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Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera &gt;36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species.<\/jats:p>","DOI":"10.1101\/2024.12.09.627636","type":"posted-content","created":{"date-parts":[[2025,1,2]],"date-time":"2025-01-02T02:48:10Z","timestamp":1735786090000},"source":"Crossref","is-referenced-by-count":15,"title":["An X-linked sex determination mechanism in cannabis and hop"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6431-0660","authenticated-orcid":false,"given":"Sarah B.","family":"Carey","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip C.","family":"Bentz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John T.","family":"Lovell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laramie 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