Remarkable Divergence of the Sex-Linked Region between Two Wild Spinach Progenitors, and .

The sex-linked region (SLR) plays an important role in determining the sex of a plant. The SLR of the Y chromosome, composed of a 14.1-Mb inversion and a 10-Mb Y-duplication region (YDR), was deciphered in previously. However, our understanding of the SLR in its wild relatives, and , remains limited. In this study, we used 63 resequencing data from the three species to infer the evolution of the SLR among the species. In the SLR, all the cultivated spinach and accessions were clustered into two distinct categories with both sexes, while the accessions of both sexes were grouped. This suggests that shared a similar SLR with , but not with , which was further confirmed based on the population structure and principal component analysis. Furthermore, we identified 3910 fully sex-linked SNPs in and 92.82% of them were available in , while none of the SNPs were adopted in . Genome coverage in males and females supported the hypothesis that the YDR increasingly expanded during its evolution. Otherwise, we identified 13 sex-linked transposable element insertion polymorphisms within the inversion in both and , demonstrating that the transposable element insertions might have occurred before the recombination suppression event of the inversion. The SLR was conserved compared with the pseudoautosomal region given that the genetic hitchhiking process occurred in the SLR during its evolution. Our findings will significantly advance our understanding of the characteristics and evolution of the SLR in species.