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

To determine identities and relationships, all bacterial strains present in inclusivity and exclusivity panels were sequenced. Pectobacterium and Enterobacter strains were amplified and sequenced using either dnaA or 16S rRNA specific primer set to confirm their identity (Table 1) . A manually corrected and proofread dnaA consensus sequence of ~742 bp was generated. Consensus sequences, produced from both strands, were queried against the NCBI GenBank database using the BLASTn tool to confirm the identity of each strain mentioned in Table 1 . The phylogenetic relationships among the bacterial strains were determined using MEGA-X and the sequence demarcation tool (v1.2), clearly grouped the strains of Dickeya species from the Pectobacterium. All Dickeya species strains were clustered together except D. paradisiaca which was out-grouped ( Figure 2 and 3) . The strains of Pectobacterium species were clustered all together. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 Enterobacter species. All Dickeya strains grouped together except two D. paradisiaca strains that form a separate clade. All Pectobacterium species clustered together.