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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
- Publication Year :
- 2019
- Publisher :
- Cold Spring Harbor Laboratory, 2019.
-
Abstract
- 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.
- Subjects :
- Dickeya
Computational biology
medicine.disease_cause
Applied Microbiology and Biotechnology
Genome
03 medical and health sciences
Species Specificity
Limit of Detection
TaqMan
False positive paradox
medicine
media_common.cataloged_instance
Multiplex
European union
Plant Diseases
Solanum tuberosum
media_common
030304 developmental biology
Comparative genomics
0303 health sciences
Genus Dickeya
biology
030306 microbiology
Pathogenic bacteria
Genomics
General Medicine
biology.organism_classification
Multiplex Polymerase Chain Reaction
Gammaproteobacteria
Genome, Bacterial
Biotechnology
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....6a9151aac43ca1e05c865928a4395093
- Full Text :
- https://doi.org/10.1101/847590