Structural variants, clonal propagation, and genome evolution in grapevine (Vitis vinifera)

Structural variants (SVs) affect plant phenotypes, but they are a largely unexplored feature of plant genomes. Little is known about the type and size of SVs, their distribution among individuals or their evolutionary dynamics. Here we identify SVs and study their evolutionary dynamics in clonally propagated grapevine cultivars and their outcrossing wild relatives. To catalog SVs, we assembled the highly heterozygous Chardonnay genome, for which one in seven genes is hemizygous. Using genomic inference as the standard, we extended SV detection to population samples. We found that negative selection acts against SVs, but particularly against inversion and translocation events. SVs nonetheless accrue as recessive heterozygotes in clonal lineages. They also define outlier regions of genomic divergence between wild and cultivated grapevines, suggesting roles in domestication. Outlier regions include the sex determination region and the berry color locus, where independent large, complex inversions drive convergent phenotypic evolution.