Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry

Abstract

When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex-determining region of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome-scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known sex-determining region on the W in strawberries. We fully characterized the previously incomplete sex-determining region, confirming its gene content, genomic location, and evolutionary history. Resolution of gaps in the previous characterization of the sex-determining region added 10 kb of sequence including a noncanonical long terminal repeat-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the sex-determining region insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.

Keywords: polyploid; sex chromosomes; strawberry; whole-genome assembly.

Fig. 1.

Genome and sex determination evolution in Fragaria. The scenario for genome evolution is simplified and adapted from Tennessen et al. (2014, 2018), Liston et al. (2020), and Session and Rokhsar (2020). The number of polyploidization events is still debated (Tennessen et al. 2014; Session and Rokhsar 2020) and is depicted here as a single event for simplification. The colors of the branches correspond to the octoploid subgenomes and their diploid progenitors: Av (red), Bi (blue), B1 (yellow), and B2 (green). ⚥♂♀ illustrates the presence of hermaphrodite, male, and female individuals, respectively, in a species. The original male sterility trait was selected against through selective breeding (Liston et al. 2014) resulting in hermaphroditism in F. × ananassa which is represented by ⚥ *. Fragaria chiloensis is predominantly dioecious with some occurrence of hermaphrodite individuals (represented by a small ⚥  ) including subspecies sandwichensis which is only hermaphrodite (Staudt 1999). The group 6 homeologous chromosomes and location of the SDR are shown on the right for the octoploid clades.

Fig. 2.

Dotplot of a minimap2 alignment between F. chiloensis group 6 homeologous chromosomes (Fchil6-Av, Fchil6-B1, Fchil6-B2, and Fchil6-Bi) and F. vesca Fvb6.

Fig. 3.

Gene and TEs on the W-specific F. chiloensis SDR and its homologous Z sequence. The W-specific region corresponds to the pink line, the Z to the blue area. Triangles represent genes, their direction shows the reading frame. Genes nomenclature follows (30). Gene colors correspond to the subgenome they originated from: Av (red), B1 (yellow), and B2 (green). An asterisk in RPP0W highlights its origin by retrotransposition from a gene on Fchil7-B2 while the other SDR genes resulted from sequential translocation from Fchil6-B2 and Fchil6-B1, respectively. The chromosomes from which the genes originated from are labeled in italics under the genes. Boxes represent TEs, and the orange arrows denote inverted repeats flanking the SDR insertion. The diagram is not to scale.

Fig. 4.

Identification and characterization of W- and Z-specific regions. Top-left: Dotplot of a nucmer alignment between the W and Z haplotype-resolved region. Specific regions of the Z-haplotype and W-haplotype sequences are highlighted by horizontal gray and vertical black arrows, respectively. Middle panels: Repeat coverage on the W (bottom) and Z (right) haplotype sequences. Bottom and far right: Coverage difference between males and females [log2(mean F) − log2(mean M)] on nonoverlapping 10-kb windows: on the W haplotig (bottom) and on the Z homologous region (right). The region highlighted in dark purple represents the SDR, in light purple a Z-specific region. Values close to 0 indicate regions shared between Z and W (PAR), −1 and > 0 potential Z- and W-specific regions, respectively.

Fig. 5.

Repeat coverage, intersexual weighted F_ST, and difference between males and females in coverage [log2(mean F) − log2(mean M)] across the sex chromosome (Fchil6-Av) in nonoverlapping 10-kb windows. The gray area represents the 95% confidence interval obtained by resampling a representative autosome (Fchil3-B1) 1,000 times. The black line on the top left panel highlights the haplotype-resolved region illustrated in Fig. 4. For the F_ST analysis, the reads were remapped on the reference sequence without the inclusion of the W haplotype which was included in the coverage analysis. The right panel represents a zoomed view of the region at the vicinity of the SDR insertion on the Z chromosome, defined by the F-box and arabinogalactan genes.

Fig. 6.

Maximum likelihood phylogenetic trees of (a) ribosomal protein P0 (RPP0), (b) GDP-mannose-3′,5′-epimerase (GME), and (c) glucan endo-1,3 beta-glucosidase (glucan). Nodes with bootstrap support <80 are represented by white circles. The copy of the genes present in the female-specific SDR is labeled “SDR” with a rectangle filled with the subgenome color of its original autosomal copy (Av = red, B1 = yellow, B2 = green, Bi = blue). Gray areas depict genes belonging to the gene families but not homeologous to the original autosomal copy of the SDR genes. The chromosomal location is given for the sister copies of the SDR genes. Tree visualization was done in R version 4.1.0 (R Core Team 2021) using ggtree v.3.0.4 (Yu 2020). The complete phylogenies are given in the Supplementary Figs. 13–15.