Аннотация
ABSTRACT Fire blight, caused by Erwinia amylovora , is one of the most important diseases of cultivated apple ( Malus domestica ) worldwide. Since 2008, this pathogen became widespread in Kazakhstan, a global centre of origin for apple. Genomic data on Central Asian populations of this pathogen remain limited. This study aimed to isolate, characterize and assess the pathogenicity and genomic diversity of E. amylovora isolates from the Almaty region. Seven isolates were obtained from symptomatic apple trees and confirmed using loop‐mediated isothermal amplification (LAMP) and real‐time quantitative PCR assays. Pathogenicity tests on apple saplings and immature pear fruits demonstrated variable virulence among isolates, depending on host and tissue type. Whole‐genome sequencing generated high‐quality draft genomes of approximately 3.7–3.8 Mb, each comprising a chromosome and the pEA29 plasmid, with an average sequencing depth of 525.8×. Comparative analysis identified 389 high‐confidence genetic variants, including 337 SNPs and 52 indels, with several impact mutations with predicted impacts detected in genes associated with virulence, stress response and cellular processes. The overall genomic similarity was extremely high (average nucleotide identity of 99.99%), confirming the low intraspecific diversity of the pathogen. Phylogenetic analysis involving 326 global genomes placed seven Kazakh isolates within a regional lineage closely related to strains from Kazakhstan, Kyrgyzstan and China. CRISPR typing classified all isolates into the (A,t,α) CRISPR haplotype typical for the Almaty region. These findings expand genomic data on E. amylovora in Central Asia and provide a foundation for improved surveillance, epidemiological tracking and disease management to protect cultivated and wild apple resources.