Fig 1.
Polyploid composition and map locations of the SDR in octoploid Fragaria.
(A) There are seven haploid Fragaria chromosomes. Diploids (e.g., F. vesca ssp. bracteata, used to generate the reference genome Fvb) have two copies of each. Octoploids have eight copies of each, within four homoeologous subgenomes (Bi, B2, B1, Av) showing high synteny with each other and with Fvb. (B) In multiple independent linkage crosses across octoploid taxa, the SDR (colored circles) had been previously mapped to three locations on different chromosomes of homoeologous group 6, corresponding to three positions (1 Mb, 13 Mb, or 37 Mb) on Fvb6. The “Linkage Cross” column indicates the taxon in which each SDR has been fine-mapped. Sex always showed ZW inheritance, but no sex-specific sequence had been previously identified. Fc, F. chiloensis; Fvb, diploid reference genome assembly informed by F. vesca ssp. bracteata; Fvp, F. virginiana ssp. platypetala; Fvv, F. virginiana ssp. virginiana; Mb, megabase; SDR, sex-determining region.
Table 1.
Fragaria taxa sequenced and SDR positions mapped in linkage crosses.
Table 2.
Elucidating the three SDR locations in octoploid Fragaria.
Fig 2.
The “SDR cassette,” a 13 kb haplotype occurring in nearly all females (29/31) and never in males (0/29), was assembled from reads containing shared female-specific sequence (S2 Table). This cassette contains two predicted genes, GMEW and RPP0W (direction of transcription indicated by arrowheads); GMEW exons downstream of the variable stop codon are faded. The locations of two assembly gaps and the diagnostic deletion are also indicated. The light blue rectangle indicates the 2.7 kb window used in phylogenetic analysis (Fig 3). SDR, sex-determining region.
Fig 3.
Phylogenetic history of the hemizygous female-specific SDR cassette.
Phylogeny of the central 2.7 kb of the hemizygous SDR cassette (blue box, Fig 2; 0%–30% missing data; mean = 16%) from females of several octoploid strawberries (S1 Table). Three major clades, α, β, and γ, are revealed. Shimodaira-Hasegawa-like (black, above branches) and bootstrap (grey, below branches) support is shown if >50%. SDRs that have been mapped are noted along with the location of the SDR. A pseudo-outgroup sequence (not shown) was generated with consistent homology to the W haplotype along this 2.7 kb portion, by concatenation of sequence from F. vesca reference genome Fvb6 position 1 Mb and orthologous Z chromosome BAC sequence, together with 1.2 kb of sequence from Fvb7 position 18 Mb corresponding to the closest autosomal paralog of RPP0W. The close evolutionary relationship between the β and γ clades is consistent with the inferred history of translocations, indicated at two points with black curved arrows to the left of the phylogeny. BAC, bacterial artificial chromosome; Fac, F. × ananassa ssp. cuneifolia; Fc, F. chiloensis; Fvb, diploid reference genome assembly informed by F. vesca ssp. bracteata; Fvg, F. virginiana ssp. glauca; Fvp, F. virginiana ssp. platypetala; Fvv, F. virginiana ssp. virginiana; Mb, megabase; SDR, sex-determining region.
Fig 4.
W-specific SDR haplotype composition across octoploid Fragaria.
Top: there are seven predicted genes in the longest haplotype (S3 Table), including two shared by all females (GMEW and RPP0W, Fig 2). Middle: all three clades (α, β, and γ) share the SDR cassette, suggesting that it is the oldest and that Fvb6 position 1 Mb is the original SDR position. Clades β and γ also share the flanking sections, suggesting a translocation to Fvb6 position 13 Mb. Only clade γ possesses the outer section, consistent with a second translocation to Fvb6 position 37 Mb unique to this clade. At either ends of the flanking sequences, terminal inverted repeats (blue nucleotides) are adjacent to target-site duplications (TA dinucleotide), a pattern consistent with transposon-mediated movement of this section. Bottom: inferred size and composition of the hemizygous W-specific insertion in each of the three clades, α, β, and γ. Z chromosome composition is inferred from the Fvb reference genome and Z-specific sequence obtained from BACs of a maternal F. virginiana ssp. virginiana linkage cross parent in clade α (S4 Fig). BAC, bacterial artificial chromosome; Fvb, diploid reference genome assembly informed by F. vesca ssp. bracteata; Mb, megabase; SDR, sex-determining region.
Fig 5.
Model of sex-chromosome evolution in Fragaria.
The eight homoeologs of Fvb6 on four subgenomes (Av, B1, B2, and Bi) are shown in a temporal sequence, starting with a presumed hermaphrodite octoploid ancestor (left). Dotted arrows indicate evolutionary descent of chromosomes. Solid arrows indicate inferred translocation or retrotransposition events. Following the move-lock-grow model, hemizygosity increases with each jump, from the retrotransposed RPP0W (red), to the SDR cassette including sequence homologous to the first SDR location (orange), to the SDR cassette plus flanking sequence (purple) representing the largest hemizygous region that is observed in the final SDR location. SDR, sex-determining region.