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

L. Pritchard, S. Humphris, G. S. Saddler, N. M. Parkinson, V. Bertrand, J. G. Elphinstone, I. K. Toth

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)587-596
Number of pages10
JournalPlant Pathology
Volume62
Issue number3
DOIs
Publication statusPublished - 30 Jun 2013

Fingerprint

Dickeya
Bacterial Genomes
plant pathogens
Genome
Polymerase Chain Reaction
genome
prediction
Genes
taxonomy
genes

Keywords

  • diagnostics
  • Erwinia spp.
  • Pectobacterium spp.
  • potato
  • real-time PCR

Cite this

Pritchard, L., Humphris, S., Saddler, G. S., Parkinson, N. M., Bertrand, V., Elphinstone, J. G., & Toth, I. K. (2013). Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. Plant Pathology, 62(3), 587-596. https://doi.org/10.1111/j.1365-3059.2012.02678.x
Pritchard, L. ; Humphris, S. ; Saddler, G. S. ; Parkinson, N. M. ; Bertrand, V. ; Elphinstone, J. G. ; Toth, I. K. / Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. In: Plant Pathology. 2013 ; Vol. 62, No. 3. pp. 587-596.
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Pritchard, L, Humphris, S, Saddler, GS, Parkinson, NM, Bertrand, V, Elphinstone, JG & Toth, IK 2013, 'Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences', Plant Pathology, vol. 62, no. 3, pp. 587-596. https://doi.org/10.1111/j.1365-3059.2012.02678.x

Detection of phytopathogens of the genus Dickeya using a PCR primer prediction pipeline for draft bacterial genome sequences. / Pritchard, L.; Humphris, S.; Saddler, G. S.; Parkinson, N. M.; Bertrand, V.; Elphinstone, J. G.; Toth, I. K.

In: Plant Pathology, Vol. 62, No. 3, 30.06.2013, p. 587-596.

Research output: Contribution to journalArticle

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AU - Humphris, S.

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AU - Bertrand, V.

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AU - Toth, I. K.

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