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Despite its significant economic value for aquaculture, existing genomic resources remain fragmented, limiting the advancement of molecular breeding and functional genomic studies. Here, we present a gap-free, telomere-to-telomere (T2T) genome assembly of\n                    <jats:italic>L. argentimaculatus<\/jats:italic>\n                    , generated using a hybrid approach combining PacBio HiFi, Oxford Nanopore ultra-long reads and Hi-C technology. The resulting assembly comprises exactly 24 scaffolds spanning 1.03\u2009Gb, perfectly matching the haploid chromosome number with a contig N50 of 46.17\u2009Mb. Notably, this assembly resolves all physical gaps present in previous versions, achieving a BUSCO completeness score of 98.2%. Comprehensive genome annotation successfully predicted 23,167 protein-coding genes. Among these, 22,067 genes (95.25%) were functionally annotated across major public databases, including eggNOG, InterPro, and Swiss-Prot. Furthermore, structural analysis successfully identified 19 telomeres and 20 centromeres, validating the chromosomal integrity. This high-fidelity, gap-free reference genome provides a robust foundation for comparative genomics, population genetics, and the genetic improvement of\n                    <jats:italic>Lutjanidae<\/jats:italic>\n                    species.\n                  <\/jats:p>","DOI":"10.1038\/s41597-026-08016-2","type":"journal-article","created":{"date-parts":[[2026,8,5]],"date-time":"2026-08-05T04:05:42Z","timestamp":1785902742000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A gap-free, telomere-to-telomere chromosome-scale genome assembly of the mangrove red snapper, Lutjanus argentimaculatus"],"prefix":"10.1038","volume":"13","author":[{"given":"Yang","family":"Xiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhencheng","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoling","family":"Jiang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yusong","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongduo","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,5]]},"reference":[{"key":"8016_CR1","doi-asserted-by":"crossref","unstructured":"Tiralongo, F., Giovos, I., Doumpas, N. Is the mangrove red snapper Lutjanus argentimaculatus (forssk\u00e5l, 1775) established in the eastern Mediterranean sea? First records from Greece through a citizen science project. in Bioinvasions Records 617\u2013626 (2019).","DOI":"10.3391\/bir.2019.8.4.19"},{"key":"8016_CR2","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1046\/j.1365-2109.2003.00892.x","volume":"34","author":"AC Emata","year":"2003","unstructured":"Emata, A. C. Reproductive performance in induced and spontaneous spawning of the mangrove red snapper, Lutjanus argentimaculatus: a potential candidate species for sustainable aquaculture. Aquac Res 34, 849\u2013857 (2003).","journal-title":"Aquac Res"},{"key":"8016_CR3","doi-asserted-by":"publisher","DOI":"10.1093\/gbe\/evad171","volume":"15","author":"Z Lai","year":"2023","unstructured":"Lai, Z. et al. The first high-quality chromosome-level genome of the Lutjanus erythropterus (Bloch, 1790) using single-tube long fragment reads and hi-C technologies. Genome Biol Evol 15, evad171 (2023).","journal-title":"Genome Biol Evol"},{"key":"8016_CR4","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-024-03633-1","volume":"11","author":"MS Shekhar","year":"2024","unstructured":"Shekhar, M. S. et al. Genome assembly, Full-length transcriptome, and isoform diversity of Red Snapper, Lutjanus argentimaculatus. Sci Data 11, 796 (2024).","journal-title":"Sci Data"},{"key":"8016_CR5","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1093\/bioinformatics\/btr011","volume":"27","author":"G Mar\u00e7ais","year":"2011","unstructured":"Mar\u00e7ais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764\u2013770 (2011).","journal-title":"Bioinformatics"},{"key":"8016_CR6","doi-asserted-by":"publisher","first-page":"2202","DOI":"10.1093\/bioinformatics\/btx153","volume":"33","author":"GW Vurture","year":"2017","unstructured":"Vurture, G. W. et al. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33, 2202\u20132204 (2017).","journal-title":"Bioinformatics"},{"key":"8016_CR7","doi-asserted-by":"publisher","first-page":"967","DOI":"10.1038\/s41592-024-02269-8","volume":"21","author":"H Cheng","year":"2024","unstructured":"Cheng, H., Asri, M., Lucas, J., Koren, S. & Li, H. Scalable telomere-to-telomere assembly for diploid and polyploid genomes with double graph. Nat Methods 21, 967\u2013970 (2024).","journal-title":"Nat Methods"},{"key":"8016_CR8","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.cels.2016.07.002","volume":"3","author":"NC Durand","year":"2016","unstructured":"Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution hi-C experiments. Cell Syst 3, 95\u201398 (2016).","journal-title":"Cell Syst"},{"key":"8016_CR9","doi-asserted-by":"publisher","DOI":"10.1101\/254797","author":"O Dudchenko","year":"2018","unstructured":"Dudchenko, O. et al. The juicebox assembly tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000. bioRxiv https:\/\/doi.org\/10.1101\/254797 (2018).","journal-title":"bioRxiv"},{"key":"8016_CR10","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1126\/science.aal3327","volume":"356","author":"O Dudchenko","year":"2017","unstructured":"Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using hi-C yields chromosome-length scaffolds. Science 356, 92\u201395 (2017).","journal-title":"Science"},{"key":"8016_CR11","doi-asserted-by":"publisher","DOI":"10.1093\/hr\/uhad127","volume":"10","author":"Y Lin","year":"2023","unstructured":"Lin, Y. et al. quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification. Hortic Res 10, uhad127 (2023).","journal-title":"Hortic Res"},{"key":"8016_CR12","unstructured":"Cao, F.-J., Li, C.-L., Liu, C.-W. Studies on the Karyotypes of Lutjanus erythopterus, Lutjanus argentimaculatus and Lutjanus bohar. Marine Sciences 43\u201346 (2002)."},{"key":"8016_CR13","doi-asserted-by":"publisher","DOI":"10.1002\/imt2.211","volume":"3","author":"H Tang","year":"2024","unstructured":"Tang, H. et al. JCVI: a versatile toolkit for comparative genomics analysis. 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PLoS One 15, e0232402 (2020).","journal-title":"PLoS One"}],"container-title":["Scientific Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-08016-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-08016-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-08016-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,7]],"date-time":"2026-09-07T10:02:19Z","timestamp":1788775339000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41597-026-08016-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,5]]},"references-count":34,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["8016"],"URL":"https:\/\/doi.org\/10.1038\/s41597-026-08016-2","relation":{"references":[{"id-type":"uri","id":"https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP661206","asserted-by":"subject"},{"id-type":"uri","id":"https:\/\/identifiers.org\/ncbi\/insdc.sra:SRP661285","asserted-by":"subject"},{"id-type":"doi","id":"10.6084\/m9.figshare.31044799","asserted-by":"subject"}]},"ISSN":["2052-4463"],"issn-type":[{"value":"2052-4463","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,5]]},"assertion":[{"value":"5 February 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Ethics"}}],"article-number":"1290"}}