Publication
Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola
Publisher:
Scientific Societies
Date:
11-2019
DOI:
10.1094/PDIS-10-18-1819-RE
Abstract: 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 lified a minority of the nontarget strains tested. The two promising candidate primer sets were trialed with DNA isolated from 116 field s les from across the United States that were previously submitted for testing. D. dianthicola was detected in 41 s les, demonstrating the applicability of our detection primers and suggesting widespread occurrence of D. dianthicola in North America.