Autopolyploidization for the wine 2 subpopulation. (A) Separation of haplotypes. Phasing the genomes of strains from the polyploid wine 2 subpopulation resolves the generally low intra-genomic variation into haplotigs along the genome. The presence of two haplotypes resolves in lower genetic variation as it does when three haplotigs are present at a given position. Maximal genetic variation between haplotypes increases from 0.93% to 1.79% with the presence of a third phased haplotype. To control that the variations in genetic difference are not artifacts coming from a variable coverage along these regions, the genome-wide coverage was calculated. The coverage is consistent across regions that harbor either two or three phased haplotypes. (B) Conserved patterns of phased haplotypes along the genomes of six strains of the wine 2 subpopulation. Having either two or three phased haplotypes at a site is conserved among different strains from the same subpopulation.
