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However, no yellow perch reference genome has been available to facilitate improvements in both fisheries and aquaculture management practices. By combining Oxford Nanopore Technologies long\u2010reads, 10X Genomics Illumina short linked reads and a chromosome contact map produced with Hi\u2010C, we generated a high\u2010continuity chromosome\u2010scale yellow perch genome assembly of 877.4 Mb. It contains, in agreement with the known diploid chromosome yellow perch count, 24 chromosome\u2010size scaffolds covering 98.8% of the complete assembly (N50\u00a0=\u00a037.4\u00a0Mb, L50\u00a0=\u00a011). We also provide a first characterization of the yellow perch sex determination locus that contains a male\u2010specific duplicate of the anti\u2010Mullerian hormone type II receptor gene (\n                    <jats:italic>amhr2by<\/jats:italic>\n                    ) inserted at the proximal end of the Y chromosome (chromosome 9). Using this sex\u2010specific information, we developed a simple PCR genotyping assay which accurately differentiates XY genetic males (\n                    <jats:italic>amhr2by<\/jats:italic>\n                    <jats:sup>+<\/jats:sup>\n                    ) from XX genetic females (\n                    <jats:italic>amhr2by<\/jats:italic>\n                    <jats:sup>\u2212<\/jats:sup>\n                    ). Our high\u2010quality genome assembly is an important genomic resource for future studies on yellow perch ecology, toxicology, fisheries and aquaculture research. In addition, characterization of the\n                    <jats:italic>amhr2by<\/jats:italic>\n                    gene as a candidate sex\u2010determining gene in yellow perch provides a new example of the recurrent implication of the transforming growth factor beta pathway in fish sex determination, and highlights gene duplication as an important genomic mechanism for the emergence of new master sex determination genes.\n                  <\/jats:p>","DOI":"10.1111\/1755-0998.13133","type":"journal-article","created":{"date-parts":[[2020,1,6]],"date-time":"2020-01-06T04:00:41Z","timestamp":1578283241000},"page":"531-543","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":106,"title":["Characterization of a Y\u2010specific duplication\/insertion of the anti\u2010Mullerian hormone type II receptor gene based on a chromosome\u2010scale genome assembly of yellow perch,\n                    <i>Perca flavescens<\/i>"],"prefix":"10.1111","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5893-6184","authenticated-orcid":false,"given":"Romain","family":"Feron","sequence":"first","affiliation":[{"name":"INRAE UR 1037 Fish Physiology and Genomics Rennes France"},{"name":"Department of Ecology and Evolution Swiss Institute of Bioinformatics University of Lausanne Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margot","family":"Zahm","sequence":"additional","affiliation":[{"name":"Plate\u2010forme bio\u2010informatique Genotoul Math\u00e9matiques et Informatique Appliqu\u00e9es de Toulouse INRAE Castanet Tolosan France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8560-4003","authenticated-orcid":false,"given":"C\u00e9dric","family":"Cabau","sequence":"additional","affiliation":[{"name":"SIGENAE, GenPhySE INRAE ENVT Universit\u00e9 de Toulouse Castanet Tolosan 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