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Fig. 1 | Genome Biology

Fig. 1

From: The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Fig. 1

Limit, gene content and synonymous divergence in the sex locus of V. sylvestris and V. vinifera. (a) Detection of sex-linked SNPs on chromosome 2. Left y axis: adjusted SNP number in 10 kb windows, black curve: XY single nucleotide polymorphisms detected by SEX-DETector++ in a cross of V. sylvestris. Purple curve: candidate XY SNPs that show heterozygosity in males and homozygosity in females in a validation dataset of public whole-genome re-sequencing is drawn in purple; right y-axis (blue curve): adjusted mean posterior probability of being XY for SNPs in 10 kb windows. (b) Genotype of nine V. sylvestris individuals (top) and thirteen grapevine cultivars (bottom) in a validation dataset of public whole-genome re-sequencing, at locations of candidates XY SNPs. Red, purple, blue, and white marks represent XX, XY, YY, and missing genotypes, respectively. In the cultivar panel, 11 cultivars are heterozygous (XY) for the sex-linked SNPs, with a Yh haplotype closely derived from Y (see text), while two cultivars (Chardonnay and Riesling) are homozygous YhYh. YhYh genotypes were previously found only in hermaphrodite cultivars [6]. The black lines highlight the limits of shared XY SNPs between the cross re-sequenced in the present study and the validation dataset. (c) Gene content and annotation and in the sex locus (approximate position). Genes highlighted in red are absent (Δ) or possess a frameshift deletion in the X haplotype (*). Genes highlighted in blue are induced in males. The yellow gene is absent in the Y haplotype. (d) Synonymous divergence between X and Y allele in the sex locus (+/− standard error), reflecting the age of recombination suppression. dS was only computed for genes present in both haplotypes

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