Chromosome-scale genome of European anchovy (Engraulis encrasicolus L., 1758) and comparative genomics uncover clupeid-specific immune gene expansions.

The European anchovy is a keystone forage species in the Mediterranean and Northeast Atlantic, yet a chromosome-scale reference genome has been lacking. Here, we present a 1.4 Gb assembly anchored to 24 chromosomes (scaffold N50 = 56.4 Mb; BUSCO 96.6%) with 27,663 annotated protein-coding genes and 44.6% repetitive content dominated by DNA transposons, which likely account for the near doubling of genome size relative to Atlantic herring. Comparative analyses across 11,755 orthogroups revealed a net contractive trend in Clupeidae, superimposed on conspicuous expansions of antiviral and innate-immune gene families (TRIM16, GTPase IMAP member 8, IFI44, Toll-like receptors), with GO enrichment exceeding 400-fold for antiviral regulatory processes. Branch-site analyses identified 216 positively selected genes in E. encrasicolus, 81 of which map to innate signaling, epigenetic regulation, ubiquitin-mediated immunity, and selective autophagy. Multitissue RNA-Seq further demonstrated that expanded, positively selected, and epithelial barrier-associated genes, including 11 claudin paralogues, zonula-occludens scaffolds, and tricellular junction components, are coordinately enriched in the gill. Together, these findings highlight a gill-enriched immune landscape potentially shaped by filter-feeding ecology, providing a genomic framework for clupeid immunogenomics and aquaculture applications.