A novel downstream factor in willows replaces the ancestral sex determining gene

Sex chromosome turnover has occurred in many groups, and is mediated by the translocation or duplication of apical sex-determining genes, or the replacement of original sex determination genes by new ones. In dioecious plants, the former frequently occurs, while the latter is rarely reported. Here, we assembled four haplotype-resolved chromosome-level genomes from four lineages of the Salix polyclona complex, including three diploids (E, E-TS, and W1) and one autotetraploid (W2). Our analyses reveal that diploids have a ZW/ZZ system, while autotetraploid has a ZZZW/ZZZZ system on chromosome 15. The apical sex-determining genes of Salicaceae, ARR17-like duplicates on chromosomes 15 and 19, which can indirectly turn-on/off the expression of PISTILLATA (PI) gene and determine sex, appears to have lost the function of sex determination in the S. polyclona complex. We found a novel sex determining factor on the 15W of the complex, namely partial PI-like duplicates, which has taken over the function from the ARR17-like duplicates. In conclusion, a new dominant sex-determining gene was recruited in the S. polyclona complex, replacing the ancestral apical sex-determining ARR17-like duplicates. The newly identified partial PI-like duplicates exhibit a direct influence on the downstream intact PI-like duplications, providing valuable insights into the evolutionary trajectory of the top-down sex determination pathway.