Diversity, evolution, and gene regulation of endogenous retroviruses in eight important poultry species.

Abstract

Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have shaped vertebrate genomes through evolution. In poultry, ERVs remain understudied despite their potential roles in genome plasticity, gene regulation, and disease resistance. Here, we presented a comprehensive analysis of ERVs across 8 poultry species from three families (Anatidae, Phasianidae, and Numidae), combining de novo mining, phylogenetic classification, and functional characterization. Our study revealed substantial variation in ERV abundance, ranging from 46,326 (Cairina moschata) to 79,018 (Meleagris gallopavo) elements per genome. We discovered 23 distinct ERV groups, including 20 novel groups, with dominance of Alpharetroviruses (10 groups), suggesting lineage-specific expansion. Several ERVs grouped closely with known poultry ERVs, indicating common evolutionary origins, they have been distributed across different families, highlighting lineage-specific expansion patterns and suggesting that they may play conserved roles in host genome regulation. Notably, ERV-derived sequences contribute significantly to both protein-coding (29.4-44.8 %) and long non-coding RNA (22.5-61.2 %) genes, with a pronounced depletion in coding regions (CDS: 63.2-98.3 %) but enrichment in regulatory regions. We further identified polymorphic ERV insertions in key developmental genes (e.g., CLC2DL4/5, TYR, CNTNAP2, CNTN5, and LUZP2), implying roles in post-transcriptional regulation. However, these polymorphic insertions were specifically observed in 2 species, Gallus gallus (4 insertions) and Numida meleagris (1 insertion). PCR genotyping confirmed active ERV polymorphisms in a small population of chickens (n = 24) and ducks (n = 24), indicating ongoing genomic dynamism. These findings underscore ERVs as dual agents of genetic innovation and structural variation, with implications for avian genome evolution, host-pathogen interactions, and poultry breeding strategies.