ArticleBMC genomics2026
Genome-wide identification and comparative analysis of endogenous retroviruses across five breed-representative pig assemblies.
Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundPorcine 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.
resultsAcross 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).
conclusionsAcross 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.
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