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

The highly conserved region present only in the core genome of D. dianthicola as well as the genus Dickeya was found by evaluating sixteen genomes of the genera Dickeya, Pectobacerium, Erwinia, Ralstonia and Clavibacter using BLAST comparisons and MAUVE (Figure 1 ). Mauve-based progressive whole genome alignments enabled the gene selection for the Dickeya species and D. dianthicola. The alcohol dehydrogenase gene region was identified as a signature gene region present in the core genome of D. dianthicola and was used for designing the robust primers and probe specifically amplifying this species. Furthermore, the galactose/methyl galactoside ABC transporter ATP-binding protein mglA/mglC region was identified as a unique target for designing the primers and probe amplifying all known species of genus Dickeya (Figure 1 ). This gene is a part of ABC transporter complex and involved in the import of galactose/methyl galactoside by ATP hydrolysis. Both sets of designed primers and probes were analyzed by BLAST against the NCBI GenBank database and showed 100% query coverage and 100% similarity only corresponding to their target species that is Dickeya and D. dianthicola (Table 2) . The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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