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Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola.
Karim, Shaista; McNally, R Ryan; Nasaruddin, Afnan S; DeReeper, Alexis; Mauleon, Ramil P; Charkowski, Amy O; Leach, Jan E; Ben-Hur, Asa; Triplett, Lindsay R.
Afiliação
  • Karim S; Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A.
  • McNally RR; Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A.
  • Nasaruddin AS; Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A.
  • DeReeper A; L'Institut de recherche pour le développement, IRD, Université Montpellier, IPME, Montpellier, France.
  • Mauleon RP; International Rice Research Institute, Los Baños, Laguna, Philippines.
  • Charkowski AO; Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A.
  • Leach JE; Colorado State University, Department of Bioagricultural Science and Pest Management, Fort Collins, CO 80523, U.S.A.
  • Ben-Hur A; Colorado State University, Department of Computer Science, Fort Collins, CO 80523, U.S.A.
  • Triplett LR; The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A.
Plant Dis ; 103(11): 2893-2902, 2019 Nov.
Article em En | MEDLINE | ID: mdl-31436473
Uniqprimer, a software pipeline developed in Python, was deployed as a user-friendly internet tool in Rice Galaxy for comparative genome analyses to design primer sets for PCRassays capable of detecting target bacterial taxa. The pipeline was trialed with Dickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato-growing regions. Dickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. Upon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with Uniqprimer, of which two were specific and sensitive when tested with D. dianthicola. The remaining four amplified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field samples from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 samples, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Solanum tuberosum / Técnicas Bacteriológicas / Primers do DNA / Agricultura / Enterobacteriaceae Tipo de estudo: Diagnostic_studies / Prognostic_studies País/Região como assunto: America do norte Idioma: En Revista: Plant Dis Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Estados Unidos

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Solanum tuberosum / Técnicas Bacteriológicas / Primers do DNA / Agricultura / Enterobacteriaceae Tipo de estudo: Diagnostic_studies / Prognostic_studies País/Região como assunto: America do norte Idioma: En Revista: Plant Dis Ano de publicação: 2019 Tipo de documento: Article País de afiliação: Estados Unidos