Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences

This study used a novel computational pipeline to exploit draft bacterial genome sequences in order to predict, automatically and rapidly, PCR primer sets for Dickeya spp. that were unbiased in terms of diagnostic gene choice. This pipeline was applied to 16 draft and four complete Dickeya genome se...

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Bibliographic Details
Published in:Plant pathology 2013-06, Vol.62 (3), p.587-596
Main Authors: Pritchard, L., Humphris, S., Saddler, G. S., Parkinson, N. M., Bertrand, V., Elphinstone, J. G., Toth, I. K.
Format: Article
Language:English
Subjects:
Bacteria
Biological and medical sciences
diagnostics
Erwinia spp
Fundamental and applied biological sciences. Psychology
Pectobacterium spp
Phytopathology. Animal pests. Plant and forest protection
potato
real‐time PCR
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Summary:This study used a novel computational pipeline to exploit draft bacterial genome sequences in order to predict, automatically and rapidly, PCR primer sets for Dickeya spp. that were unbiased in terms of diagnostic gene choice. This pipeline was applied to 16 draft and four complete Dickeya genome sequences to generate >700 primer sets predicted to discriminate between Dickeya at the species level. Predicted diagnostic primer sets for both D. dianthicola (DIA‐A and DIA‐B) and ‘D. solani’ (SOL‐C and SOL‐D) were validated against a panel of 70 Dickeya reference strains, representative of the known diversity of this genus, to confirm primer specificity. The classification of the four previously sequenced strains was re‐examined and evidence of possible misclassification of three of these strains is presented.
ISSN:0032-0862
1365-3059
DOI:10.1111/j.1365-3059.2012.02678.x