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Here we sequenced the genome of the common lumpfish (<jats:italic>Cyclopterus lumpus<\/jats:italic> Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70\u00a0K single nucleotide polymorphism array and tissue\u2010specific expression data. The chromosome\u2010level assembly identified 25 diploid chromosomes with a total size of 572.89\u00a0Mb, a scaffold N50 of 23.86\u00a0Mb and genome annotation\u2010predicted 21,480 protein\u2010coding genes. Genome\u2010wide association analysis located a highly sex\u2010associated region on chromosome 13, suggesting that anti\u2010M\u00fcllerian hormone (AMH) is the putative SD factor. Linkage disequilibrium and heterozygosity across chromosome 13\u00a0support a proto\u2010XX\/XY system, with an absence of widespread chromosome divergence between sexes. We identified three copies of <jats:italic>AMH<\/jats:italic> in the lumpfish primary and alternate haplotype assemblies localized in the SD region. Comparison to sequences from other teleosts suggested a monophyletic relationship and conservation within the Cottioidei. One <jats:italic>AMH<\/jats:italic> copy showed similarity to <jats:italic>AMH<\/jats:italic>\/<jats:italic>AMHY<\/jats:italic> in a related species and was also the only copy with expression in testis tissue, suggesting this copy may be the functional copy of <jats:italic>AMH<\/jats:italic> in lumpfish. The two other copies arranged in tandem inverted duplication were highly similar, suggesting a recent duplication event. This study provides a resource for the study of early sex chromosome evolution and novel genomic resources that benefits lumpfish conservation management and aquaculture.<\/jats:p>","DOI":"10.1111\/1755-0998.13565","type":"journal-article","created":{"date-parts":[[2021,12,3]],"date-time":"2021-12-03T09:39:27Z","timestamp":1638524367000},"page":"1427-1439","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Reference genome of lumpfish <i>Cyclopterus lumpus<\/i> Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway"],"prefix":"10.1111","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5729-6039","authenticated-orcid":false,"given":"Melissa K.","family":"Holborn","sequence":"first","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4588-3479","authenticated-orcid":false,"given":"Anthony L.","family":"Einfeldt","sequence":"additional","affiliation":[{"name":"Marine Gene Probe Laboratory Department of Biology Dalhousie University  Halifax Nova Scotia Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1079-3791","authenticated-orcid":false,"given":"Tony","family":"Kess","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steve J.","family":"Duffy","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amber M.","family":"Messmer","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barbara L.","family":"Langille","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew K.","family":"Brachmann","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Johanne","family":"Gauthier","sequence":"additional","affiliation":[{"name":"Maurice Lamontagne Institute Fisheries and Oceans Canada  Mont\u2010Joli Quebec Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4288-7730","authenticated-orcid":false,"given":"Paul","family":"Bentzen","sequence":"additional","affiliation":[{"name":"Marine Gene Probe Laboratory Department of Biology Dalhousie University  Halifax Nova Scotia Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tim Martin","family":"Knutsen","sequence":"additional","affiliation":[{"name":"AquaGen AS  Trondheim Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Kent","sequence":"additional","affiliation":[{"name":"Centre for Integrative Genetics Department of Animal and Aquacultural Sciences Faculty of Biosciences Norwegian University of Life Sciences  \u00c5s Norway"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Danny","family":"Boyce","sequence":"additional","affiliation":[{"name":"Department of Ocean Sciences Ocean Sciences Centre Memorial University of Newfoundland  St John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian\u00a0R.","family":"Bradbury","sequence":"additional","affiliation":[{"name":"Northwest Atlantic Fisheries Centre Fisheries and Oceans Canada  St. John\u2019s Newfoundland and Labrador Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2022,2,25]]},"reference":[{"key":"e_1_2_10_2_1","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E15-08-0578"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2011.05.005"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1001899"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1159\/000223077"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1534\/g3.117.042697"},{"key":"e_1_2_10_7_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.2517-6161.1995.tb02031.x"},{"key":"e_1_2_10_8_1","unstructured":"Bourdages H. 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