Investigation of the Genetic Diversity of Erwinia amylovora Strains Originating from Pome Fruits in Turkey

The present study addresses the molecular characterization of a collection of Erwinia amylovora strains obtained in 2019 from different locations in Amasya, cankiri, corum, and Isparta provinces in Turkey. Analysis revealed that all investigated strains isolated in this study (n = 27) produced the expected amplicons of 187 and 649 bp, with taxon-specific primers G1/G2 and EAPSGL3961/EAPSGL4610c for molecular identification of E. amylovora, respectively. A total of 34 strains, 27 of which were isolated in this study, as well as seven strains previously isolated from pome fruit, and six reference cultures were screened for genetic diversity using PCR fingerprints generated by repetitive DNA sequence-based polymerase chain reaction (rep-PCR) and clustered regularly interspaced short palindromic repeat (CRISPR) primers, and sequence analysis based on the nucleotides of the gapA gene. PCR fingerprints generated with rep-PCR primers were found to be homogeneous for primers REP, ERIC, and BOX. CRISPR analysis with CRISPR 1 and CRISPR 3 primers revealed the same patterns, indicating that both loci are present in the strains of this work. Four different patterns were obtained with the CRISPR-2 primers, with most of the strains tested having the same pattern (pattern 1). GEa6 from apple (pattern 2) and GEa13 from quince (pattern 3) as well as the reference strain KFB 152 (pattern 4) from apple differed in the size of the most dominant band. The obtained gapA nucleotide sequences had 100% similarity to the available complete genomes of E. amylovora strains, with the closest species being E. pyrifoliae with 94.27% similarity, allowing the taxonomic position of the strains to be determined.