Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides
Abstract Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The...
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| Veröffentlicht in: | FEMS microbiology letters 2014-06, Vol.355 (1), p.28-35 |
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| creator | Takahashi, Reiko Fukuta, Shiro Kuroyanagi, Satoru Miyake, Noriyuki Nagai, Hirofumi Kageyama, Koji Ishiguro, Yasushi |
| description | Abstract
Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.
Development of species‐specific LAMP assay for the rapid diagnosis of Pythium helicoides, a seriously problematic pathogen on poinsettia in hydroponic cultures. |
| doi_str_mv | 10.1111/1574-6968.12453 |
| format | Article |
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Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.
Development of species‐specific LAMP assay for the rapid diagnosis of Pythium helicoides, a seriously problematic pathogen on poinsettia in hydroponic cultures.</description><identifier>ISSN: 0378-1097</identifier><identifier>EISSN: 1574-6968</identifier><identifier>DOI: 10.1111/1574-6968.12453</identifier><identifier>PMID: 24797345</identifier><language>eng</language><publisher>Oxford, UK: Blackwell Publishing Ltd</publisher><subject>DNA Primers - genetics ; DNA, Ribosomal Spacer - genetics ; Euphorbia - microbiology ; High temperature ; hydroponic culture ; Hydroponics ; loop‐mediated isothermal amplification ; Microbiology ; Nucleic Acid Amplification Techniques - methods ; Oomycetes - genetics ; Oomycetes - isolation & purification ; Pathogens ; Plant Diseases - microbiology ; Plant Roots - microbiology ; Pythium helicoides ; Sensitivity and Specificity</subject><ispartof>FEMS microbiology letters, 2014-06, Vol.355 (1), p.28-35</ispartof><rights>2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved 2014</rights><rights>2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved</rights><rights>2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.</rights><rights>Copyright © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4063-aa860686e26018ac891f98d7082eb5d0a06fddd217d1248a70ead1c326d7b8393</citedby><cites>FETCH-LOGICAL-c4063-aa860686e26018ac891f98d7082eb5d0a06fddd217d1248a70ead1c326d7b8393</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%2F1574-6968.12453$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1111%2F1574-6968.12453$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,776,780,1411,27901,27902,45550,45551</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24797345$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Takahashi, Reiko</creatorcontrib><creatorcontrib>Fukuta, Shiro</creatorcontrib><creatorcontrib>Kuroyanagi, Satoru</creatorcontrib><creatorcontrib>Miyake, Noriyuki</creatorcontrib><creatorcontrib>Nagai, Hirofumi</creatorcontrib><creatorcontrib>Kageyama, Koji</creatorcontrib><creatorcontrib>Ishiguro, Yasushi</creatorcontrib><title>Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides</title><title>FEMS microbiology letters</title><addtitle>FEMS Microbiol Lett</addtitle><description>Abstract
Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.
Development of species‐specific LAMP assay for the rapid diagnosis of Pythium helicoides, a seriously problematic pathogen on poinsettia in hydroponic cultures.</description><subject>DNA Primers - genetics</subject><subject>DNA, Ribosomal Spacer - genetics</subject><subject>Euphorbia - microbiology</subject><subject>High temperature</subject><subject>hydroponic culture</subject><subject>Hydroponics</subject><subject>loop‐mediated isothermal amplification</subject><subject>Microbiology</subject><subject>Nucleic Acid Amplification Techniques - methods</subject><subject>Oomycetes - genetics</subject><subject>Oomycetes - isolation & purification</subject><subject>Pathogens</subject><subject>Plant Diseases - microbiology</subject><subject>Plant Roots - microbiology</subject><subject>Pythium helicoides</subject><subject>Sensitivity and Specificity</subject><issn>0378-1097</issn><issn>1574-6968</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkc9rFDEUx4Modq2evUnAiwjT5tckmaNUq8JKe9BzeDt5w6bMTMZkpmX_e7Nut4gUmsuD8Pl-eLwvIW85O-PlnfPaqEo32p5xoWr5jKwefp6TFZPGVpw15oS8yvmGMaYE0y_JiVCmMVLVK3L3GW-xj9OA40xh9BSmqQ8tzCGONHYUaB_jVA3oA8zoachx3mIaoKcwFLI7spAz7GgXE00wBU89ztgeLde7eRuWgW6xuGPwmF-TFx30Gd_cz1Py6_LLz4tv1frq6_eLT-uqVUzLCsBqpq1GoRm30NqGd431hlmBm9ozYLrz3gtufDmABcMQPG-l0N5srGzkKflw8E4p_l4wz24IucW-hxHjkh2vlRaCWW4L-v4_9CYuaSzbFUoqzqUxqlDnB6pNMeeEnZtSGCDtHGdu34nbN-D2Dbi_nZTEu3vvsil3fOCPJRSgPgB3ocfdUz53-WN9FH885OIyPZqq_tniD1B4oxI</recordid><startdate>201406</startdate><enddate>201406</enddate><creator>Takahashi, Reiko</creator><creator>Fukuta, Shiro</creator><creator>Kuroyanagi, Satoru</creator><creator>Miyake, Noriyuki</creator><creator>Nagai, Hirofumi</creator><creator>Kageyama, Koji</creator><creator>Ishiguro, Yasushi</creator><general>Blackwell Publishing Ltd</general><general>Oxford University Press</general><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>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>201406</creationdate><title>Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides</title><author>Takahashi, Reiko ; Fukuta, Shiro ; Kuroyanagi, Satoru ; Miyake, Noriyuki ; Nagai, Hirofumi ; Kageyama, Koji ; Ishiguro, Yasushi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4063-aa860686e26018ac891f98d7082eb5d0a06fddd217d1248a70ead1c326d7b8393</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>DNA Primers - genetics</topic><topic>DNA, Ribosomal Spacer - genetics</topic><topic>Euphorbia - microbiology</topic><topic>High temperature</topic><topic>hydroponic culture</topic><topic>Hydroponics</topic><topic>loop‐mediated isothermal amplification</topic><topic>Microbiology</topic><topic>Nucleic Acid Amplification Techniques - methods</topic><topic>Oomycetes - genetics</topic><topic>Oomycetes - isolation & purification</topic><topic>Pathogens</topic><topic>Plant Diseases - microbiology</topic><topic>Plant Roots - microbiology</topic><topic>Pythium helicoides</topic><topic>Sensitivity and Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Takahashi, Reiko</creatorcontrib><creatorcontrib>Fukuta, Shiro</creatorcontrib><creatorcontrib>Kuroyanagi, Satoru</creatorcontrib><creatorcontrib>Miyake, Noriyuki</creatorcontrib><creatorcontrib>Nagai, Hirofumi</creatorcontrib><creatorcontrib>Kageyama, Koji</creatorcontrib><creatorcontrib>Ishiguro, Yasushi</creatorcontrib><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>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>FEMS microbiology letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Takahashi, Reiko</au><au>Fukuta, Shiro</au><au>Kuroyanagi, Satoru</au><au>Miyake, Noriyuki</au><au>Nagai, Hirofumi</au><au>Kageyama, Koji</au><au>Ishiguro, Yasushi</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides</atitle><jtitle>FEMS microbiology letters</jtitle><addtitle>FEMS Microbiol Lett</addtitle><date>2014-06</date><risdate>2014</risdate><volume>355</volume><issue>1</issue><spage>28</spage><epage>35</epage><pages>28-35</pages><issn>0378-1097</issn><eissn>1574-6968</eissn><abstract>Abstract
Root rot of poinsettia, caused by Pythium helicoides at high temperatures in hydroponic cultures, has become a serious problem in many parts of the world. We have developed a species-specific, loop-mediated isothermal amplification (LAMP) assay for the rapid diagnosis of this pathogen. The primers were designed using the ribosomal DNA internal transcribed spacer sequence. Primer specificity was established using 40 Pythium species including P. helicoides, 11 Phytophthora species, and eight other soil-borne pathogens. A sensitivity test was carried out using genomic DNA extracted from P. helicoides, and the detection limit was c. 100 fg which is comparable to that of the polymerase chain reaction (PCR). In addition, we tested the ease of pathogen detection in poinsettia roots. The LAMP results were consistent with those from the conventional plating method and showed more sensitivity than the PCR results. Consequently, the LAMP method developed in this study is effective for the rapid and easy detection of P. helicoides.
Development of species‐specific LAMP assay for the rapid diagnosis of Pythium helicoides, a seriously problematic pathogen on poinsettia in hydroponic cultures.</abstract><cop>Oxford, UK</cop><pub>Blackwell Publishing Ltd</pub><pmid>24797345</pmid><doi>10.1111/1574-6968.12453</doi><tpages>8</tpages></addata></record> |
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| ispartof | FEMS microbiology letters, 2014-06, Vol.355 (1), p.28-35 |
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| source | Oxford University Press Journals All Titles (1996-Current); MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | DNA Primers - genetics DNA, Ribosomal Spacer - genetics Euphorbia - microbiology High temperature hydroponic culture Hydroponics loop‐mediated isothermal amplification Microbiology Nucleic Acid Amplification Techniques - methods Oomycetes - genetics Oomycetes - isolation & purification Pathogens Plant Diseases - microbiology Plant Roots - microbiology Pythium helicoides Sensitivity and Specificity |
| title | Development and application of a loop-mediated isothermal amplification assay for rapid detection of Pythium helicoides |
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