Lineage-specific remodeling of a conserved tRNA-Thr-associated genomic island in Edwardsiella anguillarum

Abstract Edwardsiella anguillarum is a bacterial pathogen affecting diverse aquaculture species worldwide, including red seabream, Japanese eel, and tilapia. In Japan, strains show a phenotypic dichotomy, where red seabream-derived strains are non-motile and ornithine decarboxylase (ODC)-negative, whereas eel-derived strains retain both traits. However, the evolutionary processes underlying lineage diversification within this species remain poorly understood. We performed a global comparative genomic analysis of 24 E. anguillarum strains, including seven newly sequenced genomes from Japan. Despite high ANI values (>99.6%), SNP analysis revealed lineage-level divergence, with 6500–7500 SNPs separating red seabream-associated and eel-associated lineages. Comparative analysis identified a conserved chromosomal hotspot adjacent to the tRNA-Thr gene with lineage-specific structural variation. The Japanese red seabream-associated lineage possessed a compact ∼10-kb region containing a Type I-E CRISPR/Cas system, whereas eel-associated and tilapia-derived strains carried expanded genomic islands (∼48–52 kb) enriched in DNA repair and mobile genetic element functions. These configurations were associated with phylogeographic lineages. Genes associated with motility and ODC activity were conserved across lineages, with no evidence of gene loss or major structural disruption. Phylogenetic analysis of the island-associated tyrosine-type recombinase/integrase (YR) was broadly consistent with the core genome. A shared frameshift mutation in eel- and tilapia-derived strains was consistent with a shared pseudogenization event. Overall, our findings indicate that diversification in E. anguillarum is associated with localized structural variation at a conserved tRNA-Thr-associated chromosomal hotspot within an otherwise highly conserved core genome.