Allopolyploidization from two dioecious ancestors leads to recurrent evolution of sex chromosomes and reversion to autosomes

Polyploidization presents an unusual challenge for species with sex chromosomes, as it can lead to complex combinations of sex chromosomes that disrupt reproductive development. This is particularly true for allopolyploidization between species with different sex chromosome systems. Here we assemble haplotype-resolved chromosome-level genomes of a female allotetraploid weeping willow ( Salix babylonica ) and a male diploid Salix dunnii using Hi-C and PacBio HiFi reads. We use phylogenomics of nuclear and plastid genomes to show that weeping willow arose from crosses between female ancestor from the Salix clade, having XY sex chromosomes on chromosome 7, with a male ancestor from the Vetrix clade, having ancestral XY sex chromosomes on chromosome 15. Our analysis reveals that weeping willow has one pair sex chromosomes, ZW on chromosome 15, that derive from the ancestral XY sex chromosomes in the Vetrix- clade male ancestor, and the X chromosomes on chromosome 7 from the Salix- clade female ancestor has reverted to an autosome. Taken together, our results point to rapid evolution and reversion of sex chromosomes following allopolyploidization in weeping willow. Significance Statement We assembled haplotype-resolved genomes and obtained gap-free sex chromosomes of a female allotetraploid weeping willow ( Salix babylonica ) and a male diploid Salix dunnii . The weeping willow arose from two dioecious ancestors, that have XY sex chromosomes on chromosome 7 and 15, respectively. The one pair sex chromosomes 15W and 15Z in weeping willow derived from ancestral 15X and 15Y, respectively. Inversions contributed to the evolutions of sex-linked regions (SLRs) of diploid and polyploid willows.