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

Pritchard, Leighton; Humphris, Sonia; Saddler, G. S.; Parkinson, Neil; Bertrand, Viviane; Elphinstone, J. G.; Toth, Ian K.

doi:10.1111/j.1365-3059.2012.02678.x

Cited by 97 publications

(95 citation statements)

References 33 publications

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“…Populations of D. solani were quantified using a TaqMan assay based on the primer pair SOL‐Cf/SOL‐Cr as described by Pritchard et al . (). Oligonucleotides that were used as primers and probes in the assays are listed in Table .…”

Section: Methodsmentioning

confidence: 97%

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

et al. 2018

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Dickeya and Pectobacterium are responsible for causing blackleg of plants and soft rot of tubers in storage and in the field, giving rise to losses in seed potato production. In an attempt to improve potato health, biocontrol activity of known and putative antagonists was screened using in vitro and in planta assays, followed by analysis of their persistence at various storage temperatures. Most antagonists had low survival on potato tuber surfaces at 4 °C. The population dynamics of the best low‐temperature tolerant strain and also the most efficient antagonist, Serratia plymuthica A30, along with Dickeya solani as target pathogen, was studied with TaqMan real‐time PCR throughout the storage period. Tubers of three potato cultivars were treated in the autumn with the antagonist and then inoculated with D. solani. Although the cell densities of both strains decreased during the storage period in inoculated tubers, the pathogen population was always lower in the presence of the antagonist. The treated tubers were planted in the field the following growing season to evaluate the efficiency of the bacterial antagonist for controlling disease incidence. The potato endophyte S. plymuthica A30 protected potato plants by reducing blackleg development on average by 58.5% and transmission to tuber progeny as latent infection by 47–75%. These results suggest that treatment of potato tubers with biocontrol agents after harvest can reduce the severity of soft rot disease during storage and affect the transmission of soft rot bacteria from mother tubers to progeny tubers during field cultivation.

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Section: Methodsmentioning

confidence: 97%

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

et al. 2018

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“…Multiple genome alignments with contigs of Dickeya sp. D s0432-1 were done with Mauve v.2.3.1 [22] [23]. BlastN alignment of D. solani genome to the National Center for Biotechnology Information (NCBI) nucleotide database was utilized to identify nucleotide sequences that were specific to D. solani D s0432-1.…”

Section: Genome Sequencing and Analysismentioning

confidence: 99%

Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters

et al. 2013

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Soft rot Enterobacteria in the genera Pectobacterium and Dickeya cause rotting of many crop plants. A new Dickeya isolate has been suggested to form a separate species, given the name Dickeya solani. This bacterium is spreading fast and replacing the closely related, but less virulent, potato pathogens. The genome of D. solani isolate D s0432-1 shows highest similarity at the nucleotide level and in synteny to D. dadantii strain 3937, but it also contains three large polyketide/fatty acid/non-ribosomal peptide synthetase clusters that are not present in D. dadantii 3937. These gene clusters may be involved in the production of toxic secondary metabolites, such as oocydin and zeamine. Furthermore, the D. solani genome harbors several specific genes that are not present in other Dickeya and Pectobacterium species and that may confer advantages for adaptation OPEN ACCESSDiversity 2013, 5 825 to new environments. In conclusion, the fast spreading of D. solani may be related to the acquisition of new properties that affect its interaction with plants and other microbes in the potato ecosystem.

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“…Diagnostic primers to D. dianthicola and D. solani, the two main Dickeya species that threaten potato production in Europe, were validated against a panel of 70 Dickeya and related strains (Pritchard et al 2013b). Other Dickeya species-specific primers are awaiting validation, while D. dianthicola and D. solani-specific primers are now being used or validated in laboratories across Europe.…”

Section: Bacterial Diagnostics and Classificationmentioning

confidence: 99%

Why Genomics Research on Pectobacterium and Dickeya Makes a Difference

et al. 2015

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The genome sequence of Pectobacterium atrosepticum (Pba), one of the most economically damaging bacterial diseases of potato in temperate regions, was published in 2004. Even though, at the time, the number of completely sequenced bacterial genomes numbered only in the low hundreds we were able to use comparative genomics techniques to identify novel regions of DNA that were specific to Pba or only shared with closely related bacteria. Pba was found to contain many genes that were previously undescribed in this group of pathogens but were potentially coding for pathogenicity determinants, some of which appeared to be involved in either triggering or suppressing the plant's disease resistance processes. Our work since then has employed functional genomics methods to elucidate the ways in which this pathogen interacts with plants and causes disease, and how it has acquired the means to do this. These studies have allowed us to demonstrate a role in pathogenesis for bacterial genes, and to identify potato genes involved in resistance, leading to production of a transgenic potato plant that was fully resistant to the pathogen. Pba genes involved in phenotypes suited to a plant-associated lifestyle were also identified, with roles including attachment to, and colonization of, the roots of both crops and weeds. This understanding has led us to study alternative host plants for Pba in the environment, and the importance of this mode of environmental persistence for pathogen epidemiology and its spread to and between potato crops. Recently, we sequenced 25 strains representing the species range of the related phytopathogenic Dickeya genus (all formerly Erwinia chrysanthemi). Comparative genomic analyses of these sequences enabled application of a novel bioinformatics pipeline for generating diagnostic primers, enabling assays for the soft rot potato pathogens D. dianthicola and D. solani (which are an increasing problem on potato in Europe) as well as other Dickeya species. These assays are currently being validated for molecular diagnostic testing by a number of European plant health laboratories.Resumen En el 2004 se publicó la secuencia genómica de Pectobacterium atrosepticum (Pba), una de las enfermedades bacterianas de la papa más dañinas económicamente en regiones templadas. Aun así, en ese tiempo, el número de genomas bacterianos secuenciados completamente se numeraba en pocos cientos, pudimos usar técnicas genómicas comparativas para identificar nuevas regiones de DNA que fueran específicas para Pba o solamente compartidas con bacterias estrechamente relacionadas. Se encontró que Pba contenía muchos genes que no habían sido descritos previamente en este grupo de patógenos pero que potencialmente estaban codificando para determinantes de patogenicidad, alguno de los cuales parecía estar involucrado ya fuera en disparar o en suprimir los procesos de resistencia de la planta a la enfermedad. Nuestro trabajo desde entonces ha empleado métodos genómicos funcionales para dilucidar las formas en las cuales este patógeno...

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

Cited by 97 publications

References 33 publications

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

Biological control of potato soft rot caused by Dickeya solani and the survival of bacterial antagonists under cold storage conditions

Genome Sequence of Dickeya solani, a New soft Rot Pathogen of Potato, Suggests its Emergence May Be Related to a Novel Combination of Non-Ribosomal Peptide/Polyketide Synthetase Clusters

Why Genomics Research on Pectobacterium and Dickeya Makes a Difference

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