Evolution of a ZW sex chromosome system in willows

Abstract

Transitions in the heterogamety of sex chromosomes (e.g., XY to ZW or vice versa) fundamentally alter the genetic basis of sex determination, however the details of these changes have been studied in only a few cases. In an XY to ZW transition, the X is likely to give rise to the W because they both carry feminizing genes and the X is expected to harbour less genetic load than the Y. Here, using a new reference genome for Salix exigua, we trace the X, Y, Z, and W sex determination regions during the homologous transition from an XY system to a ZW system in willow (Salix). We show that both the W and the Z arose from the Y chromosome. We find that the new Z chromosome shares multiple homologous putative masculinizing factors with the ancestral Y, whereas the new W lost these masculinizing factors and gained feminizing factors. The origination of both the W and Z from the Y was permitted by an unexpectedly low genetic load on the Y and this indicates that the origins of sex chromosomes during homologous transitions may be more flexible than previously considered.

Fig. 1. Mapping sex-associated SNPs in S. exigua.

a GWAS results show sex is strongly associated with Chr15 in S. exigua when S. exigua is used as the reference genome. The X-axis indicates the chromosomal position and SC refers to unassembled scaffolds. The Y-axis represents the significance of the association. The red dashed line is the significance threshold after using Bonferroni multiple testing correction (one sided α < 0.05). Each dot in the figure represents a single SNP after filtering. b Male genotypes of SNPs around the SDR were primarily heterozygous and females were homozygous indicating an XY sex determination system. c A magnification of the GWAS results for Chr15 in Salix exigua. d GWAS results for S. exigua genotypes from the same individuals as in 1a when the S. purpurea Chr15W chromosome is used as the reference genome. Red dashed lines represent the same significance cutoffs as in part (a).

Fig. 2. The X contigs and the Y-specific contig in S. exigua.

a Mapping read (MQ > 30) depths between 24 males and 24 females on S. exigua Chr15. The female genotypes had low depth between 0.6 and 1.3 Mb on Chr15, are highlighted by the red box, and indicate a Y-specific assembly on Chr15. The blue line and dots refer to male average and individual read depth, respectively. The orange line and dots refer to female average and individual read depth, respectively. b Alignments among the S. exigua X and Y chromosomes and the S. pururea Z chromosome. Grey lines represent syntenic genes among the S. exigua X contigs, the S. exigua male Chr15 (XY), and the S. purpurea Chr15Z. The location where contig 511 assembles is shown as a black bar. The red portion of the sex determination region (SDR) in the S. exigua male is the Y-specific region and is associated with a portion of contig 511, the blue portion of the SDR exhibits homology between the X and Y chromosomes. The SDR on S. purpurea Chr15Z is represented by an orange bar. c SNP presence between 0 and 2.2 Mb showing a low frequency of SNP calls in females between 0.6 and 1.3 Mb. Blue dots refer to the presence of SNP.

Fig. 3. Sex chromosome transitions in Salix.

The phylogeny of 8 species in the Salicaceae family shows how the sex chromosomes have changed across the phylogeny and where the sex determination system shifted from XY to ZW (Adapted from Sanderson et al. 2023).

Fig. 4. Relationships among 30 exon-anchored homologous regions on the Z, Y, and W sex determination regions.

a Alignment of the exon regions (grey bars) with Y-associated SNPs across S. exigua and S. purpurea. The relative location of contig 511 is shown in green. b A phylogeny based on the concatenated exon regions shows that the Z and W chromosomes are derived from an ancestral Y. Bootstrap support > 70 is indicated.

Fig. 5. RR17 genes and partial duplicates in S. exigua and S. purpurea chromosome 15.

a Positions (triangles) and copy names of RR17 genes and partial duplicates on the S. exigua Y, S. purpurea Z, and S. purpurea W chromosomes. Triangles are pointed in the direction of the sequence relative to the original RR17 gene (XM_024590879.1). Dashed lines show the homology between RR17 partial duplicates on the Y and Z chromosomes. Large arrows on the W chromosome indicate full length intact RR17 copies. b Homology of RR17 partial duplicates relative to the intact RR17 gene in Populus trichocarpa. Red arrows represent partial duplicated of RR17 in S. exigua and are positioned according to their homology with the full length intact RR17 gene (Blue boxes). Purple arrows represent copies in S. purpurea positioned with their homology relative to the intact copy of RR17. * indicates the duplicated palindromes within 10 bp in length.

Fig. 6. Homologous partial duplicates on the Y and Z chromosomes each have a single origin.

Phylogenies include homologous partial duplicates (highlighted in blue) on S. exigua, S. purpurea Z, and homologous regions on the intact copy of RR17 in S. exigua, S. purpurea, and P. trichocarpa. The patterns suggest that the partial duplicates on Z and Y each have a single origin. Bootstrap support > 70 is indicated. The tip labels are formatted as Species-Chromosome-Copy number. Sp: S. purpurea; Se: S. exigua; Pt: P. trichocarpa. C refers to the intact copies of RR17.

Fig. 7. The fate of sex chromosomes during the transition from XY to ZW sex systems.

a Model of sex determination evolution from XY to ZW in Salix. The X was lost during the transition while the Y developed into the Z and W. Translocations from the Chr19 copy introduced four copies of full length RR17 genes into the new W chromosome, and RR17 partial duplicates were deleted from the W. The Y and Z further differentiated by the loss (not shown) or gain (shown) of additional partial duplications of RR17. b Comparisons of the fitness of genotypes during the X, Y, W polymorphic transition assuming the Y carries genetic load under two scenarios: if the W was derived from the X or from the Y. If the W was derived from the X, and only Y carries a mutation load, YY individuals would have low fitness due to homozygous deleterious mutations. If W was derived from the Y, both the YY and the YW individuals would suffer from the homozygous genetic load.