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This study investigated the homologous XY (KarF) and XY1Y2 (KarG) sex chromosome systems present in this species by integrating cytogenetics and genomics to examine sex chromosomes\u2019 composition through characterization of repeatome (satellite DNA and transposable elements) and sex-linked markers. Our analysis indicated that both karyomorphs are little differentiated in their sex chromosomes content revealed by satDNA mapping and putative sex-linked markers. Both repeatomes were mostly composed of transposable elements, but neither intra- (male versus female) nor interspecific (KarF x KarG) variations were found. In both systems, we demonstrated the occurrence of sex-specific sequences probably located on the non-recombining region of the Y chromosome supported by the accumulation of sex-specific haplotypes of HmfSat10-28\/HmgSat31-28. This investigation offered valuable insights by highlighting the composition of homologous XY and XY1Y2 multiple sex chromosomes. Although homologous, the large Y chromosome in KarF corresponds to two separate linkage groups (Y1 and Y2) in KarG implying a specific meiotic arrangement involving the X chromosome in a meiotic trivalent chain. This scenario likely influenced recombination rates and, as a result, the genomic composition of these chromosomes.<\/jats:p>","DOI":"10.3390\/ijms26136039","type":"journal-article","created":{"date-parts":[[2025,6,24]],"date-time":"2025-06-24T06:49:38Z","timestamp":1750747778000},"page":"6039","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Repeatome Dynamics and Sex Chromosome Differentiation in the XY and XY1Y2 Systems of the Fish Hoplias malabaricus (Teleostei; Characiformes)"],"prefix":"10.3390","volume":"26","author":[{"given":"Mariannah Pravatti Barcellos","family":"de Oliveira","sequence":"first","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3374-2233","authenticated-orcid":false,"given":"Geize Aparecida","family":"Deon","sequence":"additional","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5699-5789","authenticated-orcid":false,"given":"Francisco","family":"de Menezes Cavalcante Sassi","sequence":"additional","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6209-6296","authenticated-orcid":false,"given":"Fernando Henrique Santos","family":"de Souza","sequence":"additional","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7595-0014","authenticated-orcid":false,"given":"Caio Augusto Gomes","family":"Goes","sequence":"additional","affiliation":[{"name":"Fish Genomics and Conservation Laboratory, Faculty of Sciences, S\u00e3o Paulo State University, Bauru 01049-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ricardo","family":"Utsunomia","sequence":"additional","affiliation":[{"name":"Fish Genomics and Conservation Laboratory, Faculty of Sciences, S\u00e3o Paulo State University, Bauru 01049-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8845-3845","authenticated-orcid":false,"given":"F\u00e1bio","family":"Porto-Foresti","sequence":"additional","affiliation":[{"name":"Fish Genomics and Conservation Laboratory, Faculty of Sciences, S\u00e3o Paulo State University, Bauru 01049-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5779-0443","authenticated-orcid":false,"given":"Jhon Alex Dziechciarz","family":"Vidal","sequence":"additional","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda Bueno","family":"da Silva","sequence":"additional","affiliation":[{"name":"Fish Genomics and Conservation Laboratory, Faculty of Sciences, S\u00e3o Paulo State University, Bauru 01049-010, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4763-1347","authenticated-orcid":false,"given":"Tariq","family":"Ezaz","sequence":"additional","affiliation":[{"name":"Institute of Applied Ecology, Faculty of Science and Technology, University of Canberra, Canberra 2617, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1672-3054","authenticated-orcid":false,"given":"Thomas","family":"Liehr","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Humangenetik, Universit\u00e4tsklinikum Jena, 07747 Jena, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4340-1464","authenticated-orcid":false,"given":"Marcelo","family":"de Bello Cioffi","sequence":"additional","affiliation":[{"name":"Evolutionary Cytogenetics Laboratory, Department of Genetics and Evolution, Federal University of S\u00e3o Carlos, S\u00e3o Carlos 13565-905, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,6,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Nelson, J.S., Grande, T.C., and Wilson, M.V. 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