Gap‐free X and Y chromosome assemblies of Salix arbutifolia reveal an evolutionary change from male to female heterogamety in willows, without a change in the position of the sex‐determining locus

Summary In the Vetrix clade of Salix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We studied the detailed genetic changes involved. We used genome sequencing, with chromosome conformation capture (Hi‐C) and PacBio HiFi reads to assemble chromosome level gap‐free X and Y of Salix arbutifolia, and distinguished the haplotypes in the 15X‐ and 15Y‐linked regions, to study the evolutionary history of the sex‐linked regions (SLRs). Our sequencing revealed heteromorphism of the X and Y haplotypes of the SLR, with the X‐linked region being considerably larger than the corresponding Y region, mainly due to accumulated repetitive sequences and gene duplications. The phylogenies of single‐copy orthogroups within the SLRs indicate that S. arbutifolia and Salix purpurea share an ancestral SLR within a repeat‐rich region near the chromosome 15 centromere. During the change in heterogamety, the X‐linked region changed to a W‐linked one, while the Z was derived from the Y.