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

Shefali Dobhal; Gamze Boluk; Brooke Babler; Michael J. Stulberg; John Rascoe; Mark Nakhla; Toni A. Chapman; Alex B. Crockford; Michael Melzer; Anne M. Alvarez; Mohammad Arif

Dickeya is one of the most important enteric soft rot pathogens known to cause tremendous economic losses worldwide. Dickeya species, especially D. dianthicola, is a major problem for potato growing countries, and therefore is included in the European Union A2 quarantine list of pathogens. Accurate detection, distribution and monitoring of this pathogen is critical for prevention of higher economic losses. Detection by culturing and isolation is time-consuming, especially when the pathogen can be overgrown by saprophytic bacteria commonly present in infected samples. PCR provides fast, robust and accurate detection of pathogens compared to traditional culture-based methods. Compared to traditional PCR, real-time qPCR allows faster, accurate, sensitive and quantitative monitoring of a pathogen with less chance of carry over contaminations (Arif et The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/847590 doi: bioRxiv preprint assays depends on the target gene selection and the thermodynamics of the primers and probes .