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The special transient hermaphroditic stage makes the little yellow croaker (<jats:italic>Larimichthys polyactis<\/jats:italic>) an appealing model for studying hermaphrodite formation. However, the origin and evolutionary relationship between of<jats:italic>L.\u00a0polyactis<\/jats:italic>and<jats:italic>Larimichthys crocea<\/jats:italic>, the most famous commercial fish species in East Asia, remain unclear. Here, we report the sequence of the<jats:italic>L.\u00a0polyactis<\/jats:italic>genome, which we found is ~706\u2009Mb long (contig N50\u00a0=\u00a01.21\u2009Mb and scaffold N50\u00a0=\u00a04.52\u2009Mb) and contains 25,233 protein\u2010coding genes. Phylogenomic analysis suggested that<jats:italic>L.\u00a0polyactis<\/jats:italic>diverged from the common ancestor,<jats:italic>L.\u00a0crocea<\/jats:italic>, approximately 25.4\u00a0million years ago. Our high\u2010quality genome assembly enabled comparative genomic analysis, which revealed several within\u2010chromosome rearrangements and translocations, without major chromosome fission or fusion events between the two species. The<jats:italic>dmrt1<\/jats:italic>gene was identified as the male\u2010specific gene in<jats:italic>L.\u00a0polyactis<\/jats:italic>. Transcriptome analysis showed that the expression of<jats:italic>dmrt1<\/jats:italic>and its upstream regulatory gene (<jats:italic>rnf183<\/jats:italic>) were both sexually dimorphic.<jats:italic>Rnf183<\/jats:italic>, unlike its two paralogues<jats:italic>rnf223<\/jats:italic>and<jats:italic>rnf225<\/jats:italic>, is only present in<jats:italic>Larimichthys<\/jats:italic>and<jats:italic>Lates<\/jats:italic>but not in other teleost species, suggesting that it originated from lineage\u2010specific duplication or was lost in other teleosts<jats:italic>.<\/jats:italic>Phylogenetic analysis shows that the hermaphrodite stage in male<jats:italic>L.\u00a0polyactis<\/jats:italic>may be explained by the sequence evolution of<jats:italic>dmrt1<\/jats:italic>. Decoding the<jats:italic>L.\u00a0polyactis<\/jats:italic>genome not only provides insight into the genetic underpinnings of hermaphrodite evolution, but also provides valuable information for enhancing fish aquaculture.<\/jats:p>","DOI":"10.1111\/1755-0998.13731","type":"journal-article","created":{"date-parts":[[2022,11,4]],"date-time":"2022-11-04T07:35:10Z","timestamp":1667547310000},"page":"632-658","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Whole\u2010genome assembly and annotation for the little yellow croaker (<i>Larimichthys polyactis<\/i>) provide insights into the evolution of hermaphroditism and gonochorism"],"prefix":"10.1111","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3832-5356","authenticated-orcid":false,"given":"Qing\u2010Ping","family":"Xie","sequence":"first","affiliation":[{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro\u2010Products, Institute of Hydrobiology Zhejiang Academy of Agricultural Sciences Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhan","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro\u2010Products, Institute of Hydrobiology Zhejiang Academy of Agricultural Sciences Hangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian\u2010Zhi","family":"Shi","sequence":"additional","affiliation":[{"name":"Novogene Bioinformatics Institute Beijing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro\u2010Products, Institute of Hydrobiology Zhejiang Academy of Agricultural Sciences Hangzhou 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