Gap-free X and Y chromosomes ofSalix arbutifoliareveal an evolutionary change from male to female heterogamety in willows, without a change in the sex-determining region

Abstract

In theVetrixclade ofSalix, a genus of woody flowering plants, sex determination involves chromosome 15, but an XY system has changed to a ZW system. We used genome sequencing (with chromosome conformation capture (Hi-C) and PacBio HiFi high-fidelity reads) to study the evolutionary history of the sex-linked regions before and after the transition. We assembled chromosome level gap-free X and Y chromosomes ofSalix arbutifolia, and distinguished the haplotypes in the 15X- and 15Y-linked regions. This revealed “micro-heteromorphism” differentiating the haplotypes of the Y- and X-linked regions, including insertions, deletions and duplications. Unusually, the X-linked region is considerably larger than the corresponding Y region, and we show that this primarily reflects extensive accumulation of repetitive sequences and gene duplications. The phylogenies of single-copy orthogroups within the sex-linked regions ofS. arbutifolia(X and Y) andS. purpurea(Z and W) indicate that they possess a common ancestral sex-linked region that is physically small and located in a repeat-rich region near the chromosome 15 centromere. During the change in heterogamety, the W-linked region was derived from the X-linked one and the Z from the Y. The W may subsequently have evolved a region in which recombination became suppressed. We also detected accumulation of genes with opposite sex-biases in the sex-linked regions.

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

“…In S. dunnii sex-linked region, including 5.87 Mb X-SLR and 2.95 Mb Y-SLR, this is consistent with S. arbutifolia (7.06 Mb X-SLR and 1.81 Mb Y-SLR) (34), but it is opposed to Silene latifolia, which has longer Y-SLR than X-SLR (19,40). There are 128 and 96 protein coding genes within X-SLR and Y-SLR in S. dunnii (Table S5), and the X-SLR has 2.72 Mb longer total repeated sequences than the Y-SLR (Table S12).…”

“…In 7XY and 15XY SDSs, previous studies show the correspondence between one Y chromosome with partial ARR17-like genes and four intact ARR17-like genes in two Chr19s (Table S15, Figure S18 (33)). Diploid S. chaenomeloides (7XY) and S. arbutifolia (15XY) perform this pattern (33,34), suggesting suppression effects between one Y chromosome with partial ARR17-like genes and four intact ARR17-like genes, hence determining male. The fact that partial ARR17-like duplicates are within/close inversions in the S. babylonica and S. dunnii sex chromosomes suggests that these loci act as sex determining factors in these species as well.…”

“…The nuclear and chloroplast trees imply that the female ancestor of S. babylonica most likely arose from the Salix clade, while the male ancestor most likely came from the Vetrix clade. The Vetrix clade contains both 15XY and 15ZW species, however phylogenetic analysis of ancient sex-linked genes within the Vetrix clade, the X and -Y linked genes diverged in ancestor of the Vetrix clade (34), indicating that the 15XY is the most likely sex chromosome system for the S. bablyonica male Vetrix ancestor (Figs. 1, 3, S10).…”

“…Partial ARR17 -like duplicates were also found in Y-linked regions (7Y and 15Y) of willows, which can produce small RNA and suppress the expression of intact ARR17 -like genes on chromosome 19 (33). The species of Vetrix clade inherited ancient sex-linked genes from their 15XY ancestor, ancient Y-linked genes is close to partial ARR17 -like duplicates (30, 33, 34). There were two X-Y homologous gene pairs diverged in ancestor of Vetrix clade (34).…”

“…The species of Vetrix clade inherited ancient sex-linked genes from their 15XY ancestor, ancient Y-linked genes is close to partial ARR17 -like duplicates (30, 33, 34). There were two X-Y homologous gene pairs diverged in ancestor of Vetrix clade (34). These ancient sex-linked genes of Vetrix clade should be kept in weeping willow.…”