A haplotype-resolved nutmeg genome reveals XY sex chromosome evolution and enables molecular sexing.

Nutmeg (Myristica fragrans Houtt.) is a dioecious species that produces one of the most valuable spices and has peculiar holocentric chromosomes with diffuse centromere. 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 Mb X-linked SLR and a 3.1 Mb Y-linked SLR with limited evidence for Y-degeneration. Low X:Y synonymous divergence for X- and Y-linked homologs (Ks < 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).