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...
| Autores principales: | , , , |
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| Formato: | article |
| Lenguaje: | Inglés |
| Publicado: |
2017
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| Acceso en línea: | http://hdl.handle.net/20.500.11939/4328 |
| _version_ | 1855032102274203648 |
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| author | Arahal, D. R. Llop, Pablo Alons, M. P. López, María M. |
| author_browse | Alons, M. P. Arahal, D. R. Llop, Pablo López, María M. |
| author_facet | Arahal, D. R. Llop, Pablo Alons, M. P. López, María M. |
| author_sort | Arahal, D. R. |
| collection | ReDivia |
| 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 in silico 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 oligonucleoticles being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about in silico 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. |
| format | article |
| id | ReDivia4328 |
| institution | Instituto Valenciano de Investigaciones Agrarias (IVIA) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | ReDivia43282025-04-25T14:42:51Z In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus Arahal, D. R. Llop, Pablo Alons, M. P. López, María M. 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 in silico 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 oligonucleoticles being evaluated) or even typing errors in the oligonucleotides. Although this study is an exercise about in silico 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. 2017-06-01T10:09:51Z 2017-06-01T10:09:51Z 2004 SEP 2004 article Arahal, D. R., Llop, P., Alons, M. P. & Lopez, M. M. (2004). In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus. Systematic and applied microbiology, 27(5), 581-591. 0723-2020 http://hdl.handle.net/20.500.11939/4328 10.1078/0723202041748208 en openAccess Impreso |
| spellingShingle | Arahal, D. R. Llop, Pablo Alons, M. P. López, María M. In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title | In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title_full | In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title_fullStr | In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title_full_unstemmed | In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title_short | In silico evaluation of molecular probes for detection and identification of Ralstonia solanacearum and Clavibacter michiganensis subsp sepedonicus |
| title_sort | in silico evaluation of molecular probes for detection and identification of ralstonia solanacearum and clavibacter michiganensis subsp sepedonicus |
| url | http://hdl.handle.net/20.500.11939/4328 |
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