Genome-wide identification and comparative analysis of endogenous retroviruses across five breed-representative pig assemblies

Porcine xenotransplantation offers a promising solution to human organ shortages, yet cross-species transmission of endogenous retroviruses (ERVs) remains a major safety barrier. Current risk assessments predominantly rely on a single reference genome, creating a distinct blind spot regarding ERV diversity and structural variation across diverse genetic backgrounds. We profiled ERV loci across five chromosome-level pig genome assemblies (Bama miniature pig, Duroc, Meishan, Ningxiang, and USMARC), characterizing structural completeness, phylogenetic relationships, relative insertion ages, and host-gene/QTL genomic context. ERVs were identified with the LTRharvest/LTRdigest pipeline, annotated by Pfam domain screening, and classified as complete, near-complete, or partial. Phylogenetic analysis used maximum-likelihood inference, insertion age was estimated from paired long terminal repeat (LTR) divergence, and ERV-proximal genes within 10 kb were analyzed for Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and tissue expression. Across the five chromosome-level assemblies, the paired-LTR-anchored catalog comprised 23,767 ERV candidates in the main autosome/chrX analysis set, including 75 structurally complete, 322 near-complete, and 23,370 partial loci. An additional 86 chrY records were detected in assemblies with chrY and were all classified as partial. Complete-ERV insertion-age profiles showed assembly-level variation, although Kruskal-Wallis tests did not detect a significant overall difference among assemblies. The five-assembly shared ERV-proximal host-gene set contained 278 genes at the 10 kb window; this set decreased to 229 genes at 5 kb and increased to 358 and 618 genes at 20 and 50 kb, respectively. Chromosome-stratified randomization showed that the shared 10 kb gene set overlapped pig QTL intervals more often than expected by chance (56.47% observed versus 43.23% random mean; empirical P < 0.0001). Across five breed-representative pig assemblies, we identified 23,767 paired-LTR ERV candidates, of which only 75 (0.32%) met the structural-completeness criteria, confirming that the detected porcine ERV catalog is dominated by degraded elements. Complete loci showed assembly-level variation in retroviral affinities and relative insertion-age profiles, while the five-assembly shared 10 kb ERV-proximal gene set showed non-random QTL colocalization (56.47% observed versus 43.23% random mean; empirical P < 0.0001). Benchmarking against published porcine endogenous retrovirus (PERV) and retroviral insertion polymorphism (RIP) resources linked 9 complete loci to reconstructed Sus scrofa ERV6A/B full-length ERVs (SscERV6A/B Fl-ERVs) and left 66 complete loci outside that focused set. This catalog provides concrete ERV loci and host-gene contexts for donor-line evaluation and future population-scale, T2T-informed studies of porcine ERV diversity.