In silico Evaluation of Molecular Probes for Detection and Identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus
Ralstonia solanacerum and Clavibacter michiganensis subsp. sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroug...
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| Veröffentlicht in: | Systematic and applied microbiology 2004-09, Vol.27 (5), p.581-591 |
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| creator | Arahal, David R. Llop, Pablo Alonso, Manuel Pérez López, María M. |
| description | Ralstonia solanacerum and
Clavibacter michiganensis subsp.
sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes
insilico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about
insilico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios. |
| doi_str_mv | 10.1078/0723202041748208 |
| format | Article |
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Clavibacter michiganensis subsp.
sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes
insilico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about
insilico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.</description><identifier>ISSN: 0723-2020</identifier><identifier>EISSN: 1618-0984</identifier><identifier>DOI: 10.1078/0723202041748208</identifier><identifier>PMID: 15490560</identifier><identifier>CODEN: SAMIDF</identifier><language>eng</language><publisher>Jena: Elsevier GmbH</publisher><subject>Actinomycetales - classification ; Actinomycetales - genetics ; Bacteriology ; Base Sequence ; Biological and medical sciences ; Clavibacter michiganensis ; DNA Primers ; Fundamental and applied biological sciences. Psychology ; Microbiology ; Miscellaneous ; molecular diagnostic ; oligonucleotide design ; Oligonucleotide Probes ; primer ; Ralstonia solanacearum ; Ralstonia solanacearum - classification ; Ralstonia solanacearum - genetics ; Sensitivity and Specificity ; Solanum tuberosum ; Solanum tuberosum - microbiology ; specificity</subject><ispartof>Systematic and applied microbiology, 2004-09, Vol.27 (5), p.581-591</ispartof><rights>2004 Urban & Fischer Verlag</rights><rights>2004 INIST-CNRS</rights><rights>Copyright Urban & Fischer Verlag Sep 2004</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c489t-ad70f46cdc24ffbd8b9d5903a4ab73756064da67406dab40ea7faa1902eaf2533</citedby><cites>FETCH-LOGICAL-c489t-ad70f46cdc24ffbd8b9d5903a4ab73756064da67406dab40ea7faa1902eaf2533</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0723202005702976$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16103210$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15490560$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Arahal, David R.</creatorcontrib><creatorcontrib>Llop, Pablo</creatorcontrib><creatorcontrib>Alonso, Manuel Pérez</creatorcontrib><creatorcontrib>López, María M.</creatorcontrib><title>In silico Evaluation of Molecular Probes for Detection and Identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus</title><title>Systematic and applied microbiology</title><addtitle>Syst Appl Microbiol</addtitle><description>Ralstonia solanacerum and
Clavibacter michiganensis subsp.
sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes
insilico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about
insilico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.</description><subject>Actinomycetales - classification</subject><subject>Actinomycetales - genetics</subject><subject>Bacteriology</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Clavibacter michiganensis</subject><subject>DNA Primers</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Microbiology</subject><subject>Miscellaneous</subject><subject>molecular diagnostic</subject><subject>oligonucleotide design</subject><subject>Oligonucleotide Probes</subject><subject>primer</subject><subject>Ralstonia solanacearum</subject><subject>Ralstonia solanacearum - classification</subject><subject>Ralstonia solanacearum - genetics</subject><subject>Sensitivity and Specificity</subject><subject>Solanum tuberosum</subject><subject>Solanum tuberosum - microbiology</subject><subject>specificity</subject><issn>0723-2020</issn><issn>1618-0984</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2004</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNqN0lFrFDEQB_BFFFur7z5pEPTt6iSbTXZ9k7PqQUVR-7zMJpOaspdck90Dv4cf2FzvsFAQfcrD_GaY8J-qesrhlINuX4MWtQABkmvZCmjvVcdc8XYBXSvvV8e78mJXP6oe5XwFwGWn-MPqiDeyg0bBcfVrFVj2ozeRnW1xnHHyMbDo2Kc4kplHTOxLigNl5mJi72gicyMwWLayFCbvvPnT9BXHPMXgkeU4YkBDmOb1DV6OuPUDmokSW3vzw19ioJB9Znke8uaUZdqQLb1mzo-rB65MoieH96S6eH_2fflxcf75w2r59nxhZNtNC7QanFTGGiGdG2w7dLbpoEaJg651-Z-SFpWWoCwOEgi1Q-QdCEInmro-qV7t525SvJ4pT_3aZ0NjWZ3inHulula1Qv8Tcq07oRX8B1R1UzIr8MUdeBXnFMpv-5KjbJpW7qbBHpkUc07k-k3ya0w_ew797gD6uwdQWp4d5s7DmuxtwyHxAl4eAGaDo0sYjM-3TnGoBd-553vnMPZ4mYq5-CaA18BBaF03RbzZCyoRbT2lPhtPwZD1qVxJb6P_-56_AQLa1QY</recordid><startdate>20040901</startdate><enddate>20040901</enddate><creator>Arahal, David R.</creator><creator>Llop, Pablo</creator><creator>Alonso, Manuel Pérez</creator><creator>López, María M.</creator><general>Elsevier GmbH</general><general>Elsevier</general><general>Elsevier Science Ltd</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>3V.</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AF</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>BKSAR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PCBAR</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>S0X</scope><scope>7QL</scope><scope>C1K</scope><scope>7T7</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20040901</creationdate><title>In silico Evaluation of Molecular Probes for Detection and Identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus</title><author>Arahal, David R. ; Llop, Pablo ; Alonso, Manuel Pérez ; López, María M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c489t-ad70f46cdc24ffbd8b9d5903a4ab73756064da67406dab40ea7faa1902eaf2533</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2004</creationdate><topic>Actinomycetales - classification</topic><topic>Actinomycetales - genetics</topic><topic>Bacteriology</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Clavibacter michiganensis</topic><topic>DNA Primers</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Microbiology</topic><topic>Miscellaneous</topic><topic>molecular diagnostic</topic><topic>oligonucleotide design</topic><topic>Oligonucleotide Probes</topic><topic>primer</topic><topic>Ralstonia solanacearum</topic><topic>Ralstonia solanacearum - classification</topic><topic>Ralstonia solanacearum - genetics</topic><topic>Sensitivity and Specificity</topic><topic>Solanum tuberosum</topic><topic>Solanum tuberosum - microbiology</topic><topic>specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Arahal, David R.</creatorcontrib><creatorcontrib>Llop, Pablo</creatorcontrib><creatorcontrib>Alonso, Manuel Pérez</creatorcontrib><creatorcontrib>López, María M.</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>ProQuest Central (Corporate)</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>STEM Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Earth, Atmospheric & Aquatic Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Earth, Atmospheric & Aquatic Science Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>SIRS Editorial</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Systematic and applied microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Arahal, David R.</au><au>Llop, Pablo</au><au>Alonso, Manuel Pérez</au><au>López, María M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In silico Evaluation of Molecular Probes for Detection and Identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus</atitle><jtitle>Systematic and applied microbiology</jtitle><addtitle>Syst Appl Microbiol</addtitle><date>2004-09-01</date><risdate>2004</risdate><volume>27</volume><issue>5</issue><spage>581</spage><epage>591</epage><pages>581-591</pages><issn>0723-2020</issn><eissn>1618-0984</eissn><coden>SAMIDF</coden><abstract>Ralstonia solanacerum and
Clavibacter michiganensis subsp.
sepedonicus are the two most relevant bacterial pathogens of potato for which a large number of molecular diagnostic methods using specific DNA sequences have been developed. About one hundred oligonucleotides have been described and thoroughly tested experimentally. After having compiled and evaluated all these primers and probes
insilico to check their specificity, many discrepancies were found. A detailed analysis permitted the recognition of different possible reasons for such discrepancies: sequencing errors in public sequences, wrong supposed specificity (sometimes due to more recent sequences than the oligonucleotides being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about
insilico evaluation using two potato bacterial pathogens as a model, the conclusions reflect not only information useful for phytopathologists but, in a broader scope, draw the main situations that can be found during an evaluation of probes, which can be surely found in other scenarios.</abstract><cop>Jena</cop><pub>Elsevier GmbH</pub><pmid>15490560</pmid><doi>10.1078/0723202041748208</doi><tpages>11</tpages></addata></record> |
| fulltext | fulltext |
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| ispartof | Systematic and applied microbiology, 2004-09, Vol.27 (5), p.581-591 |
| issn | 0723-2020 1618-0984 |
| language | eng |
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| subjects | Actinomycetales - classification Actinomycetales - genetics Bacteriology Base Sequence Biological and medical sciences Clavibacter michiganensis DNA Primers Fundamental and applied biological sciences. Psychology Microbiology Miscellaneous molecular diagnostic oligonucleotide design Oligonucleotide Probes primer Ralstonia solanacearum Ralstonia solanacearum - classification Ralstonia solanacearum - genetics Sensitivity and Specificity Solanum tuberosum Solanum tuberosum - microbiology specificity |
| title | In silico Evaluation of Molecular Probes for Detection and Identification of Ralstonia solanacearum and Clavibacter michiganensis subsp. sepedonicus |
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