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TECHNICAL SESSION: Advanced detection and diagnosis of plant diseases

Using whole-genome sequencing for pathogen identification: Candidatus Pectobacterium maceratum, a potato blackleg pathogen in New York State
Xing Ma - Cornell University. K. L. Perry- Cornell University, Paul Stodghill- USDA-ARS, Bryan Swingle- USDA-ARS

Blackleg and soft rot are bacterial diseases of potato that reduce plant emergence and can damage tubers in storage. Beginning in 2014 there has been an increase in blackleg disease incidence in US potato production. To help understand the cause of this disease outbreak, in 2017 we surveyed potato plants with blackleg symptoms from several locations in New York State (NYS). We isolated pathogens from these plants, confirmed their pathogenicity, and used PCR and dnaX single gene sequencing to determine the species. We found that Dickeya dianthicola and Pectobacterium parmentieri were the two most common causal agents in those plants. However, this approach could not resolve species assignments for nine Pectobacterium isolates. Here, we used whole-genome sequencing-based methods to determine the species of these nine Pectobacterium isolates. We used single gene ortholog analysis, digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) to classify the unknown isolates. We found that eight of the nine isolates were most similar to a newly designated species, Candidatus Pectobacterium maceratum; the one remaining isolate was likely P. carotovorum subsp. carotovorum. Ca. P. maceratum is not previously known to exist in the United States and data are consistent with it being a blackleg pathogen in NYS.