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

Little is known about the type and numbers of structural variants (SVs) in plant genomes, the evolutionary processes that shape SV variation, or their effects on phenotypes. Here we assembled the 605Mb genome of the Chardonnay grape (Vitis vinifera ssp. sativa), which we use to catalog SVs within and between genomes and also across 69 cultivars and wild accessions. SVs underlie widespread hemizygosity of protein coding genes within Chardonnay and genic presence-absence variation between cultivars. Negative selection acts against all SV types, but they also accrue as heterozygous, recessive mutations in clonally propagated grapevines. SV hotspots in the sex determination region and the berry color locus illustrate their impact on phenotype and the role of SVs as drivers of convergent phenotypic evolution.