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This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the <jats:italic>Solea senegalensis<\/jats:italic> genome, a flatfish of great commercial value, into 82 contigs (614\u2009Mb) combining long\u2010 and short\u2010read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC\u2010FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (<jats:italic>fshr<\/jats:italic>) consistent with an XX\/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The <jats:italic>fshr<\/jats:italic> gene displayed differential expression between male and female gonads from 86\u2009days post\u2010fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of <jats:italic>amh<\/jats:italic> and <jats:italic>cyp19a1a<\/jats:italic>, testis and ovary marker genes, respectively, in males and females. The Y\u2010linked <jats:italic>fshr<\/jats:italic> allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X\u2010linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.<\/jats:p>","DOI":"10.1111\/1755-0998.13750","type":"journal-article","created":{"date-parts":[[2023,1,1]],"date-time":"2023-01-01T08:44:14Z","timestamp":1672562654000},"page":"886-904","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["A chromosome\u2010level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex\u2010determining gene in the flatfish <i>Solea senegalensis<\/i>"],"prefix":"10.1111","volume":"23","author":[{"given":"Roberto","family":"de la Herr\u00e1n","sequence":"first","affiliation":[{"name":"Departamento de Gen\u00e9tica, Facultad de Ciencias Universidad de Granada  Granada Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miguel","family":"Hermida","sequence":"additional","affiliation":[{"name":"Departamento de Zoolog\u00eda, Gen\u00e9tica y Antropolog\u00eda F\u00edsica; 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