{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T07:19:23Z","timestamp":1791616763959,"version":"4.3.4"},"reference-count":102,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32503159"],"award-info":[{"award-number":["32503159"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32473156"],"award-info":[{"award-number":["32473156"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32172953"],"award-info":[{"award-number":["32172953"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32530106"],"award-info":[{"award-number":["32530106"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["SWU-KF25006"],"award-info":[{"award-number":["SWU-KF25006"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002865","name":"Chongqing Municipal Science and Technology Bureau","doi-asserted-by":"publisher","award":["CSTB2023NSCQ-MSX0799"],"award-info":[{"award-number":["CSTB2023NSCQ-MSX0799"]}],"id":[{"id":"10.13039\/501100002865","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Genetics and Genomics"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.jgg.2026.05.001","type":"journal-article","created":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T03:07:29Z","timestamp":1778814449000},"page":"1616-1630","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia"],"prefix":"10.1016","volume":"53","author":[{"given":"Hesheng","family":"Xiao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingrong","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuhan","family":"Niu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanyuan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baoyue","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianwen","family":"Min","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dejie","family":"Tan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deshou","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjing","family":"Tao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jgg.2026.05.001_bib1","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2020.0090","article-title":"The replaceable master of sex determination: bottom-up hypothesis revisited","volume":"376","author":"Adolfi","year":"2021","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.jgg.2026.05.001_bib2","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3390\/life11020118","article-title":"Role of transposable elements in gene regulation in the human genome","volume":"11","author":"Ali","year":"2021","journal-title":"Life"},{"key":"10.1016\/j.jgg.2026.05.001_bib3","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1093\/molehr\/gah056","article-title":"Increased expression of the FIGLA transcription factor is associated with primordial follicle formation in the human fetal ovary","volume":"10","author":"Bayne","year":"2004","journal-title":"Mol. Hum. Reprod."},{"key":"10.1016\/j.jgg.2026.05.001_bib4","doi-asserted-by":"crossref","DOI":"10.1093\/gbe\/evaf191","article-title":"Before the East African radiation: sex chromosome systems in basal haplotilapiine cichlids","volume":"18,","author":"Behrens","year":"2026","journal-title":"Genome Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib5","doi-asserted-by":"crossref","first-page":"12781","DOI":"10.1073\/pnas.1803826115","article-title":"The unusual rainbow trout sex determination gene hijacked the canonical vertebrate gonadal differentiation pathway","volume":"115","author":"Bertho","year":"2018","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jgg.2026.05.001_bib6","article-title":"Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2","author":"Bickmann","year":"2025","journal-title":"Biology, 15, 59."},{"key":"10.1016\/j.jgg.2026.05.001_bib7","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1126\/science.165.3891.349","article-title":"Gene regulation for higher cells: a theory","volume":"165","author":"Britten","year":"1969","journal-title":"Science"},{"key":"10.1016\/j.jgg.2026.05.001_bib8","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/nbt.2727","article-title":"Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions","volume":"31","author":"Burton","year":"2013","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jgg.2026.05.001_bib9","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":"10.1016\/j.jgg.2026.05.001_bib10","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1111\/jwas.12479","article-title":"A review of genetic advances related to sex control and manipulation in tilapia","volume":"49","author":"Chen","year":"2018","journal-title":"J. World Aquacult. Soc."},{"key":"10.1016\/j.jgg.2026.05.001_bib11","first-page":"44","article-title":"Wt1 directs the lineage specification of Sertoli and granulosa cells by repressing Sf1 expression","volume":"144","author":"Chen","year":"2017","journal-title":"Development"},{"key":"10.1016\/j.jgg.2026.05.001_bib12","doi-asserted-by":"crossref","first-page":"884","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":"10.1016\/j.jgg.2026.05.001_bib13","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2024.742089","article-title":"Development and application of functional gene-based SSR markers for enhancing color and genetic stability in Taiwan red Tilapia (Oreochromis spp.)","volume":"599","author":"Chiang","year":"2025","journal-title":"Aquaculture"},{"key":"10.1016\/j.jgg.2026.05.001_bib14","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nrg.2016.139","article-title":"Regulatory activities of transposable elements: from conflicts to benefits","volume":"18","author":"Chuong","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib15","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1186\/s12864-017-3723-5","article-title":"A high quality assembly of the Nile tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions","volume":"18","author":"Conte","year":"2017","journal-title":"BMC Genomics"},{"key":"10.1016\/j.jgg.2026.05.001_bib16","doi-asserted-by":"crossref","first-page":"7636","DOI":"10.3390\/ijms23147636","article-title":"Absence of figla-like gene is concordant with femaleness in cichlids harboring the LG1 sex-determination system","volume":"23","author":"Curzon","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jgg.2026.05.001_bib17","doi-asserted-by":"crossref","DOI":"10.1242\/dev.199380","article-title":"Germline sexual fate is determined by the antagonistic action of dmrt1 and foxl3\/foxl2 in tilapia","volume":"148,","author":"Dai","year":"2021","journal-title":"Development"},{"key":"10.1016\/j.jgg.2026.05.001_bib18","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"10.1016\/j.jgg.2026.05.001_bib19","doi-asserted-by":"crossref","first-page":"9150","DOI":"10.3390\/ijms22179150","article-title":"Mechanisms of binding specificity among bHLH transcription factors","volume":"22","author":"de Martin","year":"2021","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.jgg.2026.05.001_bib20","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"DePristo","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib21","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1016\/j.cels.2015.07.012","article-title":"Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom","volume":"3","author":"Durand","year":"2016","journal-title":"Cell Syst."},{"key":"10.1016\/j.jgg.2026.05.001_bib22","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"Emms","year":"2015","journal-title":"Genome Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib23","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1186\/1471-2164-15-774","article-title":"Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus)","volume":"15","author":"Eshel","year":"2014","journal-title":"BMC Genom."},{"key":"10.1016\/j.jgg.2026.05.001_bib24","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/nrg2337","article-title":"Transposable elements and the evolution of regulatory networks","volume":"9","author":"Feschotte","year":"2008","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib25","doi-asserted-by":"crossref","first-page":"416","DOI":"10.1016\/j.devcel.2013.06.018","article-title":"Homeoproteins Six1 and Six4 regulate male sex determination and mouse gonadal development","volume":"26","author":"Fujimoto","year":"2013","journal-title":"Dev. Cell"},{"key":"10.1016\/j.jgg.2026.05.001_bib26","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1186\/1471-2164-15-975","article-title":"Structure and decay of a proto-Y region in tilapia, Oreochromis niloticus","volume":"15","author":"Gammerdinger","year":"2014","journal-title":"BMC Genomics"},{"key":"10.1016\/j.jgg.2026.05.001_bib27","doi-asserted-by":"crossref","first-page":"808","DOI":"10.1186\/s12864-016-3163-7","article-title":"Comparative analysis of a sex chromosome from the blackchin tilapia, Sarotherodon melanotheron","volume":"17","author":"Gammerdinger","year":"2016","journal-title":"BMC Genomics"},{"key":"10.1016\/j.jgg.2026.05.001_bib28","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1126\/science.aap8328","article-title":"The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species","volume":"360","author":"Ge","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.jgg.2026.05.001_bib29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/bies.10207","article-title":"Masters change, slaves remain","volume":"25","author":"Graham","year":"2003","journal-title":"Bioessays"},{"key":"10.1016\/j.jgg.2026.05.001_bib30","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.ygcen.2009.03.002","article-title":"Ovarian aromatase and estrogens: a pivotal role for gonadal sex differentiation and sex change in fish","volume":"165","author":"Guiguen","year":"2010","journal-title":"Gen. Comp. Endocrinol."},{"key":"10.1016\/j.jgg.2026.05.001_bib31","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msaf239","article-title":"Transposable element-mediated cis-regulation drives the evolution of dmrt1 as a candidate master sex-determining gene in black carp","volume":"42,","author":"Guo","year":"2025","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib32","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/s41586-020-3027-9","article-title":"Reconstitution of the oocyte transcriptional network with transcription factors","volume":"589","author":"Hamazaki","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.jgg.2026.05.001_bib33","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":"Hattori","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jgg.2026.05.001_bib34","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000844","article-title":"Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements","volume":"6","author":"Herpin","year":"2010","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib35","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.15252\/embr.201540667","article-title":"Plasticity of gene-regulatory networks controlling sex determination: of masters, slaves, usual suspects, newcomers, and usurpators","volume":"16","author":"Herpin","year":"2015","journal-title":"EMBO Rep."},{"key":"10.1016\/j.jgg.2026.05.001_bib36","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1101\/gr.274266.120","article-title":"Allelic diversification after transposable element exaptation promoted gsdf as the master sex determining gene of sablefish","volume":"31","author":"Herpin","year":"2021","journal-title":"Genome Res."},{"key":"10.1016\/j.jgg.2026.05.001_bib37","doi-asserted-by":"crossref","first-page":"2253","DOI":"10.1093\/bioinformatics\/btz891","article-title":"NextPolish: a fast and efficient genome polishing tool for long-read assembly","volume":"36","author":"Hu","year":"2020","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jgg.2026.05.001_bib38","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1003629","article-title":"Gata4 is required for formation of the genital ridge in mice","volume":"9","author":"Hu","year":"2013","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib39","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1002\/mrd.22642","article-title":"gsdf is a downstream gene of dmrt1 that functions in the male sex determination pathway of the Nile tilapia","volume":"83","author":"Jiang","year":"2016","journal-title":"Mol. Reprod. Dev."},{"key":"10.1016\/j.jgg.2026.05.001_bib40","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.jgg.2026.05.001_bib41","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41587-019-0201-4","article-title":"Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype","volume":"37","author":"Kim","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.jgg.2026.05.001_bib42","doi-asserted-by":"crossref","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":"Ann. Rev. Anim. Biosci."},{"key":"10.1016\/j.jgg.2026.05.001_bib43","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1038\/348450a0","article-title":"Expression of a candidate sex-determining gene during mouse testis differentiation","volume":"348","author":"Koopman","year":"1990","journal-title":"Nature"},{"key":"10.1016\/j.jgg.2026.05.001_bib44","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1186\/s13059-019-1910-1","article-title":"Transcriptome assembly from long-read RNA-seq alignments with StringTie2","volume":"20","author":"Kovaka","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib45","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.jgg.2026.05.001_bib46","doi-asserted-by":"crossref","first-page":"1282","DOI":"10.1177\/153537020322801107","article-title":"The role of GATA in mammalian reproduction","volume":"228","author":"LaVoie","year":"2003","journal-title":"Exp. Biol. Med."},{"key":"10.1016\/j.jgg.2026.05.001_bib47","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2013","journal-title":"arXiv"},{"key":"10.1016\/j.jgg.2026.05.001_bib48","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1534\/genetics.114.163667","article-title":"Efficient and heritable gene targeting in tilapia by CRISPR\/Cas9","volume":"197","author":"Li","year":"2014","journal-title":"Genetics"},{"key":"10.1016\/j.jgg.2026.05.001_bib49","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1005678","article-title":"A tandem duplicate of anti-M\u00fcllerian hormone with a missense SNP on the Y chromosome is essential for male sex determination in Nile tilapia, Oreochromis niloticus","volume":"11","author":"Li","year":"2015","journal-title":"PLoS Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib50","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.scib.2017.01.003","article-title":"Gene editing nuclease and its application in tilapia","volume":"62","author":"Li","year":"2017","journal-title":"Sci. Bull."},{"key":"10.1016\/j.jgg.2026.05.001_bib51","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.ygcen.2018.11.015","article-title":"Roles of estrogens in fish sexual plasticity and sex differentiation","volume":"277","author":"Li","year":"2019","journal-title":"Gen. Comp. Endocrinol."},{"key":"10.1016\/j.jgg.2026.05.001_bib52","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1007\/s11427-018-9415-7","article-title":"Diverse and variable sex determination mechanisms in vertebrates","volume":"61","author":"Li","year":"2018","journal-title":"Sci. China Life Sci."},{"key":"10.1016\/j.jgg.2026.05.001_bib53","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1016\/0092-8674(94)90211-9","article-title":"A cell-specific nuclear receptor is essential for adrenal and gonadal development and sexual differentiation","volume":"77","author":"Luo","year":"1994","journal-title":"Cell"},{"key":"10.1016\/j.jgg.2026.05.001_bib54","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2021.737327","article-title":"Production of all male amelanotic red tilapia by combining MAS-GMT and tyrb mutation","volume":"546","author":"Lu","year":"2022","journal-title":"Aquaculture"},{"key":"10.1016\/j.jgg.2026.05.001_bib55","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1016\/j.jgg.2023.04.003","article-title":"The power of \u201ccontrollers\u201d: transposon-mediated duplicated genes evolve towards neofunctionalization","volume":"50","author":"Ma","year":"2023","journal-title":"J. Genet. Genomics"},{"key":"10.1016\/j.jgg.2026.05.001_bib56","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005944","article-title":"MUMmer4: a fast and versatile genome alignment system","volume":"14","author":"Mar\u00e7ais","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib57","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1186\/gb-2010-11-4-205","article-title":"Are homologies in vertebrate sex determination due to shared ancestry or to limited options?","volume":"11","author":"Marshall Graves","year":"2010","journal-title":"Genome Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib58","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":"Matsuda","year":"2002","journal-title":"Nature"},{"key":"10.1016\/j.jgg.2026.05.001_bib59","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1101\/SQB.1951.016.01.004","article-title":"Chromosome organization and genic expression","volume":"16","author":"McClintock","year":"1951","journal-title":"Cold Spring Harbor Symp. Quant. Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib60","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":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"10.1016\/j.jgg.2026.05.001_bib61","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib62","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/s10695-006-7590-2","article-title":"Molecular mechanisms of sex determination and gonadal sex differentiation in fish","volume":"31","author":"Nagahama","year":"2005","journal-title":"Fish Physiol. Biochem."},{"key":"10.1016\/j.jgg.2026.05.001_bib63","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1152\/physrev.00044.2019","article-title":"Sex determination, gonadal sex differentiation, and plasticity in vertebrate species","volume":"101","author":"Nagahama","year":"2021","journal-title":"Physiol. Rev."},{"key":"10.1016\/j.jgg.2026.05.001_bib64","doi-asserted-by":"crossref","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":"10.1016\/j.jgg.2026.05.001_bib65","first-page":"14","article-title":"GeneDoc: analysis and visualization of genetic variation","volume":"4","author":"Nicholas","year":"1997","journal-title":"Embnew News"},{"key":"10.1016\/j.jgg.2026.05.001_bib66","series-title":"Evolution by gene duplication","author":"Ohno","year":"1970"},{"key":"10.1016\/j.jgg.2026.05.001_bib67","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1186\/s12864-015-1383-x","article-title":"A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus)","volume":"16","author":"Palaiokostas","year":"2015","journal-title":"BMC Genom."},{"key":"10.1016\/j.jgg.2026.05.001_bib68","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1210\/en.2018-00648","article-title":"Roles of Figla\/figla in juvenile ovary development and follicle formation during zebrafish gonadogenesis","volume":"159","author":"Qin","year":"2018","journal-title":"Endocrinology"},{"key":"10.1016\/j.jgg.2026.05.001_bib69","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1146\/annurev-genet-110711-155621","article-title":"Transposable elements: an abundant and natural source of regulatory sequences for host genes","volume":"46","author":"Rebollo","year":"2012","journal-title":"Annu. Rev. Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib70","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baae044","article-title":"FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research","volume":"2024,","author":"Shao","year":"2024","journal-title":"Database"},{"key":"10.1016\/j.jgg.2026.05.001_bib71","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae218","article-title":"Sex chromosome evolution: hallmarks and question marks","volume":"41,","author":"Saunders","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib72","first-page":"147","article-title":"Evolution by gene duplication: in the era of genomics","volume":"47","author":"Shen","year":"2025","journal-title":"Yi Chuan"},{"key":"10.1016\/j.jgg.2026.05.001_bib73","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1093\/nar\/gkac907","article-title":"AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations","volume":"51","author":"Shen","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jgg.2026.05.001_bib74","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nature08298","article-title":"The avian Z-linked gene DMRT1 is required for male sex determination in the chicken","volume":"461","author":"Smith","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.jgg.2026.05.001_bib75","doi-asserted-by":"crossref","DOI":"10.1098\/rsob.210063","article-title":"A duplicated amh is the master sex-determining gene for Sebastes rockfish in the Northwest Pacific","volume":"11","author":"Song","year":"2021","journal-title":"Open Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib76","doi-asserted-by":"crossref","first-page":"4645","DOI":"10.1242\/dev.127.21.4645","article-title":"FIGalpha, a germ cell-specific transcription factor required for ovarian follicle formation","volume":"127","author":"Soyal","year":"2000","journal-title":"Development"},{"key":"10.1016\/j.jgg.2026.05.001_bib77","doi-asserted-by":"crossref","DOI":"10.1098\/rstb.2019.0347","article-title":"Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes","volume":"375","author":"Sundaram","year":"2020","journal-title":"Philos. Trans. R. Soc. Lond. B Biol. Sci."},{"key":"10.1016\/j.jgg.2026.05.001_bib78","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.aquaculture.2014.05.035","article-title":"Screening and characterization of sex-linked DNA markers and marker-assisted selection in the Nile tilapia (Oreochromis niloticus)","volume":"433","author":"Sun","year":"2014","journal-title":"Aquaculture"},{"key":"10.1016\/j.jgg.2026.05.001_bib79","doi-asserted-by":"crossref","first-page":"1476","DOI":"10.1210\/en.2013-1959","article-title":"Transdifferentiation of differentiated ovary into functional testis by long-term treatment of aromatase inhibitor in Nile tilapia","volume":"155","author":"Sun","year":"2014","journal-title":"Endocrinology"},{"key":"10.1016\/j.jgg.2026.05.001_bib80","doi-asserted-by":"crossref","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib81","doi-asserted-by":"crossref","DOI":"10.1002\/bies.202000161","article-title":"Network architecture and sex chromosome turnovers: do epistatic interactions shape patterns of sex chromosome replacement?","volume":"43","author":"Tao","year":"2021","journal-title":"Bioessays"},{"key":"10.1016\/j.jgg.2026.05.001_bib82","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1111\/1755-0998.13273","article-title":"High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes","volume":"21","author":"Tao","year":"2021","journal-title":"Mol. Ecol. Resour."},{"key":"10.1016\/j.jgg.2026.05.001_bib83","doi-asserted-by":"crossref","DOI":"10.3389\/fgene.2021.796211","article-title":"A chromosome-level genome assembly of Mozambique tilapia (Oreochromis mossambicus) reveals the structure of sex determining regions","volume":"12","author":"Tao","year":"2021","journal-title":"Front. Genet."},{"issue":"Unit 4.10","key":"10.1016\/j.jgg.2026.05.001_bib84","first-page":"1","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"4","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr. Protoc. Bioinform. Chapt."},{"key":"10.1016\/j.jgg.2026.05.001_bib85","doi-asserted-by":"crossref","first-page":"4627","DOI":"10.1242\/dev.129.19.4627","article-title":"Gonadal differentiation, sex determination and normal Sry expression in mice require direct interaction between transcription partners GATA4 and FOG2","volume":"129","author":"Tevosian","year":"2002","journal-title":"Development"},{"key":"10.1016\/j.jgg.2026.05.001_bib86","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1210\/me.2006-0248","article-title":"Foxl2 up-regulates aromatase gene transcription in a female-specific manner by binding to the promoter as well as interacting with ad4 binding protein\/steroidogenic factor 1","volume":"21","author":"Wang","year":"2007","journal-title":"Mol. Endocrinol."},{"key":"10.1016\/j.jgg.2026.05.001_bib87","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1210\/en.2009-0999","article-title":"Doublesex- and Mab-3-related transcription factor-1 repression of aromatase transcription, a possible mechanism favoring the male pathway in tilapia","volume":"151","author":"Wang","year":"2010","journal-title":"Endocrinology"},{"key":"10.1016\/j.jgg.2026.05.001_bib88","doi-asserted-by":"crossref","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. Genomics"},{"key":"10.1016\/j.jgg.2026.05.001_bib89","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.jgg.2026.05.001_bib90","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s12915-021-01205-y","article-title":"Transposon-induced epigenetic silencing in the X chromosome as a novel form of dmrt1 expression regulation during sex determination in the fighting fish","volume":"20","author":"Wang","year":"2022","journal-title":"BMC Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib91","doi-asserted-by":"crossref","DOI":"10.1093\/molbev\/msae169","article-title":"Genomic anatomy of homozygous XX females and YY males reveals early evolutionary trajectory of sex-determining gene and sex chromosomes in Silurus fishes","volume":"41","author":"Wang","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"10.1016\/j.jgg.2026.05.001_bib92","doi-asserted-by":"crossref","DOI":"10.1016\/j.aquaculture.2026.743808","article-title":"Genome-wide population structure and a molecular system to precise identification of tilapia genetic resources in China","volume":"618","author":"Wang","year":"2026","journal-title":"Aquaculture"},{"key":"10.1016\/j.jgg.2026.05.001_bib93","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1186\/s13059-019-1727-y","article-title":"Performance of neural network basecalling tools for Oxford Nanopore sequencing","volume":"20","author":"Wick","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib94","doi-asserted-by":"crossref","first-page":"1839","DOI":"10.1101\/gad.220102","article-title":"The Wilms tumor suppressor WT1 regulates early gonad development by activation of Sf1","volume":"16","author":"Wilhelm","year":"2002","journal-title":"Genes Dev."},{"key":"10.1016\/j.jgg.2026.05.001_bib95","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/s42003-023-05551-1","article-title":"Genetic evidence for differential functions of figla and nobox in zebrafish ovarian differentiation and folliculogenesis","volume":"6","author":"Wu","year":"2023","journal-title":"Commun. Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib96","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/s41588-024-02059-0","article-title":"Functional innovation through new genes as a general evolutionary process","volume":"57","author":"Xia","year":"2025","journal-title":"Nat. Genet."},{"key":"10.1016\/j.jgg.2026.05.001_bib97","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1038\/s42003-024-06853-8","article-title":"Steroid hormone-deprived sex reversal in cyp11a1 mutant XX tilapia experiences an ovary-like stage at molecular level","volume":"7","author":"Xiao","year":"2024","journal-title":"Commun. Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib98","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1073\/pnas.1109047109","article-title":"Divergence of duplicate genes in exon-intron structure","volume":"109","author":"Xu","year":"2012","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jgg.2026.05.001_bib99","doi-asserted-by":"crossref","DOI":"10.1210\/endocr\/bqab205","article-title":"Cyp17a1 is required for female sex determination and male fertility by regulating sex steroid biosynthesis in fish","volume":"162,","author":"Yang","year":"2021","journal-title":"Endocrinology"},{"key":"10.1016\/j.jgg.2026.05.001_bib100","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":"Yano","year":"2012","journal-title":"Curr. Biol."},{"key":"10.1016\/j.jgg.2026.05.001_bib101","doi-asserted-by":"crossref","first-page":"2469","DOI":"10.1073\/pnas.0712244105","article-title":"A W-linked DM-domain gene, DM-W, participates in primary ovary development in Xenopus laevis","volume":"105","author":"Yoshimoto","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.jgg.2026.05.001_bib102","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/s12915-025-02160-8","article-title":"The origin, evolution, and translocation of sex chromosomes in Silurus catfish mediated by transposons","volume":"23","author":"Zheng","year":"2025","journal-title":"BMC Biol."}],"container-title":["Journal of Genetics and Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1673852726001657?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1673852726001657?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T20:29:11Z","timestamp":1788985751000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1673852726001657"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":102,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S1673852726001657"],"URL":"https:\/\/doi.org\/10.1016\/j.jgg.2026.05.001","relation":{},"ISSN":["1673-8527"],"issn-type":[{"value":"1673-8527","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"A duplicated female pathway gene figla-like evolves as the male sex-determining gene in tilapia","name":"articletitle","label":"Article Title"},{"value":"Journal of Genetics and Genomics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jgg.2026.05.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}