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Using a high\u2010quality super\u2010pangenome comprising 12\n                    <jats:italic>Trichinella<\/jats:italic>\n                    species, we compared extensive genomic variations between encapsulating and non\u2010encapsulating lineages. Pangenomic analysis revealed an open\u2010genome architecture dominated by dispensable genes, with nonencapsulated lineages exhibiting a high load of structural variation (SV). These findings suggest that the capsule represents an evolutionary innovation that arose in the common ancestor of\n                    <jats:italic>Trichinella<\/jats:italic>\n                    as an adaptation to mammalian hosts, dating back approximately 18 million years. Branch\u2010specific selection analysis further revealed distinct host adaptation strategies between the two lineages. By integrating cross\u2010species and cross\u2010developmental transcriptomic atlases, we constructed a secreted protein\u2010host interaction network and identified encapsulation\u2010associated parasite\u2010secreted proteins. Additionally, we identified\n                    <jats:italic>dpy\u201031<\/jats:italic>\n                    as a promising drug target. Collectively, our work establishes a comprehensive genomic and functional framework that deepens the understanding of host\u2013parasite interactions and opens avenues for therapeutic intervention.\n                  <\/jats:p>","DOI":"10.1002\/advs.202523161","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T15:30:45Z","timestamp":1775835045000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The\n                    <i>Trichinella<\/i>\n                    Super\u2010Pangenome Reveals the Evolution of Encapsulation and Predicted Host\u2013Parasite Protein Interactions"],"prefix":"10.1002","volume":"13","author":[{"given":"Qingbo","family":"Lv","sequence":"first","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Xu","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaming","family":"Yang","sequence":"additional","affiliation":[{"name":"Yunnan Institute of Parasitic Diseases  Yunnan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengyao","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"},{"name":"China Conservation and Research Center For the Giant Panda Key Laboratory of SFGA On the Giant panda  Chengdu Sichuan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanhai","family":"Mao","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingyuan","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory For Diagnosis and Treatment of Severe Zoonotic Infectious Diseases Institute of Zoonosis and College of Veterinary Medicine Key Laboratory for Zoonosis Research of the Ministry of Education Jilin University  Changchun China"},{"name":"Jiangsu Co\u2010innovation Center For Prevention and Control of Important Animal Infectious Diseases and Zoonoses  Yangzhou 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