@article{fdi:010077161,
  title = {{D}evelopment of the automated primer design workflow uniqprimer and diagnostic primers for the broad-host-range plant pathogen {D}ickeya dianthicola},
  author = {{K}arim, {S}. and {M}c{N}ally, {R}. {R}. and {N}asaruddin, {A}. {S}. and {D}ereeper, {A}lexis and {M}auleon, {R}. {P}. and {C}harkowski, {A}. {O}. and {L}each, {J}. {E}. and {B}en-{H}ur, {A}. and {T}riplett, {L}. {R}.},
  editor = {},
  language = {{ENG}},
  abstract = {{U}niqprimer, a software pipeline developed in {P}ython, was deployed as a user-friendly interne tool in {R}ice {G}alaxy for comparative genome analyses to design primer sets for {PCR}assays capable of detecting target bacterial taxa. {T}he pipeline was trialed with {D}ickeya dianthicola, a destructive broad-host-range bacterial pathogen found in most potato growing regions. {D}ickeya is a highly variable genus, and some primers available to detect this genus and species exhibit common diagnostic failures. {U}pon uploading a selection of target and nontarget genomes, six primer sets were rapidly identified with {U}niqprimer, of which two were specific and sensitive when tested with {D}. dianthicola. {T}he remaining four amplified a minority of the nontarget strains tested. {T}he two promising candidate primer sets were trialed with {DNA} isolated from 116 field samples from across the {U}nited {S}tates 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 {N}orth {A}merica.},
  keywords = {blackleg ; diagnostics ; {G}alaxy ; primer design},
  booktitle = {},
  journal = {{P}lant {D}isease},
  volume = {103},
  numero = {11},
  pages = {2893--2902},
  ISSN = {0191-2917},
  year = {2019},
  DOI = {10.1094/pdis-10-18-1819-re},
  URL = {https://www.documentation.ird.fr/hor/fdi:010077161},
}