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

In this study, we have presented a multiplex TaqMan qPCR for sensitive and simultaneous detection of genus Dickeya and D. dianthicola. The developed multiplex TaqMan qPCR was validated in the lab extracted DNA from purified cultures and naturally infected potato samples. Comparative genomics using Mauve identified signature genomic regions; the gene mglA/mglC region was used to design the primers/probe for the genus Dickeya, while the alcohol dehydrogenase gene was used for designing the primers targeting D. dianthicola. The developed assay has applications in farm management, seed certification, biosecurity and to discover new reservoir hosts.