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The impact of holocentricity on the evolution of sex chromosomes is not well understood. Here, we present the first fully annotated haplotype-resolved chromosome-level genome of a male nutmeg plant, identify its sex chromosomes and analyse evolution of the sex-linked region (SLR). We demonstrate that nutmeg has a male heterogametic (XY) system, with a 0.23\u2009Mb X-linked SLR and a 3.1\u2009Mb Y-linked SLR with limited evidence for Y-degeneration. Low X:Y synonymous divergence for X- and Y-linked homologs (K\n                    <jats:sub>s<\/jats:sub>\n                    &lt; 2.5%) indicates recent evolution of sex linkage, likely through loss(es) of homologous X-linked region(s). Leveraging the new genome and SLR sequences, we developed PCR-based molecular marker for reliable sexing of nutmeg seedlings, enabling efficient management of plantations by ensuring the optimal male to female ratio (1:10).\n                  <\/jats:p>","DOI":"10.1038\/s42003-026-10355-0","type":"journal-article","created":{"date-parts":[[2026,5,28]],"date-time":"2026-05-28T14:15:27Z","timestamp":1779977727000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing"],"prefix":"10.1038","volume":"9","author":[{"given":"Katarina","family":"Matvijev","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sufang","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mengjun","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashini D.","family":"Mahadura","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9417-5789","authenticated-orcid":false,"given":"Ray","family":"Ming","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8077-5452","authenticated-orcid":false,"given":"Dmitry A.","family":"Filatov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,28]]},"reference":[{"key":"10355_CR1","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1038\/s41559-019-1050-8","volume":"3","author":"B Vicoso","year":"2019","unstructured":"Vicoso, B. 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