Remarkable Divergence of the Sex-Linked Region between Two Wild Spinach Progenitors, Spinacia turkestanica and Spinacia tetrandra

SIMPLE SUMMARY: There remain substantial gaps in our understanding of the sex-linked region (SLR) in two wild spinach progenitors, Spinacia turkestanica and S. tetrandra, although SLR in cultivated spinach is well understood. Using 63 Spinacia accessions comprising 32 S. oleracea, 19 S. turkestanica and 12 S. tetrandra, we found that S. oleracea shared a similar SLR with S. turkestanica, while the SLR was remarkably divergent between S. oleracea/S. turkestanica and S. tetrandra. Additionally, the SLR increasingly expanded via accumulating repetitive sequences and was more conserved than the pseudoautosomal region (PAR) during the evolution of S. tetrandra to S. oleracea. The results obtained in this study provide a broader understanding of the evolution of SLR in Spinacia species. ABSTRACT: 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 Spinacia oleracea previously. However, our understanding of the SLR in its wild relatives, S. turkestanica and S. tetrandra, remains limited. In this study, we used 63 resequencing data from the three Spinacia species to infer the evolution of the SLR among the Spinacia species. In the SLR, all the cultivated spinach and S. turkestanica accessions were clustered into two distinct categories with both sexes, while the S. tetrandra accessions of both sexes were grouped. This suggests that S. oleracea shared a similar SLR with S. turkestanica, but not with S. tetrandra, which was further confirmed based on the population structure and principal component analysis. Furthermore, we identified 3910 fully sex-linked SNPs in S. oleracea and 92.82% of them were available in S. turkestanica, while none of the SNPs were adopted in S. tetrandra. 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 S. oleracea and S. turkestanica, 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 Spinacia species.