Molecular methods as tools to control plant diseases caused by Dickeya and Pectobacterium spp: A minireview

Motyka, Agata; Żołędowska, Sabina; Śledź, Wojciech; Łojkowska, Ewa

doi:10.1016/j.nbt.2017.08.010

Cited by 53 publications

(50 citation statements)

References 89 publications

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“…At present, neither resistant varieties nor effective physical, chemical or biological controls have been reported to manage D. dianthicola diseases under field conditions (Czajkowski et al ). Only preventive measures are recommended, which include planting certified seeds, eradicating contaminated plant materials, screening for latent infections, monitoring appropriate storage conditions and inspecting fields (Motyka et al ). Therefore, early, accurate and sensitive detection of Dickeya species is important to identify inoculum sources before they become a problem.…”

Section: Introductionmentioning

confidence: 99%

“…Several assays have been reported for detection of Dickeya from infected samples including selective and semi‐selective media (Hayman et al ; Helias et al ), microscopic observations and biochemical and serological identification methods (Czajkowski et al ; Motyka et al ). Detection based on molecular methods such as PCR, quantitative PCR and loop‐mediated isothermal amplification (LAMP) are implemented routinely due to their high sensitivity, speed, specificity, accuracy, discriminatory ability and reproducibility (Ouyang et al ; Czajkowski et al ; Larrea‐Sarmiento et al ; Ocenar et al ).…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real‐time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

et al. 2020

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Aims Dickeya species are high consequence plant pathogenic bacteria; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, Dickeya dianthicola. Methods and Results A signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome‐based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed a detection limit of 10 fg DNA. Conclusion The developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials. Significance and Impact of the Study The developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding programme. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real‐time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

et al. 2020

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“…At present, neither resistant varieties nor effective physical, chemical or biological controls have been reported to manage D. dianthicola diseases under field conditions (Czajkowski et al 2014). Only preventive measures are recommended, which include planting certified seeds, eradicating contaminated plant materials, screening for latent infections, monitoring appropriate storage conditions and inspecting fields (Motyka et al 2017). Therefore, early, accurate and sensitive detection of Dickeya species is important to identify inoculum sources before they become a problem.…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

Dobhal

Bölük

Babler

et al. 2019

Preprint

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AimsDickeya species are high consequence plant pathogenic bacteria listed among the quarantine pathogens of the European Union; associated with potato disease outbreaks and subsequent economic losses worldwide. Early, accurate, and reliable detection of Dickeya spp. is needed to prevent establishment and further dissemination of this pathogen. Therefore, a multiplex TaqMan qPCR was developed for sensitive detection of Dickeya spp. and specifically, D. dianthicola. Methods and ResultsA signature genomic region for the genus Dickeya (mglA/mglC) and unique genomic region for D. dianthicola (alcohol dehydrogenase) were identified using a whole genome based comparative genomics approach. The developed multiplex TaqMan qPCR was validated using extensive inclusivity and exclusivity panels, and naturally/artificially infected samples to confirm broad range detection capability and specificity. Both sensitivity and spiked assays showed detection limit of 10 fg DNA. ConclusionThe developed multiplex assay is sensitive and reliable to detect Dickeya spp. and D. dianthicola with no false positives or false negatives. It was able to detect mixed infection from naturally and artificially infected plant materials. Significance and ImpactThe developed assay will serve as a practical tool for screening of propagative material, monitoring the presence and distribution, and quantification of target pathogens in a breeding program. The assay also has applications in routine diagnostics, biosecurity and microbial forensics.

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“…Assessment of the total economic impact of these diseases is demanding as Pectobacterium and Dickeya spp. are present on various plant hosts in diverse geographical regions where miscellaneous seed certi cation policies remain in force [11].…”

Section: Introductionmentioning

confidence: 99%

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

Motyka-Pomagruk

Żołędowska

Misztak

et al. 2020

Preprint

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Abstract Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population. Results: High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported. Conclusions: The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

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Molecular methods as tools to control plant diseases caused by Dickeya and Pectobacterium spp: A minireview

Cited by 53 publications

References 89 publications

Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real‐time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real‐time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

Comparative genomics reveals signature regions used to develop a robust and sensitive multiplex TaqMan real-time qPCR assay to detect the genus Dickeya and Dickeya dianthicola

Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani

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