdQeReCRy1Hb3rwB0mJXHySe7nYIRc75OKTvPdJ3kbpy2OPuY0D_is8GhOB10cAggKrPQzKhAeO0ZrHuSzcu5X7ZSwe_vsB8vPFlyWK-lerXoOTsPWxx_V3tnwUKoTgtOR_AF7YuxU</recordid><startdate>200909</startdate><enddate>200909</enddate><creator>Li, X</creator><creator>Nie, J</creator><creator>Ward, L</creator><creator>Madani, M</creator><creator>Hsiang, T</creator><creator>Zhao, Y</creator><creator>De Boer, S.H</creator><general>Oxford, UK : Blackwell Publishing Ltd</general><general>Blackwell Publishing Ltd</general><general>Blackwell</general><scope>FBQ</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7T7</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>200909</creationdate><title>Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola</title><author>Li, X ; Nie, J ; Ward, L ; Madani, M ; Hsiang, T ; Zhao, Y ; De Boer, S.H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4532-537feeaeb26f2fde35966e7145d4ab4eb8e6b718d5d3f00f6e620f126a7fcbba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2009</creationdate><topic>Bacterial Proteins - genetics</topic><topic>Biological and medical sciences</topic><topic>characterization</topic><topic>comparative genomics</topic><topic>detection</topic><topic>DNA Primers - genetics</topic><topic>Erwinia</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>loop-mediated isothermal amplification</topic><topic>Microbiology</topic><topic>Nucleic Acid Amplification Techniques - methods</topic><topic>Pectobacterium</topic><topic>Phaseolus - virology</topic><topic>Phaseolus vulgaris</topic><topic>Polyketide Synthases - genetics</topic><topic>Pseudomonas aeruginosa</topic><topic>Pseudomonas aeruginosa - genetics</topic><topic>Pseudomonas fluorescens - genetics</topic><topic>Pseudomonas syringae</topic><topic>Pseudomonas syringae - genetics</topic><topic>Pseudomonas syringae - isolation & purification</topic><topic>Pseudomonas syringae pv. phaseolicola</topic><topic>Sensitivity and Specificity</topic><topic>Sequence Alignment</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, X</creatorcontrib><creatorcontrib>Nie, J</creatorcontrib><creatorcontrib>Ward, L</creatorcontrib><creatorcontrib>Madani, M</creatorcontrib><creatorcontrib>Hsiang, T</creatorcontrib><creatorcontrib>Zhao, Y</creatorcontrib><creatorcontrib>De Boer, S.H</creatorcontrib><collection>AGRIS</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, X</au><au>Nie, J</au><au>Ward, L</au><au>Madani, M</au><au>Hsiang, T</au><au>Zhao, Y</au><au>De Boer, S.H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola</atitle><jtitle>Journal of applied microbiology</jtitle><addtitle>J Appl Microbiol</addtitle><date>2009-09</date><risdate>2009</risdate><volume>107</volume><issue>3</issue><spage>717</spage><epage>726</epage><pages>717-726</pages><issn>1364-5072</issn><eissn>1365-2672</eissn><abstract>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.). 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. 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. 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.</abstract><cop>Oxford, UK</cop><pub>Oxford, UK : Blackwell Publishing Ltd</pub><pmid>19486391</pmid><doi>10.1111/j.1365-2672.2009.04262.x</doi><tpages>10</tpages></addata></record> |
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| ispartof | Journal of applied microbiology, 2009-09, Vol.107 (3), p.717-726 |
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| source | MEDLINE; Oxford Academic Journals (OUP); Wiley Online Library All Journals |
| subjects | Bacterial Proteins - genetics Biological and medical sciences characterization comparative genomics detection DNA Primers - genetics Erwinia Fundamental and applied biological sciences. Psychology loop-mediated isothermal amplification Microbiology Nucleic Acid Amplification Techniques - methods Pectobacterium Phaseolus - virology Phaseolus vulgaris Polyketide Synthases - genetics Pseudomonas aeruginosa Pseudomonas aeruginosa - genetics Pseudomonas fluorescens - genetics Pseudomonas syringae Pseudomonas syringae - genetics Pseudomonas syringae - isolation & purification Pseudomonas syringae pv. phaseolicola Sensitivity and Specificity Sequence Alignment Sequence Analysis, DNA |
| title | Comparative genomics-guided loop-mediated isothermal amplification for characterization of Pseudomonas syringae pv. phaseolicola |
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