{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T22:26:47Z","timestamp":1792794407656,"version":"4.5.0"},"reference-count":82,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Regional Government Xunta de Galicia","award":["ED431C 2022\/33"],"award-info":[{"award-number":["ED431C 2022\/33"]}],"id":[{"id":"https:\/\/ror.org\/0181xnw06","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Regional Government Xunta de Galicia","award":["101066785"],"award-info":[{"award-number":["101066785"]}],"id":[{"id":"https:\/\/ror.org\/0181xnw06","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Regional Government Xunta de Galicia","award":["PID2022-137821OB-C31"],"award-info":[{"award-number":["PID2022-137821OB-C31"]}],"id":[{"id":"https:\/\/ror.org\/0181xnw06","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Sex determination is exceptionally diverse and shows a high evolutionary rate in fish. European hake (Merluccius merluccius) is a species of great commercial value distributed throughout European coasts, which displays a significant sexual growth dimorphism. We present a chromosome-level genome of M. merluccius, composed of 215 contigs using long- and short-read sequencing, further scaffolded into the species\u2019 21 chromosomes using Hi-C technique (715\u2005Mb). RNA-seq on several tissues from pooled individuals improved annotation (26,625 protein-coding genes and 11,083 ncRNAs). Five males and 5 females from an Atlantic population were re-sequenced at 30\u00d7 depth to look for association with sex across the whole genome. Genetic differentiation between males and females (FST) and intrapopulation fixation index (FIS) pointed to a region on chromosome 9 spanning \u223c10\u2005Mb which included several genes related to gonad differentiation and showed strong linkage disequilibrium associated with a putative inversion. Near sox3 gene (\u223c25\u2005kb), SNPs were mostly heterozygous in males and homozygous in females, consistent with an XX\/XY sex-determining (SD) system. These SNP markers were validated in a larger sample of 56 males and 63 females from the same population using MassARRAY. Other genomic regions that were differentiated between males and females and suggestive of sexual conflict were also explored across the genome. Results support a candidate master SD gene in M. merluccius and indicate some differentiated regions potentially under sexual conflict. This information will be useful for the fisheries management of M. merluccius in the context of climate change, where noninvasive sex identification tools are essential.<\/jats:p>","DOI":"10.1093\/g3journal\/jkaf127","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T08:57:00Z","timestamp":1749459420000},"source":"Crossref","is-referenced-by-count":3,"title":["Screening a new European hake (\n                    <i>Merluccius merluccius<\/i>\n                    ) chromosome-level genome assembly suggests an XX\/XY sex-determining system driven by the SRY-box transcription factor 3 (\n                    <i>sox3<\/i>\n                    )"],"prefix":"10.1093","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8438-9305","authenticated-orcid":false,"given":"Paulino","family":"Mart\u00ednez","sequence":"first","affiliation":[{"name":"Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela , 27002 Lugo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6617-8731","authenticated-orcid":false,"given":"Laura","family":"Casas","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Marinas (IIM-CSIC) , 36208 Vigo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natalia","family":"Petit-Marty","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Marinas (IIM-CSIC) , 36208 Vigo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9s","family":"Blanco","sequence":"additional","affiliation":[{"name":"Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela , 27002 Lugo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maialen","family":"Carballeda","sequence":"additional","affiliation":[{"name":"Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela , 27002 Lugo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nair","family":"Vilas-Arrondo","sequence":"additional","affiliation":[{"name":"Centro Oceanogr\u00e1fico de Vigo, Instituto Espa\u00f1ol de Oceanograf\u00eda (IEO-CSIC) , 36390 Vigo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"G\u00f3mez-Garrido","sequence":"additional","affiliation":[{"name":"Centre Nacional D'An\u00e0lisi Gen\u00f2mica (CNAG) , 08028 Barcelona ,","place":["Spain"]},{"name":"Universitat de Barcelona , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando","family":"Cruz","sequence":"additional","affiliation":[{"name":"Centre Nacional D'An\u00e0lisi Gen\u00f2mica (CNAG) , 08028 Barcelona ,","place":["Spain"]},{"name":"Universitat de Barcelona , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julio","family":"Valeiras","sequence":"additional","affiliation":[{"name":"Centro Oceanogr\u00e1fico de Vigo, Instituto Espa\u00f1ol de Oceanograf\u00eda (IEO-CSIC) , 36390 Vigo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Alioto","sequence":"additional","affiliation":[{"name":"Centre Nacional D'An\u00e0lisi Gen\u00f2mica (CNAG) , 08028 Barcelona ,","place":["Spain"]},{"name":"Universitat de Barcelona , 08028 Barcelona ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2760-8169","authenticated-orcid":false,"given":"Fran","family":"Saborido-Rey","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Marinas (IIM-CSIC) , 36208 Vigo ,","place":["Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,9]]},"reference":[{"issue":"1","key":"2025081214122341100_jkaf127-B1","doi-asserted-by":"publisher","first-page":"e56","DOI":"10.1002\/cpbi.56","article-title":"Using geneid to identify genes","volume":"64","author":"Alioto","year":"2018","journal-title":"Curr Protoc Bioinformatics"},{"issue":"3","key":"2025081214122341100_jkaf127-B2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"2025081214122341100_jkaf127-B3","doi-asserted-by":"publisher","first-page":"103281","DOI":"10.1016\/j.rsma.2023.103281","article-title":"Reproductive aspects of European hake, (Merluccius merluccius, Linnaeus, 1758) based on histological depiction of both sexes in the Eastern Mediterranean (Aegean Sea)","volume":"68","author":"Apostologamvrou","year":"2023","journal-title":"Reg Stud Mar Sci"},{"issue":"7","key":"2025081214122341100_jkaf127-B4","doi-asserted-by":"publisher","first-page":"e1001899","DOI":"10.1371\/journal.pbio.1001899","article-title":"Sex determination: why so many ways of doing it?","volume":"12","author":"Bachtrog","year":"2014","journal-title":"PLoS Biol"},{"issue":"12","key":"2025081214122341100_jkaf127-B5","doi-asserted-by":"crossref","first-page":"1761","DOI":"10.1111\/jeb.14242","article-title":"How chromosomal inversions reorient the evolutionary process","volume":"36","author":"Berdan","year":"2023","journal-title":"J Evol Biol"},{"issue":"1","key":"2025081214122341100_jkaf127-B6","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/s00251-020-01194-2","article-title":"The intersection of stress, sex and immunity in fishes","volume":"73","author":"Campbell","year":"2021","journal-title":"Immunogenetics"},{"key":"2025081214122341100_jkaf127-B7","doi-asserted-by":"publisher","first-page":"1238133","DOI":"10.3389\/fmars.2023.1238133","article-title":"Editorial: prospects and challenges for the implementation of HTS genetic methods in fisheries research surveys and stock assessments","volume":"10","author":"Casas","year":"2023","journal-title":"Front Mar Sci"},{"key":"2025081214122341100_jkaf127-B8","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/978-94-011-1300-7_5","volume-title":"Hake. Chapman and Hall Fish and Fisheries Series","author":"Casey","year":"1995"},{"key":"2025081214122341100_jkaf127-B9","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.fishres.2013.11.010","article-title":"Estimating growth from sex ratio-at-length data in species with sexual size dimorphism","volume":"160","author":"Cervi\u00f1o","year":"2014","journal-title":"Fish Res"},{"key":"2025081214122341100_jkaf127-B10","doi-asserted-by":"publisher","first-page":"1361","DOI":"10.1534\/g3.119.400908","article-title":"BlobToolKit\u2014interactive quality assessment of genome assemblies","volume":"10","author":"Challis","year":"2020","journal-title":"G3 (Bethesda)"},{"key":"2025081214122341100_jkaf127-B11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-1-4939-9173-0_1","article-title":"tRNAscan-SE: searching for tRNA genes in genomic sequences","volume":"1962","author":"Chan","year":"2019","journal-title":"Methods Mol Biol"},{"key":"2025081214122341100_jkaf127-B12","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"2025081214122341100_jkaf127-B13","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B14","doi-asserted-by":"publisher","first-page":"e12618","DOI":"10.1111\/gbb.12618","article-title":"Sex differences in main olfactory system pathways involved in psychosexual function","volume":"19","author":"Cherry","year":"2020","journal-title":"Genes Brain Behav"},{"key":"2025081214122341100_jkaf127-B15","doi-asserted-by":"publisher","first-page":"258","DOI":"10.3390\/genes8100258","article-title":"Chromosomal evolution in lower vertebrates: sex chromosomes in neotropical fishes","volume":"8","author":"Cioffi","year":"2017","journal-title":"Genes (Basel)."},{"key":"2025081214122341100_jkaf127-B16","doi-asserted-by":"publisher","first-page":"i332","DOI":"10.1093\/bioinformatics\/btw271","article-title":"CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction","volume":"32","author":"Cui","year":"2016","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B17","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1111\/1755-0998.13750","article-title":"A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis","volume":"23","author":"De la Herr\u00e1n","year":"2023","journal-title":"Mol Ecol Resour"},{"key":"2025081214122341100_jkaf127-B18","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1111\/jfb.15241","article-title":"Sex reversal of pejerrey (Odontesthes bonariensis), a species with temperature-dependent sex determination, in a seminatural environment","volume":"102","author":"Del Fresno","year":"2023","journal-title":"J Fish Biol"},{"key":"2025081214122341100_jkaf127-B19","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B20","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1016\/j.fishres.2009.09.002","article-title":"New bioenergetic perspective of European hake (Merluccius merluccius L.) reproductive ecology","volume":"104","author":"Dom\u00ednguez-Petit","year":"2010","journal-title":"Fisheries Res"},{"key":"2025081214122341100_jkaf127-B21","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.ejar.2021.12.003","article-title":"Growth and mortality of the European hake Merluccius merluccius (Linnaeus, 1758) from the North of Moroccan Atlantic coasts","volume":"48","author":"El Bouzidi","year":"2022","journal-title":"Egypt J Aquat Res"},{"key":"2025081214122341100_jkaf127-B22","doi-asserted-by":"publisher","author":"FAO","DOI":"10.4060\/cb2429en"},{"key":"2025081214122341100_jkaf127-B23","doi-asserted-by":"publisher","first-page":"101886","DOI":"10.1016\/j.isci.2020.101886","article-title":"Fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations","volume":"24","author":"Ferraresso","year":"2021","journal-title":"iScience"},{"key":"2025081214122341100_jkaf127-B24","doi-asserted-by":"publisher","first-page":"eabq5072","DOI":"10.1126\/sciadv.abq5072","article-title":"ESPRESSO: robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data","volume":"9","author":"Gao","year":"2023","journal-title":"Sci Adv"},{"key":"2025081214122341100_jkaf127-B25","doi-asserted-by":"publisher","first-page":"e0146150","DOI":"10.1371\/journal.pone.0146150","article-title":"Molecular cytogenetic analysis of the European hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA gene clusters map to the same location","volume":"10","author":"Garc\u00eda-Souto","year":"2015","journal-title":"PLoS One"},{"key":"2025081214122341100_jkaf127-B26","doi-asserted-by":"publisher","DOI":"10.48546\/WORKFLOWHUB.WORKFLOW.567.2","article-title":"CLAWS (CNAG's long-read assembly workflow in Snakemake)","author":"Gomez-Garrido","year":"2024","journal-title":"WorkflowHub"},{"key":"2025081214122341100_jkaf127-B27","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1093\/bioinformatics\/btaa025","article-title":"Identifying and removing haplotypic duplication in primary genome assemblies","volume":"36","author":"Guan","year":"2020","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B28","first-page":"35","volume-title":"Sex Control in Aquaculture","author":"Guiguen","year":"2019"},{"key":"2025081214122341100_jkaf127-B29","doi-asserted-by":"publisher","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol"},{"key":"2025081214122341100_jkaf127-B30","doi-asserted-by":"publisher","first-page":"1576","DOI":"10.1002\/humu.24458","article-title":"A survey of current methods to detect and genotype inversions","volume":"43","author":"Hanlon","year":"2022","journal-title":"Hum Mutat."},{"key":"2025081214122341100_jkaf127-B31","doi-asserted-by":"publisher","first-page":"4800","DOI":"10.1016\/j.cub.2021.08.030","article-title":"A supernumerary \u201cB-sex\u201d chromosome drives male sex determination in the Pach\u00f3n cavefish, Astyanax mexicanus","volume":"31","author":"Imarazene","year":"2021","journal-title":"Curr Biol"},{"key":"2025081214122341100_jkaf127-B32","doi-asserted-by":"publisher","first-page":"614675","DOI":"10.3389\/fmars.2021.614675","article-title":"Spatio-temporal assessment of the European hake (Merluccius merluccius) recruits in the Northern Iberian Peninsula","volume":"8","author":"Izquierdo","year":"2021","journal-title":"Front Mar Sci"},{"key":"2025081214122341100_jkaf127-B33","doi-asserted-by":"publisher","first-page":"jkae183","DOI":"10.1093\/g3journal\/jkae183","article-title":"Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing","volume":"14","author":"Johnson","year":"2024","journal-title":"G3 (Bethesda) Genes, Genomes, Genetics"},{"key":"2025081214122341100_jkaf127-B34","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/s12862-018-1119-z","article-title":"The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs","volume":"18","author":"Katsura","year":"2018","journal-title":"BMC Evol Biol"},{"key":"2025081214122341100_jkaf127-B35","doi-asserted-by":"publisher","first-page":"91","DOI":"10.3389\/fnins.2014.00091","article-title":"Gender-typical olfactory regulation of sexual behavior in goldfish","volume":"8","author":"Kawaguchi","year":"2014","journal-title":"Front Neurosci"},{"key":"2025081214122341100_jkaf127-B36","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1038\/s41598-018-36748-8","article-title":"Characterization of a male specifc region containing a candidate sex determining gene in Atlantic cod","volume":"9","author":"Kirubakaran","year":"2019","journal-title":"Sci Rep"},{"key":"2025081214122341100_jkaf127-B37","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1146\/annurev-animal-021122-113935","article-title":"Diversity and convergence of sex-determination mechanisms in Teleost fish","volume":"12","author":"Kitano","year":"2024","journal-title":"Annu Rev Anim Biosci"},{"key":"2025081214122341100_jkaf127-B38","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1038\/nri.2016.90","article-title":"Sex differences in immune responses","volume":"16","author":"Klein","year":"2016","journal-title":"Nat Rev Immunol"},{"key":"2025081214122341100_jkaf127-B39","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/bs.ctdb.2019.02.004","article-title":"Genetic regulation of sex determination and maintenance in zebrafish (Danio rerio)","volume":"134","author":"Kossack","year":"2019","journal-title":"Curr Top Dev Biol"},{"key":"2025081214122341100_jkaf127-B40","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1134\/S003294522401003X","article-title":"Finding of the European hake Merluccius merluccius (Merlucciidae) off the Black Sea shore of Crimea","volume":"64","author":"Kutsyn","year":"2024","journal-title":"J Ichthyol"},{"key":"2025081214122341100_jkaf127-B41","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1111\/j.1558-5646.1993.tb02108.x","article-title":"Variation in environmental and genotypic sex-determining mechanisms across a latitudinal gradient in the fish, Menidia menidia","volume":"47","author":"Lagomarsino","year":"1993","journal-title":"Evolution"},{"key":"2025081214122341100_jkaf127-B42","doi-asserted-by":"publisher","first-page":"e17236","DOI":"10.1111\/GCB.17236","article-title":"Predicting the future of our oceans\u2014evaluating genomic forecasting approaches in marine species","volume":"30","author":"Layton","year":"2024","journal-title":"Glob Chang Biol"},{"key":"2025081214122341100_jkaf127-B43","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B44","doi-asserted-by":"publisher","first-page":"btad014","DOI":"10.1093\/bioinformatics\/btad014","article-title":"Protein-to-genome alignment with miniprot","volume":"39","author":"Li","year":"2023","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B45","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B46","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B47","doi-asserted-by":"publisher","first-page":"e119","DOI":"10.1093\/nar\/gku557","article-title":"Integration of mapped RNA-seq reads into automatic training of eukaryotic gene finding algorithm","volume":"42","author":"Lomsadze","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2025081214122341100_jkaf127-B48","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","article-title":"BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes","volume":"38","author":"Manni","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025081214122341100_jkaf127-B49","author":"Mart\u00ednez"},{"key":"2025081214122341100_jkaf127-B50","doi-asserted-by":"publisher","first-page":"1705","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 undifferentiated ZZ\/ZW sex determination of turbot (Scophthalmus maximus)","volume":"113","author":"Mart\u00ednez","year":"2021","journal-title":"Genomics"},{"key":"2025081214122341100_jkaf127-B51","doi-asserted-by":"publisher","first-page":"340","DOI":"10.3389\/fgene.2014.00340","article-title":"Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture","volume":"5","author":"Mart\u00ednez","year":"2014","journal-title":"Front Genet"},{"key":"2025081214122341100_jkaf127-B52","doi-asserted-by":"publisher","first-page":"106419","DOI":"10.1016\/j.fishres.2022.106419","article-title":"European hake (Merluccius merluccius) stock structure in the Mediterranean as assessed by otolith shape and microchemistry","volume":"254","author":"Morales-Nin","year":"2022","journal-title":"Fish Res"},{"key":"2025081214122341100_jkaf127-B53","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/B978-0-12-381015-1.00002-2","article-title":"The biology and fisheries of European hake, Merluccius merluccius, in the North-East Atlantic","volume":"58","author":"Murua","year":"2010","journal-title":"Adv Mar Biol"},{"key":"2025081214122341100_jkaf127-B54","doi-asserted-by":"publisher","first-page":"2685","DOI":"10.1534\/g3.115.021543","article-title":"Turnover of sex chromosomes in celebensis group medaka fishes","volume":"5","author":"Myosho","year":"2015","journal-title":"G3 (Bethesda)."},{"key":"2025081214122341100_jkaf127-B55","doi-asserted-by":"publisher","first-page":"e1009705","DOI":"10.1371\/journal.pgen.1009705","article-title":"A Y-linked anti-M\u00fcllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis","volume":"17","author":"Nakamoto","year":"2021","journal-title":"PLoS Genet"},{"key":"2025081214122341100_jkaf127-B56","doi-asserted-by":"publisher","first-page":"2933","DOI":"10.1093\/bioinformatics\/btt509","article-title":"Infernal 1.1: 100-fold faster RNA homology searches","volume":"29","author":"Nawrocki","year":"2013","journal-title":"Bioinformatics"},{"key":"2025081214122341100_jkaf127-B57","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1038\/nmeth.4078","article-title":"TACO produces robust multisample transcriptome assemblies from RNA-seq","volume":"14","author":"Niknafs","year":"2017","journal-title":"Nat Methods"},{"key":"2025081214122341100_jkaf127-B58","doi-asserted-by":"publisher","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":"2025081214122341100_jkaf127-B59","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1038\/hdy.2012.73","article-title":"Genetic interactions controlling sex and color establish the potential for sexual conflict in Lake Malawi cichlid fishes","volume":"110","author":"Parnell","year":"2013","journal-title":"Heredity (Edinb)."},{"key":"2025081214122341100_jkaf127-B60","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat Biotechnol"},{"key":"2025081214122341100_jkaf127-B61","doi-asserted-by":"publisher","first-page":"1086","DOI":"10.1016\/S1054-3139(03)00086-9","article-title":"Age estimation, growth and maturity of the European hake (Merluccius merluccius (Linnaeus, 1758)) from Iberian Atlantic waters","volume":"60","author":"Pi\u00f1eiro","year":"2003","journal-title":"ICES J Mar Sci"},{"key":"2025081214122341100_jkaf127-B62","doi-asserted-by":"publisher","first-page":"110277","DOI":"10.1016\/j.ygeno.2022.110277","article-title":"Decoding sex: elucidating sex determination and how high-quality genome assemblies are untangling the evolutionary dynamics of sex chromosomes","volume":"114","author":"Ramos","year":"2022","journal-title":"Genomics"},{"key":"2025081214122341100_jkaf127-B63","doi-asserted-by":"publisher","first-page":"1432","DOI":"10.1038\/s41467-020-14998-3","article-title":"GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes","volume":"11","author":"Ranallo-Benavidez","year":"2020","journal-title":"Nat Commun"},{"key":"2025081214122341100_jkaf127-B64","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1093\/oxfordjournals.jhered.a111573","article-title":"GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism","volume":"86","author":"Raymond","year":"1995","journal-title":"J Hered"},{"key":"2025081214122341100_jkaf127-B65","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1126\/science.1174705","article-title":"Sexual conflict resolved by invasion of a novel sex determiner in Lake Malawi cichlid fishes","volume":"26","author":"Roberts","year":"2009","journal-title":"Science"},{"key":"2025081214122341100_jkaf127-B66","doi-asserted-by":"publisher","first-page":"1095171","DOI":"10.3389\/fmars.2023.1095171","article-title":"The potential use of genomic methods in bottom trawl surveys to improve stock assessments in Europe","volume":"10","author":"Rodr\u00edguez-Mendoza","year":"2023","journal-title":"Front Mar Sci"},{"key":"2025081214122341100_jkaf127-B67","doi-asserted-by":"publisher","first-page":"18411","DOI":"10.1038\/s41598-019-54672-3","article-title":"New insights in oocyte dynamics shed light on the complexities associated with fish reproductive strategies","volume":"9","author":"Serrat","year":"2019","journal-title":"Sci Rep"},{"key":"2025081214122341100_jkaf127-B68","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1007\/s12562-020-01454-w","article-title":"Sexual bipotentiality of the olfactory pathway for sexual behavior in goldfish","volume":"86","author":"Shinohara","year":"2020","journal-title":"Fish Sci"},{"key":"2025081214122341100_jkaf127-B69","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1186\/1471-2105-7-62","article-title":"Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources","volume":"7","author":"Stanke","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2025081214122341100_jkaf127-B70","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41586-020-2700-3","article-title":"Sex differences in immune responses that underlie COVID-19 disease outcomes","volume":"588","author":"Takahashi","year":"2020","journal-title":"Nature"},{"key":"2025081214122341100_jkaf127-B71","doi-asserted-by":"publisher","first-page":"4157","DOI":"10.1038\/ncomms5157","article-title":"Co-option of Sox3 as the male-determining factor on the Y chromosome in the fish Oryzias dancena","volume":"5","author":"Takehana","year":"2014","journal-title":"Nat Commun"},{"key":"2025081214122341100_jkaf127-B72","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1002\/pro.4193","article-title":"PANNZER\u2014a practical tool for protein function prediction","volume":"31","author":"Toronen","year":"2022","journal-title":"Protein Sci"},{"key":"2025081214122341100_jkaf127-B73","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/s00441-024-03906-6","article-title":"In-depth histological, lectin-histochemical, immunohistochemical and ultrastructural description of the olfactory rosettes and olfactory bulbs of turbot (Scophthalmus maximus)","volume":"397","author":"Torres","year":"2024","journal-title":"Cell Tissue Res"},{"key":"2025081214122341100_jkaf127-B74","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/nature06178","article-title":"Turnover of sex chromosomes induced by sexual conflict","volume":"449","author":"Van Doorn","year":"2007","journal-title":"Nature"},{"key":"2025081214122341100_jkaf127-B75","doi-asserted-by":"publisher","first-page":"1351","DOI":"10.1016\/j.jgg.2024.08.008","article-title":"Sex chromosome turnover and biodiversity in fishes","volume":"51","author":"Wang","year":"2024","journal-title":"J Genet Genom"},{"key":"2025081214122341100_jkaf127-B76","doi-asserted-by":"publisher","first-page":"592","DOI":"10.3390\/genes11060592","article-title":"Transcriptome analysis of zebrafish olfactory epithelium reveals sexual differences in odorant detection","volume":"11","author":"Wang","year":"2020","journal-title":"Genes (Basel)"},{"key":"2025081214122341100_jkaf127-B77","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1016\/j.tree.2018.04.002","article-title":"Eco-evolutionary genomics of chromosomal inversions","volume":"33","author":"Wellenreuther","year":"2018","journal-title":"Trends Ecol Evol"},{"key":"2025081214122341100_jkaf127-B78","doi-asserted-by":"publisher","first-page":"1300","DOI":"10.1093\/icesjms\/fsw249","article-title":"Large and fine scale population structure in European hake (Merluccius merluccius) in the northeast Atlantic","volume":"74","author":"Westgaard","year":"2017","journal-title":"ICES J Mar Sci"},{"key":"2025081214122341100_jkaf127-B79","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2025081214122341100_jkaf127-B80","author":"Winter"},{"key":"2025081214122341100_jkaf127-B81","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1111\/j.1469-1809.1949.tb02451.x","article-title":"The genetical structure of populations","volume":"15","author":"Wright","year":"1949","journal-title":"Ann Eugen"},{"key":"2025081214122341100_jkaf127-B82","doi-asserted-by":"publisher","first-page":"btac808","DOI":"10.1093\/bioinformatics\/btac808","article-title":"YaHS: yet another Hi\u2013C scaffolding tool","volume":"39","author":"Zhou","year":"2023","journal-title":"Bioinformatics"}],"container-title":["G3: Genes, Genomes, Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/g3journal\/advance-article-pdf\/doi\/10.1093\/g3journal\/jkaf127\/63455943\/jkaf127.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/15\/8\/jkaf127\/63455943\/jkaf127.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/g3journal\/article-pdf\/15\/8\/jkaf127\/63455943\/jkaf127.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T18:12:27Z","timestamp":1755022347000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/g3journal\/article\/doi\/10.1093\/g3journal\/jkaf127\/8158669"}},"subtitle":[],"editor":[{"given":"C","family":"Palaiokostas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,6,9]]},"references-count":82,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2025,6,9]]},"published-print":{"date-parts":[[2025,8,6]]}},"URL":"https:\/\/doi.org\/10.1093\/g3journal\/jkaf127","relation":{},"ISSN":["2160-1836"],"issn-type":[{"value":"2160-1836","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,8]]},"published":{"date-parts":[[2025,6,9]]},"article-number":"jkaf127"}}