{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T16:20:27Z","timestamp":1791822027700,"version":"4.3.4"},"reference-count":111,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2021,8,26]],"date-time":"2021-08-26T00:00:00Z","timestamp":1629936000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"The Japan Society for the Promotion of Science","doi-asserted-by":"crossref","award":["16K14972, 20H00431"],"award-info":[{"award-number":["16K14972, 20H00431"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001691","name":"The Japan Society for the Promotion of Science","doi-asserted-by":"crossref","award":["18K05816"],"award-info":[{"award-number":["18K05816"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004532","name":"The Japan International Cooperation Agency","doi-asserted-by":"crossref","award":["Science and Technology Research Partnership for Sustainable Development (SATREPS)"],"award-info":[{"award-number":["Science and Technology Research Partnership for Sustainable Development (SATREPS)"]}],"id":[{"id":"10.13039\/501100004532","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"crossref","award":["PhyloSex project, 2014-2016"],"award-info":[{"award-number":["PhyloSex project, 2014-2016"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["PhyloSex project, 2014-2016"],"award-info":[{"award-number":["PhyloSex project, 2014-2016"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"name":"The USA National Institutes of Health","award":["R01OD011116, 5R01GM085318"],"award-info":[{"award-number":["R01OD011116, 5R01GM085318"]}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"abstract":"<jats:p>Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), <jats:italic>Plecoglossus altivelis<\/jats:italic>, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Thus, ayu holds an important position in the fish tree of life. Although ayu is economically important for the food industry and recreational fishing in Japan, few genomic resources are available for this species. To address this problem, we produced a draft genome sequence of ayu by whole-genome shotgun sequencing and constructed linkage maps using a genotyping-by-sequencing approach. Syntenic analyses of ayu and other teleost fish provided information about chromosomal rearrangements during the divergence of Stomiati, Protacanthopterygii and Neoteleostei. The size of the ayu genome indicates that genome compaction occurred after the divergence of the family Osmeridae. Ayu has an XX\/XY sex-determination system for which we identified sex-associated loci by a genome-wide association study by genotyping-by-sequencing and whole-genome resequencing using wild populations. Genome-wide association mapping using wild ayu populations revealed three sex-linked scaffolds (total, 2.03 Mb). Comparison of whole-genome resequencing mapping coverage between males and females identified male-specific regions in sex-linked scaffolds. A duplicate copy of the anti-M\u00fcllerian hormone type-II receptor gene (<jats:italic>amhr2bY<\/jats:italic>) was found within these male-specific regions, distinct from the autosomal copy of <jats:italic>amhr2<\/jats:italic>. Expression of the Y-linked <jats:italic>amhr2<\/jats:italic> gene was male-specific in <jats:italic>sox9b<\/jats:italic>-positive somatic cells surrounding germ cells in undifferentiated gonads, whereas autosomal <jats:italic>amhr2<\/jats:italic> transcripts were detected in somatic cells in sexually undifferentiated gonads of both genetic males and females. Loss-of-function mutation for <jats:italic>amhr2bY<\/jats:italic> induced male to female sex reversal. Taken together with the known role of <jats:italic>Amh<\/jats:italic> and <jats:italic>Amhr2<\/jats:italic> in sex differentiation, these results indicate that the paralog of <jats:italic>amhr2<\/jats:italic> on the ayu Y chromosome determines genetic sex, and the male-specific amh-amhr2 pathway is critical for testicular differentiation in ayu.<\/jats:p>","DOI":"10.1371\/journal.pgen.1009705","type":"journal-article","created":{"date-parts":[[2021,8,26]],"date-time":"2021-08-26T17:26:59Z","timestamp":1629998819000},"page":"e1009705","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":63,"title":["A Y-linked anti-M\u00fcllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2819-7303","authenticated-orcid":true,"given":"Masatoshi","family":"Nakamoto","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsubasa","family":"Uchino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eriko","family":"Koshimizu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yudai","family":"Kuchiishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8377-0120","authenticated-orcid":true,"given":"Ryota","family":"Sekiguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0073-9262","authenticated-orcid":true,"given":"Liu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ryusuke","family":"Sudo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masato","family":"Endo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5464-6219","authenticated-orcid":true,"given":"Yann","family":"Guiguen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9882-5948","authenticated-orcid":true,"given":"Manfred","family":"Schartl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5476-2137","authenticated-orcid":true,"given":"John H.","family":"Postlethwait","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8399-851X","authenticated-orcid":true,"given":"Takashi","family":"Sakamoto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,8,26]]},"reference":[{"key":"pgen.1009705.ref001","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/S0925-4773(99)00327-5","article-title":"The battle of the sexes","volume":"92","author":"B Capel","year":"2000","journal-title":"Mech Dev"},{"key":"pgen.1009705.ref002","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1530\/rep.0.1240447","article-title":"Vertebrate sex determination: many means to an end","volume":"124","author":"BC Morrish","year":"2002","journal-title":"Reproduction"},{"key":"pgen.1009705.ref003","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1002\/dvdy.23927","article-title":"Novel Sex-Determining Genes in Fish and Sex Chromosome Evolution","volume":"242","author":"K Kikuchi","year":"2013","journal-title":"Dev Dyn"},{"key":"pgen.1009705.ref004","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1038\/nature751","article-title":"DMY is a Y-specific DM-domain gene required for male development in the medaka. fish","volume":"417","author":"M Matsuda","year":"2002","journal-title":"Nature"},{"key":"pgen.1009705.ref005","doi-asserted-by":"crossref","first-page":"11778","DOI":"10.1073\/pnas.182314699","article-title":"A duplicated copy of DMRT1 in the sex-determining region of the Y chromosome of the medaka, Oryzias latipes","volume":"99","author":"I Nanda","year":"2002","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref006","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1534\/genetics.111.137497","article-title":"Tracing the emergence of a novel sex-determining gene in medaka, Oryzias luzonensis","volume":"191","author":"T Myosho","year":"2012","journal-title":"Genetics"},{"key":"pgen.1009705.ref007","doi-asserted-by":"crossref","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":"Y Takehana","year":"2014","journal-title":"Nat Commun"},{"key":"pgen.1009705.ref008","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1016\/j.cub.2012.05.045","article-title":"An immune-related gene evolved into the master sex-determining gene in rainbow trout, Oncorhynchus mykiss","volume":"22","author":"A Yano","year":"2012","journal-title":"Curr Biol"},{"key":"pgen.1009705.ref009","doi-asserted-by":"crossref","first-page":"1901","DOI":"10.1016\/j.cub.2019.04.069","article-title":"A SNP in a Steroidogenic Enzyme Is Associated with Phenotypic Sex in Seriola Fishes","volume":"29","author":"T Koyama","year":"2019","journal-title":"Curr Biol"},{"key":"pgen.1009705.ref010","doi-asserted-by":"crossref","first-page":"2955","DOI":"10.1073\/pnas.1018392109","article-title":"A Y-linked anti-M\u00fcllerian hormone duplication takes over a critical role in sex determination","volume":"109","author":"RS Hattori","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref011","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":"Q Pan","year":"2019","journal-title":"Plos Genet"},{"key":"pgen.1009705.ref012","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-020-02097-x","article-title":"Assembly of the threespine stickleback Y chromosome reveals convergent signatures of sex chromosome evolution","volume":"21","author":"CL Peichel","year":"2020","journal-title":"Genome Biol"},{"key":"pgen.1009705.ref013","doi-asserted-by":"crossref","first-page":"e1002798","DOI":"10.1371\/journal.pgen.1002798","article-title":"A Trans-Species Missense SNP in Amhr2 Is Associated with Sex Determination in the Tiger Pufferfish, Takifugu rubripes (Fugu)","volume":"8","author":"T Kamiya","year":"2012","journal-title":"Plos Genet"},{"key":"pgen.1009705.ref014","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1111\/1755-0998.13133","article-title":"Characterization of a Y-specific duplication\/insertion of 1 the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens","volume":"20","author":"R Feron","year":"2020","journal-title":"Mol Ecol Resour"},{"key":"pgen.1009705.ref015","doi-asserted-by":"crossref","first-page":"63","DOI":"10.2331\/fishsci.65.63","article-title":"Genetic Variation and Geographic Population Structure of Amphidromous Ayu Plecoglossus altivelis as Examined by Mitochondrial DNA Sequencing","volume":"65","author":"K Iguchi","year":"1999","journal-title":"Fisheries Sci"},{"key":"pgen.1009705.ref016","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1023\/A:1026582922248","article-title":"Genetic biogeography among insular populations of the amphidromous fish Plecoglossus altivelis assessed from mitochondrial DNA analysis","volume":"1","author":"K Iguchi","year":"2000","journal-title":"Conserv Genet"},{"key":"pgen.1009705.ref017","doi-asserted-by":"crossref","first-page":"279","DOI":"10.5635\/ASED.2012.28.4.279","article-title":"Population Genetic Structure and Evidence of Demographic Expansion of the Ayu (Plecoglossus altivelis) in East Asia","volume":"28","author":"YS Kwan","year":"2012","journal-title":"Anim Syst Evol Divers"},{"key":"pgen.1009705.ref018","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/S1055-7903(02)00418-9","article-title":"Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the \u201cProtacanthopterygii\u201d","volume":"27","author":"NB Ishiguro","year":"2003","journal-title":"Mol Phylogenetics Evol"},{"key":"pgen.1009705.ref019","doi-asserted-by":"crossref","first-page":"13698","DOI":"10.1073\/pnas.1206625109","article-title":"Resolution of ray-finned fish phylogeny and timing of diversification","volume":"109","author":"TJ Near","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref020","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1186\/s12864-016-2709-z","article-title":"Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database","volume":"17","author":"J Pasquier","year":"2016","journal-title":"BMC Genomics"},{"key":"pgen.1009705.ref021","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1186\/s12862-017-0958-3","article-title":"Phylogenetic classification of bony fishes","volume":"17","author":"R Betancur-R","year":"2017","journal-title":"BMC Evol Biol"},{"key":"pgen.1009705.ref022","doi-asserted-by":"crossref","first-page":"6249","DOI":"10.1073\/pnas.1719358115","article-title":"Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data","volume":"115","author":"LC Hughes","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref023","unstructured":"MAFF Japan. Ministry of Agriculture Forestry and Fisheries. Annual Statistics of Fishery and Aquaculture Production. (in Japanese). 2017; (http:\/\/www.maff.go.jp\/j\/tokei\/kouhyou\/naisui_gyosei\/index.html)."},{"key":"pgen.1009705.ref024","first-page":"1","article-title":"Study on the reproduction of all female ayu","volume":"17","author":"A Tsujimura","year":"1991","journal-title":"Wakayama Pref. Inland Fish Center Report"},{"key":"pgen.1009705.ref025","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1111\/j.1444-2906.2003.00769.x","article-title":"Detection of ayu sex-linked DNA markers using homologous clones","volume":"70","author":"T Watanabe","year":"2004","journal-title":"Fisheries Sci"},{"key":"pgen.1009705.ref026","article-title":"RADSex: a computational workflow to study sex determination using Restriction Site-Associated DNA Sequencing data","author":"R Feron","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"pgen.1009705.ref027","doi-asserted-by":"crossref","first-page":"3726","DOI":"10.1093\/bioinformatics\/btx494","article-title":"Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data","volume":"33","author":"P Rastas","year":"2017","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref028","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1266\/jjg.61.71","article-title":"Potentiality of application of Triploidy to the culture of Ayu, Plecoglossus altivelis temminck et Schlegel","volume":"61","author":"K Ueno","year":"1986","journal-title":"Jpn J Genet"},{"key":"pgen.1009705.ref029","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13059-014-0573-1","article-title":"ALLMAPS: robust scaffold ordering based on multiple maps","volume":"16","author":"H Tang","year":"2015","journal-title":"Genome Biol"},{"key":"pgen.1009705.ref030","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":"FA Sim\u00e3o","year":"2015","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref031","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/bioinformatics\/btn013","article-title":"Using native and syntenically mapped cDNA alignments to improve de novo gene finding","volume":"24","author":"M Stanke","year":"2008","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref032","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1038\/nature05846","article-title":"The medaka draft genome and insights into vertebrate genome evolution","volume":"447","author":"M Kasahara","year":"2007","journal-title":"Nature"},{"key":"pgen.1009705.ref033","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1017\/S1464793100005613","article-title":"Chromosome evolution in the Salmonidae (Pisces): an update","volume":"76","author":"R Phillips","year":"2001","journal-title":"Biol Rev Camb Philos Soc"},{"key":"pgen.1009705.ref034","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1126\/science.282.5394.1711","article-title":"Zebrafish hox Clusters and Vertebrate Genome Evolution","volume":"282","author":"A Amores","year":"1998","journal-title":"Science"},{"key":"pgen.1009705.ref035","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/ng0498-345","article-title":"Vertebrate genome evolution and the zebrafish gene map","volume":"18","author":"JH Postlethwait","year":"1998","journal-title":"Nat Genet"},{"key":"pgen.1009705.ref036","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1101\/gr.164800","article-title":"Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes","volume":"10","author":"JH Postlethwait","year":"2000","journal-title":"Genome Res"},{"key":"pgen.1009705.ref037","first-page":"27","article-title":"The karyotype of the zebrafish (Brachydanio rerio)","volume":"36","author":"KH Schreeb","year":"1993","journal-title":"J Exp Anim Sci"},{"key":"pgen.1009705.ref038","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1038\/nature12111","article-title":"The zebrafish reference genome sequence and its relationship to the human genome","volume":"496","author":"K Howe","year":"2013","journal-title":"Nature"},{"key":"pgen.1009705.ref039","doi-asserted-by":"crossref","first-page":"1291","DOI":"10.1534\/genetics.114.169284","article-title":"Wild Sex in Zebrafish: Loss of the Natural Sex Determinant in Domesticated Strains","volume":"198","author":"CA Wilson","year":"2014","journal-title":"Genetics"},{"key":"pgen.1009705.ref040","doi-asserted-by":"crossref","first-page":"e48140","DOI":"10.1371\/journal.pone.0048140","article-title":"Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains","volume":"7","author":"J Xu","year":"2012","journal-title":"Plos one"},{"key":"pgen.1009705.ref041","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1007\/s00239-004-2613-z","article-title":"Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish","volume":"59","author":"S Hoegg","year":"2004","journal-title":"J Mol Evol"},{"key":"pgen.1009705.ref042","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1002\/jez.b.22761","article-title":"Analysis of the spotted gar genome suggests absence of causative link between ancestral genome duplication and transposable element diversification in teleost fish","volume":"328","author":"D Chalopin","year":"2017","journal-title":"J Exp Zool. (Mol Dev Evol.)"},{"key":"pgen.1009705.ref043","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/ng.3526","article-title":"The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons","volume":"48","author":"I Braasch","year":"2016","journal-title":"Nat Genet"},{"key":"pgen.1009705.ref044","doi-asserted-by":"crossref","first-page":"2","DOI":"10.3835\/plantgenome2015.08.0073","article-title":"Software for Genome-Wide Association Studies in Autopolyploids and Its Application to Potato","volume":"9","author":"UR Rosyara","year":"2016","journal-title":"Plant Genome"},{"key":"pgen.1009705.ref045","article-title":"The Variety of Vertebrate Mechanisms of Sex Determination","author":"AV Trukhina","year":"2013","journal-title":"BioMed Res. Int"},{"key":"pgen.1009705.ref046","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref047","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gku1221","article-title":"CDD: NCBI\u2019s conserved domain database","volume":"43","author":"A Marchler-Bauer","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref048","doi-asserted-by":"crossref","first-page":"W296","DOI":"10.1093\/nar\/gky427","article-title":"SWISS-MODEL: homology modelling of protein structures and complexes","volume":"46","author":"A Waterhouse","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref049","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1101\/gr.2004004","article-title":"A medaka gene map: the trace of ancestral vertebrate proto-chromosomes revealed by comparative gene mapping","volume":"14","author":"K Naruse","year":"2004","journal-title":"Genome Res"},{"key":"pgen.1009705.ref050","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":"M Nakamura","year":"1998","journal-title":"J Exp Zool"},{"key":"pgen.1009705.ref051","first-page":"1017.1","article-title":"The function and regulation of vasa-like genes in germ-cell development","volume":"1","author":"E. Raz","year":"2000","journal-title":"Genome Biol"},{"key":"pgen.1009705.ref052","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1046\/j.1440-169x.2000.00521.x","article-title":"The vasa-like gene, olvas, identifies the migration path of primordial germ cells during embryonic body formation stage in the medaka, Oryzias latipes","volume":"42","author":"A Shinomiya","year":"2000","journal-title":"Dev Growth Differ"},{"key":"pgen.1009705.ref053","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1016\/j.bbrc.2005.05.158","article-title":"Testicular type Sox9 is not involved in sex determination but might be in the development of testicular structures in the medaka, Oryzias latipes","volume":"333","author":"M Nakamoto","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"key":"pgen.1009705.ref054","doi-asserted-by":"crossref","first-page":"e29982","DOI":"10.1371\/journal.pone.0029982","article-title":"Analysis of medaka sox9 orthologue reveals a conserved role in germ cell maintenance","volume":"7","author":"S Nakamura","year":"2012","journal-title":"Plos one"},{"key":"pgen.1009705.ref055","first-page":"249","article-title":"Sex differentiation and its manipulation in ayu","volume":"34","author":"T Sasaki","year":"1987","journal-title":"Suisanzoshoku"},{"key":"pgen.1009705.ref056","doi-asserted-by":"crossref","first-page":"e102089","DOI":"10.1371\/journal.pone.0102089","article-title":"The Genome and Linkage Map of the Northern Pike (Esox lucius): Conserved Synteny Revealed between the Salmonid Sister Group and the Neoteleostei","volume":"9","author":"EB Rondeau","year":"2014","journal-title":"Plos one"},{"key":"pgen.1009705.ref057","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0014-5793(00)01659-8","article-title":"Fugu: a compact vertebrate reference genome","volume":"476","author":"B Venkatesh","year":"2000","journal-title":"FEBS Letters"},{"key":"pgen.1009705.ref058","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1007\/s10126-008-9089-6","article-title":"Rainbow Smelt (Osmerus mordax) Genomic Library and EST Resources","volume":"10","author":"KR von Schalburg","year":"2008","journal-title":"Mar. Biotechnol"},{"key":"pgen.1009705.ref059","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/s10709-006-9110-9","article-title":"Karyotype and chromosomal characteristics of Ag\u2013NOR sites and 5S rDNA in European smelt, Osmerus eperlanus","volume":"131","author":"K Ocalewicz","year":"2007","journal-title":"Genetica"},{"key":"pgen.1009705.ref060","doi-asserted-by":"crossref","first-page":"4155","DOI":"10.1073\/pnas.94.8.4155","article-title":"Excitatory Amino Acid Transporter 5, a Retinal Glutamate Transporter Coupled to a Chloride Conductance","volume":"94","author":"JL Arriza","year":"1997","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref061","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1017\/S0952523804214067","article-title":"Differential cellular and subcellular distribution of glutamate transporters in the cat retina","volume":"21","author":"B Fyk-Kolodziej","year":"2004","journal-title":"Vis Neurosci"},{"key":"pgen.1009705.ref062","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1089\/hyb.1984.3.201","article-title":"Production of monoclonal antibodies for affinity purification of bovine m\u00fcllerian inhibiting substance activity","volume":"3","author":"H Shima","year":"1984","journal-title":"Hybridoma"},{"key":"pgen.1009705.ref063","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/0303-7207(84)90155-2","article-title":"Purification of testicular anti-M\u00fcllerian hormone allowing direct visualization of the pure glycoprotein and determination of yield and purification factor","volume":"34","author":"JY Picard","year":"1984","journal-title":"Mol Cell Endocrinol"},{"key":"pgen.1009705.ref064","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1146\/annurev-animal-020518-114955","article-title":"Intersex, Hermaphroditism, and Gonadal Plasticity in Vertebrates: Evolution of the M\u00fcllerian Duct and Amh\/Amhr2 Signaling","volume":"7","author":"MC Adolfi","year":"2019","journal-title":"Annu Rev Anim Biosci"},{"key":"pgen.1009705.ref065","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1002\/dvdy.24579","article-title":"Gonadal Soma Controls Ovarian Follicle Proliferation Through Gsdf in Zebrafish","volume":"246","author":"YL Yan","year":"2017","journal-title":"Dev Dyn"},{"key":"pgen.1009705.ref066","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.gep.2010.06.005","article-title":"Expression of gonadal soma derived factor (GSDF) is spatially and temporally correlated with early testicular differentiation in medaka","volume":"10","author":"Y Shibata","year":"2010","journal-title":"Gene Expr Patterns"},{"key":"pgen.1009705.ref067","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1242\/dev.102.2.443","article-title":"Cell-autonomous action of the testis-determining gene: Sertoli cells are exclusively XY in XX->XY chimaeric mouse testes","volume":"102","author":"PS Burgoyne","year":"1988","journal-title":"Development"},{"key":"pgen.1009705.ref068","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1006\/dbio.2001.0438","article-title":"Evidence that Sry is expressed in pre-Sertoli cells and Sertoli and granulosa cells have a common precursor","volume":"240","author":"KH Albrecht","year":"2001","journal-title":"Dev Biol"},{"key":"pgen.1009705.ref069","doi-asserted-by":"crossref","first-page":"9691","DOI":"10.1073\/pnas.0611379104","article-title":"The hotei mutation of medaka in the anti-M\u00fcllerian hormone receptor causes the dysregulation of germ cell and sexual development","volume":"104","author":"C Morinaga","year":"2007","journal-title":"Proc Natl Acad Sci USA"},{"key":"pgen.1009705.ref070","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1093\/hmg\/5.9.1269","article-title":"A 27 Base-Pair Deletion of the anti-m\u00fcllerian Type II Receptor Gene Is the Most Common Cause of the Persistent m\u00fcllerian Duct Syndrome","volume":"5","author":"S Imbeaud","year":"1996","journal-title":"Hum Mol Genet"},{"key":"pgen.1009705.ref071","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1093\/aob\/mci019","article-title":"The origin, evolution and proposed stabilization of the terms \u2019genome size\u2019 and \u2019C-value\u2019 to describe nuclear DNA contents","volume":"95","author":"J Greilhuber","year":"2005","journal-title":"Ann Bot"},{"key":"pgen.1009705.ref072","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for Illumina Sequence Data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref073","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1101\/gr.170720.113","article-title":"Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads","volume":"24","author":"R Kajitani","year":"2014","journal-title":"Genome Res"},{"key":"pgen.1009705.ref074","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/1471-2105-15-211","article-title":"SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information","volume":"15","author":"M Boetzer","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"pgen.1009705.ref075","doi-asserted-by":"crossref","first-page":"R56","DOI":"10.1186\/gb-2012-13-6-r56","article-title":"Toward almost closed genomes with GapFiller","volume":"13","author":"M Boetzer","year":"2012","journal-title":"Genome Biol"},{"key":"pgen.1009705.ref076","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"S Koren","year":"2017","journal-title":"Genome Res"},{"key":"pgen.1009705.ref077","doi-asserted-by":"crossref","first-page":"31900","DOI":"10.1038\/srep31900","article-title":"DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies","volume":"6","author":"C Ye","year":"2016","journal-title":"Sci Rep"},{"key":"pgen.1009705.ref078","first-page":"e147","article-title":"Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage","volume":"44","author":"M Chakraborty","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref079","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/s13059-015-0764-4","article-title":"Metassembler: merging and optimizing de novo genome assemblies","volume":"16","author":"AH Wences","year":"2015","journal-title":"Genome Biol"},{"key":"pgen.1009705.ref080","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"Plos one"},{"key":"pgen.1009705.ref081","doi-asserted-by":"crossref","first-page":"e19379","DOI":"10.1371\/journal.pone.0019379","article-title":"A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species","volume":"6","author":"RJ Elshire","year":"2011","journal-title":"Plos one"},{"key":"pgen.1009705.ref082","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler Transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref083","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"key":"pgen.1009705.ref084","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The Variant Call Format and VCFtools","volume":"27","author":"P Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref085","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/978-3-642-60441-6_23","article-title":"Pseudo-Testcross Mapping Strategy Using RAPD Markers","author":"D Grattapaglia","year":"1997","journal-title":"Fingerprinting Methods Based on Arbitrarily Primed PCR"},{"key":"pgen.1009705.ref086","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1093\/bioinformatics\/btx576","article-title":"LinkageMapView\u2014rendering high-resolution linkage and QTL maps","volume":"34","author":"LA Ouellette","year":"2018","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref087","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13100-015-0041-9","article-title":"Repbase Update, a database of repetitive elements in eukaryotic genomes","volume":"6","author":"W Bao","year":"2015","journal-title":"Mob DNA"},{"key":"pgen.1009705.ref088","doi-asserted-by":"crossref","first-page":"6494","DOI":"10.1093\/nar\/gki937","article-title":"Gene identification in novel eukaryotic genomes by self-training algorithm","volume":"33","author":"A Lomsadze","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref089","doi-asserted-by":"crossref","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":"A Lomsadze","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref090","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-4939-9173-0_5","article-title":"Whole-Genome Annotation with BRAKER","volume":"1962","author":"KJ Hoff","year":"2019","journal-title":"Methods Mol Biol"},{"key":"pgen.1009705.ref091","doi-asserted-by":"crossref","first-page":"3420","DOI":"10.1093\/nar\/gkn176","article-title":"High-throughput functional annotation and data mining with the Blast2GO suite","volume":"36","author":"S G\u00f6tz","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref092","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"The UniProt Consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref093","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1186\/s12859-017-1939-7","article-title":"Synima: a Synteny imaging tool for annotated genome assemblies","volume":"18","author":"RA Farrer","year":"2017","journal-title":"BMC Bioinformatics"},{"key":"pgen.1009705.ref094","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: An information aesthetic for comparative genomics","volume":"19","author":"M Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"pgen.1009705.ref095","article-title":"VGSC2: Second generation vector graph toolkit of genome synteny and collinearity","author":"Y Xu","year":"2019","journal-title":"Genomics"},{"key":"pgen.1009705.ref096","doi-asserted-by":"crossref","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","article-title":"Ensembl 2018","volume":"46","author":"DR Zerbino","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref097","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"F Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref098","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative Genomics Viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"key":"pgen.1009705.ref099","doi-asserted-by":"crossref","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: rising to the challenge of larger and richer datasets","volume":"4","author":"CC Chang","year":"2015","journal-title":"GigaScience"},{"key":"pgen.1009705.ref100","volume-title":"R package version 2.1.0","author":"M Maechler","year":"2019"},{"key":"pgen.1009705.ref101","first-page":"1358","article-title":"Estimating F-Statistics for the Analysis of Population Structure","volume":"38","author":"BS Weir","year":"1984","journal-title":"Evolution"},{"key":"pgen.1009705.ref102","doi-asserted-by":"crossref","first-page":"731","DOI":"10.21105\/joss.00731","article-title":"qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots","volume":"3","author":"SD Turner","year":"2018","journal-title":"J. Open Source Softw"},{"key":"pgen.1009705.ref103","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v016.c03","article-title":"LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms","volume":"16","author":"J Shin","year":"2006","journal-title":"J Stat Soft"},{"key":"pgen.1009705.ref104","doi-asserted-by":"crossref","first-page":"18351","DOI":"10.1038\/s41598-019-54830-7","article-title":"Structural consequences of BMPR2 kinase domain mutations causing pulmonary arterial hypertension","volume":"9","author":"A Chaikuad","year":"2019","journal-title":"Sci Rep"},{"key":"pgen.1009705.ref105","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"pgen.1009705.ref106","unstructured":"Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University. 2007; (http:\/\/www.bx.psu.edu\/~rsharris\/lastz\/)."},{"key":"pgen.1009705.ref107","first-page":"2019","article-title":"CiiiDER: A tool for predicting and analysing transcription factor binding sites","volume":"4","author":"LJ Gearing","journal-title":"Plos one September"},{"key":"pgen.1009705.ref108","first-page":"D87","article-title":"JASPAR 2020: update of the open-access database of transcription factor binding profiles","volume":"48","author":"O Fornes","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"pgen.1009705.ref109","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1093\/molbev\/msy096","article-title":"MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms","volume":"35","author":"S Kumar","year":"2018","journal-title":"Mol Biol Evol"},{"key":"pgen.1009705.ref110","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2-a multiple sequence alignment editor and analysis workbench","volume":"25","author":"AM Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"pgen.1009705.ref111","doi-asserted-by":"crossref","first-page":"e0124633","DOI":"10.1371\/journal.pone.0124633","article-title":"CCTop: an intuitive, flexible and reliable CRISPR\/Cas9 target prediction tool","volume":"10","author":"M Stemmer","year":"2015","journal-title":"Plos one"}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009705","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,26]],"date-time":"2021-08-26T17:29:32Z","timestamp":1629998972000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1009705"}},"subtitle":[],"editor":[{"given":"Cecilia","family":"Moens","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,8,26]]},"references-count":111,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1009705","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,26]]}}}