{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T09:27:28Z","timestamp":1786958848407,"version":"build-2736575974"},"reference-count":53,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T00:00:00Z","timestamp":1786924800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","award":["NIFA Evans-Allen-1013186"],"award-info":[{"award-number":["NIFA Evans-Allen-1013186"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","award":["NIFA AFRI 2020-67016-31347"],"award-info":[{"award-number":["NIFA AFRI 2020-67016-31347"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","award":["NIFA AFRI 2025-38821-45500"],"award-info":[{"award-number":["NIFA AFRI 2025-38821-45500"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000199","name":"USDA","doi-asserted-by":"publisher","award":["NSF-IOS-1831988"],"award-info":[{"award-number":["NSF-IOS-1831988"]}],"id":[{"id":"10.13039\/100000199","id-type":"DOI","asserted-by":"publisher"}]},{"award":["NIFA Evans-Allen-1013186"],"award-info":[{"award-number":["NIFA Evans-Allen-1013186"]}],"id":[{"id":"https:\/\/ror.org\/01na82s61","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NIFA AFRI 2020-67016-31347"],"award-info":[{"award-number":["NIFA AFRI 2020-67016-31347"]}],"id":[{"id":"https:\/\/ror.org\/01na82s61","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NIFA AFRI 2025-38821-45500"],"award-info":[{"award-number":["NIFA AFRI 2025-38821-45500"]}],"id":[{"id":"https:\/\/ror.org\/01na82s61","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NSF-IOS-1831988"],"award-info":[{"award-number":["NSF-IOS-1831988"]}],"id":[{"id":"https:\/\/ror.org\/01na82s61","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>The porcine interferon (IFN) system is highly diversified, particularly within Type I subfamilies, yet its evolutionary trajectory across domestication and breed formation remains poorly characterized. We performed a comprehensive comparative genomic and structural analysis of 432 IFN sequences spanning all IFN types across 11 Sus scrofa breeds representing commercial, indigenous, and wild\/outgroup lineages. Phylogenetic reconstruction, pairwise dN\/dS selection pressure analysis, and AlphaFold2-based 3D structure prediction coupled with DALI structural similarity mapping were integrated to resolve repertoire architecture, evolutionary constraints, and domestication-associated divergence. IFN repertoire organization is governed primarily by family identity rather than breed origin, with Type I IFN-\u03b1, -\u03b4, and -\u03c9 subfamilies showing pronounced gene expansion in domestic breeds. Phylogenetic clustering and structural similarity consistently grouped sequences by subtype, independent of domestication history. Pervasive purifying selection (median \u03c9 = 0.48) maintained functional constraints across all lineages. Commercial breeds exhibited significantly higher within-category structural convergence alongside expanded repertoires, while structural conservation was evolutionarily decoupled from sequence-level selective pressure. Domestication potentially drove coordinated IFN repertoire expansion and structural conservation with related purifying selection at the gene level. These findings establish a genomic framework linking breed-specific IFN architecture to antiviral capacity and provide a foundation for immunogenetic-informed breeding strategies in the swine model.<\/jats:p>","DOI":"10.3390\/biom16081195","type":"journal-article","created":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T08:05:41Z","timestamp":1786953941000},"page":"1195","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Domestication-Driven Expansion and Structural Convergence of the Porcine Antiviral Interferon Repertoire"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-3649-7100","authenticated-orcid":false,"given":"Jiuyi","family":"Li","sequence":"first","affiliation":[{"name":"Department of Food and Animal Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN 37209, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niya","family":"Tu","sequence":"additional","affiliation":[{"name":"Department of Food and Animal Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN 37209, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8946-9416","authenticated-orcid":false,"given":"Laura C.","family":"Miller","sequence":"additional","affiliation":[{"name":"Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, 1800 Denison Ave, Manhattan, KS 66506, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2980-2854","authenticated-orcid":false,"given":"Yongming","family":"Sang","sequence":"additional","affiliation":[{"name":"Department of Food and Animal Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN 37209, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"309","DOI":"10.12688\/f1000research.12450.1","article-title":"Recent advances in antiviral interferon-stimulated gene biology","volume":"7","author":"Schoggins","year":"2018","journal-title":"F1000Research"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1146\/annurev-virology-092818-015756","article-title":"Interferon-Stimulated Genes: What Do They All Do?","volume":"6","author":"Schoggins","year":"2019","journal-title":"Annu. Rev. 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