Differential activation and gene-coupled transcriptional dynamics of transposable elements during Piscirickettsiosis...

Transposable elements (TE) are increasingly recognized as dynamic regulatory components of vertebrate genomes, particularly under stress and disease conditions. However, their transcriptional role during bacterial infections in teleost fish remains largely unexplored. Here, we performed a genome-wide analysis of TE expression in Atlantic salmon using RNA-seq datasets derived from head kidney tissue of control and Piscirickettsia salmonis-infected individuals. A curated species-specific TE library comprising 1641 consensus sequences was constructed to ensure intergenic accurate annotation and quantification. We identified widespread TE transcriptional activity, with 4550 locus-specific differentially expressed TEs, of which 84.35% were upregulated in infected fish. DNA transposons (Class II), particularly TIR elements, represented the largest fraction of upregulated loci. Importantly, 84 TE-gene pairs exhibited significant expression coupling, predominantly showing positive correlations. Functional enrichment of associated genes revealed overrepresentation of metabolic and immune-related pathways. These findings reveal extensive TE transcriptional activation during bacterial infection in Atlantic salmon and suggest coordinated TE-gene expression dynamics as part of the host response. Although causal regulatory relationships cannot be inferred from correlation-based analyses alone, this study provides a quantitative framework for investigating mobilome dynamics during host-pathogen interactions in salmonids.