Phased chromosome-level genomes reveal young evolutionary origin of sex determination in Magnolia kwangsiensis.

While sex determination has been extensively studied in animals, the origin and early evolution of sex chromosomes in plants remain poorly understood. Magnolia kwangsiensis, an early-diverging dioecious flowering plant, provides a unique opportunity to investigate sex chromosome evolution at early stages. Here we generated phased chromosome-level genome assemblies for male and female M. kwangsiensis individuals (~2.4-2.5 Gb of 19 chromosomes) and uncovered a nascent XY sex chromosome system. The sex-determining region (SDR) is located on chromosome 4 and spans ~10.4 Mb on the X chromosome and ~ 17.3 Mb on the Y chromosome. Comparative of X- and Y-linked SDR haplotypes revealed recombination suppression accompanied by partial gene loss, of tandem repeat accumulation, and elevated substitution rates within the Y. The presence of two evolutionary strata indicates sequential recombination suppression during the SDR formation, likely initiated by two inversions. Molecular-clock analyses date the SDR to ~7.74 million years ago. Within the SDR, we identified several putative sex-determining genes, including TPD1 and CRN, which are potentially associated with male or female sterility, respectively, and fit well with the classic two-gene model of sex determination. Our findings capture an early stage of XY chromosome development in a magnoliid lineage and provide novel insights into the origin and evolution of sex chromosomes in flowering plants.