Genome-wide identification and comparative analysis of endogenous retroviruses across five breed-representative pig assemblies
Year: 2026
Type: article
Abstract: Background 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 breed-specific ERV diversity and structural variations 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 associations with host genes and quantitative trait loci (QTLs). 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-associated genes within 10 kb were analysed for Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and tissue expression. Results A total of 23,767 ERV loci were identified across five pig breeds, with consistent counts and length distributions across assemblies. Most were structurally degraded, comprising 75 complete (0.32%), 322 near-complete (1.35%), and 23,370 partial loci (98.33%). Complete ERVs were classified into four retroviral clades and showed counter-intuitive breed differences in relative insertion age: Ningxiang, a Chinese indigenous breed with a comparatively small effective population size, showed the lowest median insertion age (0.81 Myr), whereas USMARC, a composite outbred line derived from multiple Western breeds, showed the highest (7.85 Myr). A core set of 278 ERV-associated genes shared across breeds was enriched in synaptic signaling and vesicle transport pathways, showed tissue-specific expression, and substantially overlapped with QTLs for meat quality, growth, and reproduction. Conclusions The porcine ERV landscape is dominated by degraded elements. Among complete loci, the unexpectedly lower median insertion ages in Ningxiang compared to USMARC align with reduced purifying selection efficiency in small-Ne breeds rather than commercial selection models. Furthermore, the tissue-specific expression and clustering of ERV-associated genes within host QTL regions for meat quality, growth, and reproduction highlight their regulatory roles in porcine biology. Ultimately, this study establishes a comprehensive, breed-resolved pan-genome framework for porcine ERVs, providing practical benchmarks and target catalogs for donor strain selection and precise CRISPR-mediated viral inactivation in xenotransplantation.
Source: BMC Genomics
Authors: Xiaotong Zhao, Yongping Hu, Zhidong Zhang, Xun Xiang, Hua Chang
Institution: Yunnan Agricultural University
Language: English
Subfield: Plant Science
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,090
OpenAlex ID: W7170137212