{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T02:08:12Z","timestamp":1790820492605,"version":"4.1.0"},"reference-count":100,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,11,15]],"date-time":"2021-11-15T00:00:00Z","timestamp":1636934400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.nationalarchives.gov.uk\/doc\/open-government-licence\/version\/3\/"}],"funder":[{"name":"Canada 150 Sequencing Initiative","award":["Canseq150"],"award-info":[{"award-number":["Canseq150"]}]},{"name":"Genome Canada Technology Platform grants to Jiannis Ragoussis"},{"name":"National Sciences and Engineering Research Council of Canada (NSERC"},{"name":"Louis Bernatchez, C\u00e9line Audet"},{"name":"Pascal Sirois"},{"name":"R\u00e9jean Tremblay"},{"name":"Canadian Research Chair in Genomics and Conservation of Aquatic Resources"},{"name":"Ressources Aquatiques Qu\u00e9bec"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1594 scaffolds (scaffold N50\u2009=\u200925\u2009Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.<\/jats:p>","DOI":"10.1093\/g3journal\/jkab376","type":"journal-article","created":{"date-parts":[[2021,11,18]],"date-time":"2021-11-18T04:05:29Z","timestamp":1637208329000},"source":"Crossref","is-referenced-by-count":23,"title":["Chromosome-level assembly reveals a putative Y-autosomal fusion in the sex determination system of the Greenland Halibut (<i>Reinhardtius hippoglossoides<\/i>)"],"prefix":"10.1093","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9577-5508","authenticated-orcid":false,"given":"Anne-Laure","family":"Ferchaud","sequence":"first","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval, Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire","family":"M\u00e9rot","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval, Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Normandeau","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval, Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiannis","family":"Ragoussis","sequence":"additional","affiliation":[{"name":"McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, QC H3A 0G1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles","family":"Babin","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval, Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haig","family":"Djambazian","sequence":"additional","affiliation":[{"name":"McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, QC H3A 0G1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"B\u00e9rub\u00e9","sequence":"additional","affiliation":[{"name":"McGill Genome Centre and Department for Human Genetics, McGill University, Montreal, Quebec, QC H3A 0G1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3366-210X","authenticated-orcid":false,"given":"C\u00e9line","family":"Audet","sequence":"additional","affiliation":[{"name":"D\u00e9partement de l'Institut des Sciences de la Mer de Rimouski, Universit\u00e9 du Qu\u00e9bec \u00e0 Rimouski, Rimouski, QC G5L 3A1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9365-2398","authenticated-orcid":false,"given":"Margaret","family":"Treble","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada, Arctic Aquatic Research Division, Winnipeg Department, Freshwater Institute Winnipeg, Manitoba, MB R3T2N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wojciech","family":"Walkusz","sequence":"additional","affiliation":[{"name":"Fisheries and Oceans Canada, Arctic Aquatic Research Division, Winnipeg Department, Freshwater Institute Winnipeg, Manitoba, MB R3T2N6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8085-9709","authenticated-orcid":false,"given":"Louis","family":"Bernatchez","sequence":"additional","affiliation":[{"name":"D\u00e9partement de Biologie, Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS), Universit\u00e9 Laval, Qu\u00e9bec, QC G1V 0A6, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,15]]},"reference":[{"key":"2022013117312180700_jkab376-B1","first-page":"20162806","article-title":"Sex chromosome evolution: historical insights and future","volume":"284","author":"Abbott","year":"2016","journal-title":"Proc Biol Sci"},{"key":"2022013117312180700_jkab376-B2","doi-asserted-by":"crossref","first-page":"4692","DOI":"10.1093\/nar\/25.22.4692","article-title":"Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques","volume":"25","author":"Aljanabi","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2022013117312180700_jkab376-B3","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1016\/j.gde.2006.10.007","article-title":"A dynamic view of sex chromosome evolution","volume":"16","author":"Bachtrog","year":"2006","journal-title":"Curr Opin Genet Dev"},{"key":"2022013117312180700_jkab376-B4","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1038\/nrg3366","article-title":"Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration","volume":"14","author":"Bachtrog","year":"2013","journal-title":"Nat Rev Genet"},{"key":"2022013117312180700_jkab376-B5","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s12915-019-0627-7","article-title":"The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish","volume":"17","author":"Bao","year":"2019","journal-title":"BMC Biol"},{"key":"2022013117312180700_jkab376-B6","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1159\/000223077","article-title":"Environmental effects on fish sex determination and differentiation","volume":"3","author":"Baroiller","year":"2009","journal-title":"Sex Dev"},{"key":"2022013117312180700_jkab376-B7","doi-asserted-by":"crossref","first-page":"e0128036","DOI":"10.1371\/journal.pone.0128036","article-title":"Inexpensive multiplexed library preparation for megabase-sized genomes","volume":"10","author":"Baym","year":"2015","journal-title":"PLoS One"},{"key":"2022013117312180700_jkab376-B8","doi-asserted-by":"crossref","first-page":"6767","DOI":"10.1111\/mec.14217","article-title":"Sex matters in massive parallel sequencing: evidence for biases in genetic parameter estimation and investigation of sex determination systems","volume":"26","author":"Benestan","year":"2017","journal-title":"Mol Ecol"},{"key":"2022013117312180700_jkab376-B9","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1016\/j.tree.2017.06.010","article-title":"Harnessing the power of genomics to secure the future of seafood","volume":"32","author":"Bernatchez","year":"2017","journal-title":"Trends Ecol Evol"},{"key":"2022013117312180700_jkab376-B10","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.ympev.2014.01.006","article-title":"Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes)","volume":"73","author":"Betancur","year":"2014","journal-title":"Mol Phylogenet Evol"},{"key":"2022013117312180700_jkab376-B14","volume-title":"Evolution of Sex Determining Mechanisms","author":"Bull","year":"1983"},{"key":"2022013117312180700_jkab376-B15","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1038\/nrg.2017.60","article-title":"Vertebrate sex determination: evolutionary plasticity of a fundamental switch","volume":"18","author":"Capel","year":"2017","journal-title":"Nat Rev Genet"},{"key":"2022013117312180700_jkab376-B16","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/sj.hdy.6800697","article-title":"Steps in the evolution of heteromorphic sex chromosomes","volume":"95","author":"Charlesworth","year":"2005","journal-title":"Heredity (Edinb)"},{"key":"2022013117312180700_jkab376-B17","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/ng.2890","article-title":"Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle","volume":"46","author":"Chen","year":"2014","journal-title":"Nat Genet"},{"key":"2022013117312180700_jkab376-B18","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13578-020-00432-0","article-title":"Whole genome-wide chromosome fusion and new gene birth in the Monopterus albus genome","volume":"10","author":"Cheng","year":"2020","journal-title":"Cell Biosci"},{"key":"2022013117312180700_jkab376-B520560","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1006\/dbio.2000.0129","article-title":"Two sox9 genes on duplicated zebrafish chromosomes: expression of similar transcription activators in distinct sites","volume":"231","author":"Chiang","year":"2001","journal-title":"Developmental biology"},{"key":"2022013117312180700_jkab376-B19","first-page":"1","article-title":"Temperature-dependent sex determination: the interplay of steroid hormones and temperature","volume":"3","author":"Crews","year":"1976","journal-title":"Zoolog Sci"},{"key":"2022013117312180700_jkab376-B22","article-title":"Assessment of the Greenland Halibut Stock in the Gulf of St. Lawrence (4RST) in 2017","year":"2018"},{"key":"2022013117312180700_jkab376-B23","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1093\/icesjms\/fsx162","article-title":"Original article evaluating the use of the autodiametric method for estimating fecundity of Reinhardtius hippoglossoides, a species with an unusual oocyte development strategy","volume":"75","author":"Dominguez-Petit","year":"2018","journal-title":"ICES J Mar Sci"},{"key":"2022013117312180700_jkab376-B24","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1093\/jhered\/esx102","article-title":"Identification of genomic regions associated with sex in Pacific Halibut (S Grant, Ed)","volume":"109","author":"Drinan","year":"2018","journal-title":"J Hered"},{"key":"2022013117312180700_jkab376-B25","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/s12041-007-0013-z","article-title":"Cloning and study of adult-tissue-specific expression of\u00a0Sox9\u00a0in Cyprinus carpio","volume":"86","author":"Du","year":"2007","journal-title":"J Genet"},{"key":"2022013117312180700_jkab376-B26","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1093\/genetics\/162.3.1355","article-title":"Chromosomal rearrangements and evolution of recombination: comparison of chiasma distribution patterns in standard and Robertsonian populations of the house mouse","volume":"162","author":"Dumas","year":"2002","journal-title":"Genetics"},{"key":"2022013117312180700_jkab376-B28","first-page":"1:1686\u20131696","article-title":"Chromosome level reference of Atlantic Halibut Hippoglossus hippoglossus provides insight into the evolution of sexual determination systems","author":"Einfeldt","year":"2021","journal-title":"Mol Ecol Resources"},{"key":"2022013117312180700_jkab376-B30","first-page":"673","article-title":"The state of the gonads of the Barents sea Greenland Halibut, Reinhardtius hippoglossoides (Walb.) in connection with failure to spawn","volume":"11","author":"Fedorov","year":"1971","journal-title":"Vop Ichtiol"},{"key":"2022013117312180700_jkab376-B31","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1093\/dnares\/dsw007","article-title":"Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life","volume":"23","author":"Figueras","year":"2016","journal-title":"DNA Res"},{"key":"2022013117312180700_jkab376-B32","doi-asserted-by":"crossref","first-page":"3855","DOI":"10.1093\/bioinformatics\/btz200","article-title":"ngsLD: evaluating linkage disequilibrium using genotype likelihoods","volume":"35","author":"Fox","year":"2019","journal-title":"Bioinformatics"},{"key":"2022013117312180700_jkab376-B33","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1093\/gbe\/evaa081","article-title":"Sex chromosome evolution: so many exceptions to the rules","volume":"12","author":"Furman","year":"2020","journal-title":"Genome Biol Evol"},{"key":"2022013117312180700_jkab376-B34","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.gene.2014.04.062","article-title":"Identification and characterization of a\u00a0Sox2\u00a0homolog in the Japanese flounder Paralichthys olivaceus","volume":"544","author":"Gao","year":"2014","journal-title":"Gene"},{"key":"2022013117312180700_jkab376-B35","doi-asserted-by":"crossref","first-page":"105332","DOI":"10.1016\/j.fishres.2019.105332","article-title":"Influence of sex on growth of juvenile Greenland Halibut (Reinhardtius hippoglossoides) in the Estuary and Gulf of St. Lawrence","volume":"219","author":"Ghinter","year":"2019","journal-title":"Fisheries Res"},{"key":"2022013117312180700_jkab376-B37","doi-asserted-by":"crossref","first-page":"2747","DOI":"10.1111\/evo.12481","article-title":"Local adaptation and the evolution of chromosome fusions","volume":"68","author":"Guerrero","year":"2014","journal-title":"Evolution"},{"key":"2022013117312180700_jkab376-B38","first-page":"101","article-title":"Sexual determination and differentiation in teleost fish","author":"Guerrero-Est\u00e9vez","year":"2010","journal-title":"Rev Fish Biol Fisheries"},{"key":"2022013117312180700_jkab376-B39","doi-asserted-by":"crossref","first-page":"326","DOI":"10.3389\/fgene.2019.00326","article-title":"A high-density genetic linkage map and QTL mapping for sex in black tiger shrimp (Penaeus monodon)","volume":"10","author":"Guo","year":"2019","journal-title":"Front Genet"},{"key":"2022013117312180700_jkab376-B40","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1016\/j.aquaculture.2006.09.026","article-title":"Sexual dimorphism of fast muscle fibre recruitment in farmed Atlantic Halibut (Hippoglossus hippoglossus L.)","volume":"261","author":"Hagen","year":"2006","journal-title":"Aquaculture"},{"key":"2022013117312180700_jkab376-B41","doi-asserted-by":"crossref","first-page":"679","DOI":"10.3390\/genes10090679","article-title":"The duplicated Y-specific amhy gene is conserved and linked to maleness in silversides of the genus Odontesthes","volume":"10","author":"Hattori","year":"2019","journal-title":"Genes"},{"key":"2022013117312180700_jkab376-B43","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1095\/biolreprod.107.064246","article-title":"Sexual dimorphic expression of genes in gonads during early differentiation of a teleost fish, the Nile tilapia Oreochromis niloticus","volume":"78","author":"Ijiri","year":"2008","journal-title":"Biol Reprod"},{"key":"2022013117312180700_jkab376-B44","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1111\/j.1365-2109.1997.tb01022.x","article-title":"Sexual dimorphism in growth and maturation of turbot, Scophthalmus maximus (Rafinesque, 1810)","volume":"28","author":"Imsland","year":"1997","journal-title":"Aquaculture Res"},{"key":"2022013117312180700_jkab376-B46","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1111\/jfb.12579","article-title":"Sexual size dimorphism in three North Sea gadoids","volume":"86","author":"Keyl","year":"2015","journal-title":"J Fish Biol"},{"key":"2022013117312180700_jkab376-B47","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1101\/gr.113985.110","article-title":"Adaptive seeds tame genomic sequence comparison","volume":"21","author":"Kie\u0142basa","year":"2011","journal-title":"Genome Res"},{"key":"2022013117312180700_jkab376-B48","doi-asserted-by":"crossref","first-page":"e1000501","DOI":"10.1371\/journal.pbio.1000501","article-title":"How and why chromosome inversions evolve","volume":"8","author":"Kirkpatrick","year":"2010","journal-title":"PLoS Biol"},{"key":"2022013117312180700_jkab376-B49","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1007\/s10641-011-9853-8","article-title":"Turnover of sex chromosomes and speciation in fishes","volume":"94","author":"Kitano","year":"2012","journal-title":"Environ Biol Fishes"},{"key":"2022013117312180700_jkab376-B50","doi-asserted-by":"crossref","first-page":"1079","DOI":"10.1038\/nature08441","article-title":"A role for a neo-sex chromosome in stickleback speciation","volume":"461","author":"Kitano","year":"2009","journal-title":"Nature"},{"key":"2022013117312180700_jkab376-B51","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1101\/gr.5016106","article-title":"Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka","volume":"16","author":"Kondo","year":"2006","journal-title":"Genome Res"},{"key":"2022013117312180700_jkab376-B52","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1186\/s12859-014-0356-4","article-title":"ANGSD: analysis of Next Generation Sequencing Data","volume":"15","author":"Korneliussen","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2022013117312180700_jkab376-B53","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol"},{"key":"2022013117312180700_jkab376-B54","volume-title":"Numerical Ecology","author":"Legendre","year":"1998"},{"key":"2022013117312180700_jkab376-B55","doi-asserted-by":"crossref","first-page":"2074","DOI":"10.1111\/mec.15065","article-title":"Chromosome polymorphisms track trans-Atlantic divergence and secondary contact in Atlantic salmon","volume":"28","author":"Lehnert","year":"2019","journal-title":"Mol Ecol"},{"key":"2022013117312180700_jkab376-B56","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1534\/genetics.118.301747","article-title":"Local PCA shows how the effect of population structure differs along the genome","volume":"211","author":"Li","year":"2018","journal-title":"Genetics"},{"key":"2022013117312180700_jkab376-B57","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.3390\/ijms19092641","article-title":"Characteristics of\u00a0Cyp11a\u00a0during Gonad Differentiation of the Olive Flounder Paralichthys olivaceus","volume":"19","author":"Liang","year":"2018","journal-title":"Int J Mol Sci"},{"key":"2022013117312180700_jkab376-B58","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1038\/s41598-018-35983-3","article-title":"SOX2 participates in spermatogenesis of Zhikong scallop Chlamys farreri","volume":"9","author":"Liang","year":"2019","journal-title":"Sci Rep"},{"key":"2022013117312180700_jkab376-B59","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1126\/science.1181369","article-title":"Comprehensive mapping of long-range-interactions reveals folding principles of the human genome","volume":"326","author":"Lieberman-Aiden","year":"2009","journal-title":"Science"},{"key":"2022013117312180700_jkab376-B60","first-page":"1","article-title":"A beginner\u2019s guide to low-coverage whole genome sequencing for population genomics","author":"Lou","year":"2021","journal-title":"Mol Ecol"},{"key":"2022013117312180700_jkab376-B61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ygeno.2021.04.007","article-title":"A genome-wide association study, supported by a new chromosome-level genome assembly, suggests sox2 as a main driver of the undifferentiatiated ZZ\/ZW sex determination of turbot (Scophthalmus maximus)","volume":"113","author":"Martinez","year":"2021","journal-title":"Genomics"},{"key":"2022013117312180700_jkab376-B62","first-page":"340","article-title":"Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture","volume":"5","author":"Martinez","year":"2014","journal-title":"Front Genet"},{"key":"2022013117312180700_jkab376-B63","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1093\/genetics\/165.3.1317","article-title":"sequence differentiation associated with an inversion on the neo-x chromosome of Drosophila americana","volume":"165","author":"McAllyster","year":"2003","journal-title":"Genetics"},{"key":"2022013117312180700_jkab376-B64","doi-asserted-by":"crossref","first-page":"764","DOI":"10.1093\/gbe\/evaa092","article-title":"Highlight: exceptions are the rule in sex determination","volume":"12","author":"McGrath","year":"2020","journal-title":"Genome Biol Evol"},{"key":"2022013117312180700_jkab376-B65","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1534\/genetics.118.301336","article-title":"Inferring population structure and admixture proportions in low-depth NGS data","volume":"210","author":"Meisner","year":"2018","journal-title":"Genetics"},{"key":"2022013117312180700_jkab376-B66","doi-asserted-by":"crossref","first-page":"msab143","DOI":"10.1093\/molbev\/msab143","article-title":"Locally adaptive inversions modulate genetic variation at different geographic scales in a seaweed fly","volume":"38","author":"M\u00e9rot","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2022013117312180700_jkab376-B67","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.bbrc.2005.05.158","article-title":"Testicular type\u00a0Sox9\u00a0is not involved in sex determination but might be in the development of testicular structures in the medaka, Oryzias latipes","volume":"333","author":"Nakamoto","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"key":"2022013117312180700_jkab376-B68","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1002\/(SICI)1097-010X(19980801)281:5<362::AID-JEZ3>3.0.CO;2-M","article-title":"Gonadal sex differentiation in teleost fish","volume":"281","author":"Nakamura","year":"1998","journal-title":"J Exp Zool"},{"key":"2022013117312180700_jkab376-B69","doi-asserted-by":"crossref","first-page":"11778","DOI":"10.1073\/pnas.182314699","article-title":"A duplicated copy of\u00a0DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes","volume":"99","author":"Nanda","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"2022013117312180700_jkab376-B70","first-page":"443","volume":"12","author":"Nielsen","year":"2011","journal-title":"Genotype and SNP Calling from Next-Generation Sequencing Data"},{"key":"2022013117312180700_jkab376-B71","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/B978-0-12-394815-1.00011-2","volume-title":"Vertebrate Endocrinology","author":"Norris","year":"2013","edition":"5th ed."},{"key":"2022013117312180700_jkab376-B72","doi-asserted-by":"crossref","first-page":"e2837","DOI":"10.1371\/journal.pone.0002837","article-title":"Temperature-dependent sex determination in fish revisited: prevalence, a single sex ratio response pattern, and possible effects of climate change","volume":"3","author":"Ospina-Alvarez","year":"2008","journal-title":"PLoS One"},{"key":"2022013117312180700_jkab376-B73","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/faf.12052","article-title":"Ocean's eleven: a critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries","volume":"16","author":"Ovenden","year":"2013","journal-title":"Fish Fish"},{"key":"2022013117312180700_jkab376-B74","doi-asserted-by":"crossref","first-page":"e1008013","DOI":"10.1371\/journal.pgen.1008013","article-title":"Identification of the master sex determining gene in Northern pike (Esox lucius) reveals restricted sex chromosome differentiation","volume":"15","author":"Pan","year":"2019","journal-title":"PLoS Genet"},{"key":"2022013117312180700_jkab376-B75","doi-asserted-by":"crossref","first-page":"e62858","DOI":"10.7554\/eLife.62858","article-title":"The rise and fall of the ancient Northern pike master sex-determining gene","volume":"10","author":"Pan","year":"2021","journal-title":". eLife"},{"key":"2022013117312180700_jkab376-B76","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1186\/1471-2164-14-566","article-title":"Mapping the sex determination locus in the Atlantic Halibut (Hippoglossus hippoglossus) using RAD sequencing","volume":"14","author":"Palaiokostas","year":"2013","journal-title":"BMC Genomics"},{"key":"2022013117312180700_jkab376-B77","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.theriogenology.2015.03.017","article-title":"First evidence of molecular characterization of rohu carp\u00a0Sox2\u00a0gene being expressed in proliferating spermatogonial cells","volume":"84","author":"Patra","year":"2015","journal-title":"Theriogenology"},{"key":"2022013117312180700_jkab376-B78","doi-asserted-by":"crossref","first-page":"e1005237","DOI":"10.1371\/journal.pgen.1005237","article-title":"Y fuse? sex chromosome fusions in fishes and reptiles","volume":"11","author":"Pennell","year":"2015","journal-title":"PLoS Genet"},{"key":"2022013117312180700_jkab376-B80","doi-asserted-by":"crossref","first-page":"R93","DOI":"10.1530\/REP-15-0106","article-title":"The role of non-coding RNAs in male sex determination and differentiation","volume":"150","author":"Rastetter","year":"2015","journal-title":"Reproduction"},{"key":"2022013117312180700_jkab376-B81","volume-title":": A Language and Environment for Statistical Computing","author":"Core Team","year":"2020"},{"key":"2022013117312180700_jkab376-B82","doi-asserted-by":"crossref","first-page":"1527","DOI":"10.1016\/j.cell.2015.10.071","article-title":"Insights into sex chromosome evolution and aging from the genome of a short-lived fish","volume":"163","author":"Reichwald","year":"2015","journal-title":"Cell"},{"key":"2022013117312180700_jkab376-B83","doi-asserted-by":"crossref","first-page":"15","DOI":"10.2960\/J.v44.m679","article-title":"Oocyte development and vitellogenin production in Northwest Atlantic Greenland Halibut Reinhardtius hippoglossoides","volume":"44","author":"Rideout","year":"2012","journal-title":"J Northwest Atlantic Fish Sci"},{"key":"2022013117312180700_jkab376-B84","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1111\/jfb.12664","article-title":"High-density aggregations of rodlet cells in the gonads of Greenland Halibut Reinhardtius hippoglossoides, a deep-water marine flatfish","volume":"86","author":"Rideout","year":"2015","journal-title":"J Fish Biol"},{"key":"2022013117312180700_jkab376-B85","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1111\/j.1095-8649.1989.tb02992.x","article-title":"Sexual dimorphism in the energetics of reproduction and growth of the North Sea plaice, Pleuronectes platessa L","volume":"35","author":"Rljnsdorp","year":"1989","journal-title":"J Fish Biol"},{"key":"2022013117312180700_jkab376-B86","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.cbd.2016.12.001","article-title":"Integrating genomic resources of flatfish (Pleuronectiformes) to boost aquaculture production","volume":"21","author":"Robledo","year":"2017","journal-title":"Comp Biochem Physiol Part D Genomics Proteomics"},{"key":"2022013117312180700_jkab376-B87","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1186\/s13104-016-2030-6","article-title":"A PCR assay detects a male-specific duplicated copy of Anti-M\u00fcllerian hormone (amh) in the lingcod (Ophiodon elongatus)","volume":"9","author":"Rondeau","year":"2016","journal-title":"BMC Res Notes"},{"key":"2022013117312180700_jkab376-B88","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41592-019-0669-3","article-title":"Fast and accurate long-read assembly with wtdbg2","volume":"17","author":"Ruan","year":"2020","journal-title":"Nat Methods"},{"key":"2022013117312180700_jkab376-B90","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/ng.3732","article-title":"The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry","volume":"49","author":"Shao","year":"2017","journal-title":"Nat Genet"},{"key":"2022013117312180700_jkab376-B91","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1007\/s10695-007-9131-z","article-title":"Cloning of the full-length coding sequence and expression analysis of\u00a0Sox9b\u00a0in guppy (Poecilia reticulata)","volume":"33","author":"Shen","year":"2007","journal-title":"Fish Physiol Biochem"},{"key":"2022013117312180700_jkab376-B92","doi-asserted-by":"crossref","first-page":"3210","DOI":"10.1093\/bioinformatics\/btv351","article-title":"BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs","volume":"31","author":"Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"2022013117312180700_jkab376-B93","author":"Smit","year":"2013"},{"key":"2022013117312180700_jkab376-B94","doi-asserted-by":"crossref","first-page":"e68","DOI":"10.1093\/nar\/gkr123","article-title":"SyMAP v3.4: a turnkey synteny system with application to plant genomes","volume":"39","author":"Soderlund","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2022013117312180700_jkab376-B95","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1101\/gr.5396706","article-title":"SyMAP: a system for discovering and viewing syntenic regions of FPC maps","volume":"16","author":"Soderlund","year":"2006","journal-title":"Genome Res"},{"key":"2022013117312180700_jkab376-B96","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.1534\/g3.117.040915","article-title":"Sex chromosome evolution, Heterochiasmy, and Physiological QTL in the salmonid brook charr Salvelinus fontinalis","volume":"7","author":"Sutherland","year":"2017","journal-title":"G3 (Bethesda)"},{"key":"2022013117312180700_jkab376-B97","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/S0378-1119(97)00483-6","article-title":"Rainbow trout\u00a0SOX9: cDNA cloning, gene structure and expression","volume":"202","author":"Takamatsu","year":"1997","journal-title":"Gene"},{"key":"2022013117312180700_jkab376-B98","author":"Tavares","year":"2021"},{"key":"2022013117312180700_jkab376-B99","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1111\/1755-0998.12593","article-title":"Practical low-coverage genomewide sequencing of hundreds of individually barcoded samples for population and evolutionary genomics in nonmodel species","volume":"17","author":"Therkildsen","year":"2017","journal-title":"Mol Ecol Resour"},{"key":"2022013117312180700_jkab376-B101","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.tree.2007.03.008","article-title":"The evolution of sex ratios and sex-determining systems","volume":"22","author":"Uller","year":"2007","journal-title":"Trends Ecol Evol"},{"key":"2022013117312180700_jkab376-B102","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.ympev.2018.03.014","article-title":"Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling","volume":"125","author":"Vinnikov","year":"2018","journal-title":"Mol Phylogenet Evol"},{"key":"2022013117312180700_jkab376-B103","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1002\/dvdy.21212","article-title":"Characterization of early molecular sex differentiation in rainbow trout, Oncorhynchus mykiss","volume":"236","author":"Vizziano","year":"2007","journal-title":"Dev Dyn"},{"key":"2022013117312180700_jkab376-B104","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1186\/1477-7827-3-63","article-title":"Zebrafish sex determination and differentiation: involvement of\u00a0FTZ-F1\u00a0genes","volume":"3","author":"VonHofsten","year":"2005","journal-title":"Rep Biol Endocrinol"},{"key":"2022013117312180700_jkab376-B105","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1111\/mec.14965","article-title":"Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon","volume":"28","author":"Wellband","year":"2019","journal-title":"Mol Ecol"},{"key":"2022013117312180700_jkab376-B106","doi-asserted-by":"crossref","first-page":"641","DOI":"10.1111\/1755-0998.13312","article-title":"The changing face of genome assemblies: guidance on achieving high-quality reference genomes","volume":"21","author":"Whibley","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2022013117312180700_jkab376-B107","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2022013117312180700_jkab376-B109","doi-asserted-by":"crossref","first-page":"12087","DOI":"10.1038\/ncomms12087","article-title":"How to make a sex chromosome","volume":"7","author":"Wright","year":"2016","journal-title":"Nat Commun"},{"key":"2022013117312180700_jkab376-B111","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1002\/mrd.10169","article-title":"Sox9\u00a0in a teleost fish, medaka (Oryzias latipes): evidence for diversified function of Sox9 in gonad differentiation","volume":"63","author":"Yokoi","year":"2002","journal-title":"Mol Reprod Dev"},{"key":"2022013117312180700_jkab376-B112","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1111\/eva.12032","article-title":"The sexually dimorphic on the Y chromosome gene (sdY) is a conserved male specific Y chromosome sequence in many salmonids","volume":"6","author":"Yano","year":"2013","journal-title":"Evol Appl"},{"key":"2022013117312180700_jkab376-B115","doi-asserted-by":"crossref","first-page":"305","DOI":"10.4252\/wjsc.v6.i3.305","article-title":"Sox2, a key factor in the regulation of pluripotency and neural differentiation","volume":"6","author":"Zhang","year":"2014","journal-title":"World journal of stem cells"},{"key":"2022013117312180700_jkab376-B114","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1002\/mrd.10271","article-title":"Similar gene structure of two\u00a0Sox9a\u00a0genes and their expression patterns during gonadal differentiation in a teleost fish, rice field eel (Monopterus albus)","volume":"66","author":"Zhou","year":"2003","journal-title":"Mol Reprod Dev"}],"container-title":["G3 Genes|Genomes|Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkab376\/41365405\/jkab376.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/12\/1\/jkab376\/42341237\/jkab376.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/12\/1\/jkab376\/42341237\/jkab376.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T18:03:41Z","timestamp":1643652221000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkab376\/6428537"}},"subtitle":[],"editor":[{"given":"M","family":"Arbeitman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,11,15]]},"references-count":100,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,11,15]]},"published-print":{"date-parts":[[2022,1,4]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkab376","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,1,1]]},"published":{"date-parts":[[2021,11,15]]},"article-number":"jkab376"}}