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However, the absence of a complete reference genome has impeded advanced genetic research on this species, and the phylogenetic position of Epinephelidae within Perciformes remains unresolved. Here, we generated a complete telomere\u2010to\u2010telomere (T2T) genome assembly (887.20\u2009Mb; contig N50: 39.03\u2009Mb; QV: 67) for\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>P. leopardus<\/jats:italic>\n                    <\/jats:styled-content>\n                    with no need for gap\u2010filling. Leveraging this genome combined with other available genome resources, we conducted a large\u2010scale genomic re\u2010annotation and reconstructed a robust genome\u2010level phylogeny of the Perciformes. Our analysis revealed that Epinephelidae and Anthiadidae form a monophyletic clade situated at the base of the Perciformes, indicating that the traditional suborder Serranoidei is non\u2010monophyletic. Comparative genomic analysis revealed that differential expansions of transposable elements represented the primary driver of genome size variation among\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>P. leopardus<\/jats:italic>\n                    <\/jats:styled-content>\n                    and other groupers. Furthermore, we constructed a high\u2010density haplotype reference panel using 110 individuals and annotated 1068 loss\u2010of\u2010function (LoF) mutations. Enrichment analysis indicated that genes with stop\u2010gain LoF mutations are involved in the immune response and skin color variation. This study provides an essential genomic resource for\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>P. leopardus<\/jats:italic>\n                    <\/jats:styled-content>\n                    and offers fundamental evolutionary insights into the Epinephelidae and, more broadly, the order Perciformes.\n                  <\/jats:p>","DOI":"10.1111\/eva.70296","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T06:02:14Z","timestamp":1783663334000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A Complete Telomere\u2010To\u2010Telomere Assembly of\n                    <i>Plectropomus leopardus<\/i>\n                    and Phylogenomic Insights Into Perciformes"],"prefix":"10.1111","volume":"19","author":[{"given":"Baojun","family":"Zhao","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-0865-5340","authenticated-orcid":false,"given":"Chaofan","family":"Jin","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingjian","family":"Liu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haizhan","family":"Tang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Da","family":"Zheng","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengya","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0089-5812","authenticated-orcid":false,"given":"Bo","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenmin","family":"Bao","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"},{"name":"Southern Marine Science and Engineer Guangdong Laboratory  Guangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjie","family":"Hu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences\/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China  Qingdao China"},{"name":"Southern Marine Science and Engineer Guangdong Laboratory  Guangzhou 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