Whole Genome Analysis of Two Pectobacterium Species Isolated from Blackleg Disease of Potato Occurred in Nagasaki Prefecture, Japan

In Japan, Dickeya dianthicola, D. chrysanthemi, Pectobacterium atrosepticum, P. parmentieri, and P. brasiliense are known as blackleg disease pathogens of potato. A transient outbreak of the blackleg disease occurred in Nagasaki Prefecture, and the pathogens were identified as P. parmentieri and P. brasiliense. Because repetitive extragenic palindromic PCR showed clonal relatedness among strains in each species, two Nagasaki strains (NK5 and NK14) were selected as the representative strains, and their whole genome sequences were determined. Average nucleotide identity analysis supported the identification in the previous study. Multilocus sequence analysis with seven housekeeping genes indicated the relationship between NK14 and other strains isolated in Japan, Russia, China, Switzerland, Poland, and Belgium. NK5 was related to the strains from various geographic locations including Syria, China, Canada, South Korea, Netherlands, Algeria, South Africa, Mexico, and Belarus. Subsequently, core genome multilocus sequence typing was performed with publicly available sequences, indicating that NK14 and NK5 were most closely related to the strains Poland/Russian and Netherlands/Belarus/Russia, respectively. This study concerns the first phylogenetic analyses based on the whole genome sequences of Japanese strains of P. parmentieri and P. brasiliense, and contributes to the molecular epidemiological analysis of the pathogen of potato blackleg.