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Recently, we created YY-supermale yellow catfish by crossing XY males with sex-reversed XY females, providing a valuable model for Y-chromosome assembly and evolution. Here, we assembled highly homomorphic Y and X chromosomes by sequencing genomes of the YY supermale and XX female in yellow catfish, revealing their nucleotide divergences with only less than 1% and with the same gene compositions. The sex-determining region (SDR) was identified to locate within a physical distance of 0.3\u00a0Mb by FST scanning. Strikingly, the incipient sex chromosomes were revealed to originate via autosome\u2013autosome fusion and were characterized by a highly rearranged region with an SDR downstream of the fusion site. We found that the Y chromosome was at a very early stage of differentiation, as no clear evidence of evolutionary strata and classical structure features of recombination suppression for a rather late stage of Y-chromosome evolution were observed. Significantly, a number of sex-antagonistic mutations and the accumulation of repetitive elements were discovered in the SDR, which might be the main driver of the initial establishment of recombination suppression between young X and Y chromosomes. Moreover, distinct three-dimensional chromatin organizations of the Y and X chromosomes were identified in the YY supermales and XX females, as the X chromosome exhibited denser chromatin structure than the Y chromosome, while they respectively have significantly spatial interactions with female- and male-related genes compared with other autosomes. The chromatin configuration of the sex chromosomes as well as the nucleus spatial organization of the XX neomale were remodeled after sex reversal and similar to those in YY supermales, and a male-specific loop containing the SDR was found in the open chromatin region. Our results elucidate the origin of young sex chromosomes and the chromatin remodeling configuration in the catfish sexual plasticity.<\/jats:p>","DOI":"10.1093\/nsr\/nwac239","type":"journal-article","created":{"date-parts":[[2022,10,29]],"date-time":"2022-10-29T04:31:52Z","timestamp":1667017912000},"source":"Crossref","is-referenced-by-count":47,"title":["Origin and chromatin remodeling of young X\/Y sex chromosomes in catfish with sexual plasticity"],"prefix":"10.1093","volume":"10","author":[{"given":"Gaorui","family":"Gong","sequence":"first","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Xiong","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shijun","family":"Xiao","sequence":"additional","affiliation":[{"name":"Jiaxing Key Laboratory for New Germplasm Breeding of Economic Mycology , Jiaxing 314000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi-Yin","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences , Wuhan 430072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peipei","family":"Huang","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University , Wuhan 430023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Liao","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingqing","family":"Han","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaohong","family":"Lin","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences , Wuhan 430072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Dan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences , Wuhan 430072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhou","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences , Wuhan 430072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fan","family":"Ren","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7419-2047","authenticated-orcid":false,"given":"Qi","family":"Zhou","sequence":"additional","affiliation":[{"name":"MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University , Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4969-1482","authenticated-orcid":false,"given":"Jian-Fang","family":"Gui","sequence":"additional","affiliation":[{"name":"Hubei Hongshan Laboratory, College of Fisheries, Huazhong Agricultural University , Wuhan 430070, China"},{"name":"State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Institute of Hydrobiology, Chinese Academy of Sciences, University of the Chinese Academy of Sciences , Wuhan 430072, 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