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This primary genetic cue is often located on a single locus\u2014referred to as sex chromosomes\u2014and can be limited to females (in a ZZ\/ZW system) or males (in an XX\/XY system). One trademark of sex chromosomes is a restriction or cessation of recombination surrounding the sex-limited region (to prevent its inheritance in the homogametic sex). This may lead to\u2014through a variety of mechanisms\u2014higher amounts of genetic divergence within this region, i.e. between the X\/Z and Y\/W chromosomes, especially when compared to their autosomal counterparts. Recent advances in genome sequencing and computation have brought with them the ability to resolve haplotypes within a diploid individual, permitting assembly of previously challenging genomic regions like sex chromosomes. Leveraging these advances, we identified replicable diagnostic characteristics between typical autosomes and sex chromosomes (within a single genome assembly). Under this framework, we can use this information to identify putative sex chromosome linkage groups across divergent vertebrate taxa and simultaneously curate misassembled regions on autosomes. Here, we present this conceptual framework and associated tool for identifying candidate sex chromosome linkage groups from a single, diploid individual dubbed Sex Chromosome Identification by Negating Kmer Densities, or SCINKD.<\/jats:p>","DOI":"10.1101\/2025.07.07.660342","type":"posted-content","created":{"date-parts":[[2025,7,11]],"date-time":"2025-07-11T01:50:36Z","timestamp":1752198636000},"source":"Crossref","is-referenced-by-count":0,"title":["Sex chromosome identification and genome curation from a single individual with SCINKD"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4243-5788","authenticated-orcid":false,"given":"Brendan J.","family":"Pinto","sequence":"first","affiliation":[{"name":"Comparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA"},{"name":"Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA"},{"name":"Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6656-4034","authenticated-orcid":false,"given":"Simone M.","family":"Gable","sequence":"additional","affiliation":[{"name":"Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2601-0816","authenticated-orcid":false,"given":"Shannon E.","family":"Keating","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Marquette University, Milwaukee, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1499-0311","authenticated-orcid":false,"given":"Chase H.","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology, University of Texas, Austin, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0204-8003","authenticated-orcid":false,"given":"Tony","family":"Gamble","sequence":"additional","affiliation":[{"name":"Department of Zoology, Milwaukee Public Museum, Milwaukee, WI USA"},{"name":"Department of Biological Sciences, Marquette University, Milwaukee, WI, USA"},{"name":"Bell Museum of Natural History, University of Minnesota, St. Paul, MN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3114-1469","authenticated-orcid":false,"given":"Stuart V.","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Museum of Life Sciences, Department of Biological Sciences, Louisiana State University Shreveport, Shreveport, LA, USA"},{"name":"Department of Natural History, Florida Museum of Natural History, Gainesville, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2614-0285","authenticated-orcid":false,"given":"Melissa A.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Comparative Genomics and Reproductive Health Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA"},{"name":"Center for Evolution and Medicine, Arizona State University, Tempe, AZ USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026011009000570000_2025.07.07.660342v2.1","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02823-7"},{"key":"2026011009000570000_2025.07.07.660342v2.2","unstructured":"Andrews, S. 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