Ralstonia solanacearum is an aerobic nonspore-forming, Gram-negative, pathogenic bacterium that can infect up to 200 different plant species. R. solanacearum species produces four phylogenetically distinct groups that are directly related to their geographical origin. Phylotype I is composed of strains from Asia. The strains of Phylotype II are from the Americas. Phylotype II has two clearly recognizable branches: Phylotype IIA and Phylotype IIB. The members of Phylotype III originated from Africa. Phylotype IV isolates originate from the Philippines, Japan, Indonesia, and Australia. In this study, Georgian isolates of R. solanacearum were characterized using Average Nucleotide Identity (ANI). ANI is a method to compare genetic relatedness among prokaryotic strains and gives the ability to infer species from isolates.
The reference strains and Georgian isolates whole genome pairwise comparison has been carried out using ANI to establish genetic similarity of the Georgian isolates with other R. solanacearum strains. Complete genome sequences of reference R. solanacearum were obtained from the National Center for Biotechnology Information (NCBI). The database contains complete genome information about fifteen strains of the pathogen. Provided by the NCBI, we used the following genomes for analysis: Phylotype I (OE1-1, EP1, YC45, GMI1000, KACC10709, FJAT-1458, FQY_4, and YC40-M); Phylotype IIA (CFBP2957); Phylotype IIB (Po82, UW163, IBSBF1503 and UY031); Phylotype III (CMR15; Phylotype IV – SPI07, and KACC10722).
According to pairwise ANI, the reference strains and Georgian isolates formed three distinct groups. Group one formed strains from Asia (Phylotype I) and Africa (Phylotype III). The Asian strains are very similar with an ANI more than 99%. African strain CMR15 is clustered to the strains from Asia. The ANI values of the strain CMR15 versus the strains from Phylotype I accounts values more than 95%. The second group consists of closely related strains KACC10722 and PSI07 with ANI value of 99%. The third group is created from American strains (Phylotype II) and isolates from Georgia. The ANI values for these strains are more than 95%. Georgian isolates and strain UY031 have about 100% pairwise ANI. Three strains IBSBF1503, Po82 and UW163 are closely related (ANI value 99.94%). Pairwise, ANI of CFBP2957 (Phylotype IIA and Phylotype IIB) is relatively low; we found strains belonging to the same Phylotype with an ANI value of 96%.
Strains with more than 95% ANI were the same species. According to interstrain ANI, R. solanacearum should be treated as three species. The first species includes strains from Phylotype I (OE1-1, EP1, YC45, GMI1000, KACC10709, FGAT-1458, YC40-M, FQY_4) and Phylotype III (CMR15). The second species comprises strains from Phylotype IV (PSI07, KACC10722). The third species encompasses strains from Phylotype IIA (Po82, IBSBF1503, UW163, UY031, Georgian isolates) and Phylotype IIB (CFBP2957).
Gene editing, synthetic genomics, forensics, and biosurveillance
