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.. 2019. Development of the automated primer design workflow uniqprimer and diagnostic primers for the broad-host-range plant pathogen Dickeya dianthicola. Plant Disease, 103 (11) : 2893-2902.

Url - autres données associées : https://github.com/SouthGreenPlatform/Uniqprimer/tree/master/uniqprimer-0.5.0 / Url - autres données associées : https://github.com/SouthGreenPlatform/Uniqprimer

Quartile : Q1, Sujet : PLANT SCIENCES

Résumé : 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.

Mots-clés Agrovoc : internet, génome, agent pathogène, génomique, identification, pouvoir pathogène, Dickeya

Mots-clés libres : Blackleg, Diagnostics, Galaxy, Primer design

Agences de financement hors UE : U.S. Department of Agriculture, University of Agriculture, Faisalabad, Taiwan Council of Agriculture, Institut de Recherche pour le Développement, Consortium of International Agricultural Research Centers

Auteurs et affiliations

• Karim Shaista, Colorado State University (USA)
• McNally R. Ryan, Colorado State University (USA)
• Nasaruddin Afnan S., Colorado State University (USA)
• Dereeper Alexis, CIRAD-BIOS-UMR AGAP (GLP)
• Mauleon Ramil P., IRRI [International Rice Research Institute] (PHL)
• Charkowski Amy O., Colorado State University (USA)
• Leach Jan E., Colorado State University (USA)
• Ben-Hur Asa, Colorado State University (USA)
• Triplett Lindsay R., Colorado State University (USA) - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/605030/)

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