Construction of genus-wide core genome  

To construct the Vitis core-genome, nine genomes were aligned to the 12X.v2 version of the PN40024 reference genome\cite{Canaguier2017}. Due to the fact the 41.4% of the grape genome is composed of transposable elements, we masked the repetitive genome regions before the alignment. The pairwise syntenic alignments were further filtered to ensure one-to-one match between the assembly and PN40024, as shown in Figure 1c. On average, the total length for the one-to-one match ranged from 160  to 226 Mbp, depending on their genetic distance to V. vinifera. The collinearity between the assembly and the reference at genome level was high, further indicating that the overall quality of the assembly was good. The assembly had even coverage in arm and pericentromeric regions, but the scaffolds were smaller and less continuous in the pericentromeric regions than in the arms, which indicates the pericentromeric regions are still challenging to assemble when using the 10X de novo genome technology. As expected, the wild species represented larger genetic divergence to the reference than domesticated cultivars. For example, on chromosome 2, on average 66% of the chromosome was collinear with wild species versus 88% with cultivars. (Figure 1d, Supplementary Table 1). We defined the coverage as how many times a chromosome region occurred in a collinear alignment between the genome assemblies and the reference PN40024. About 10% of the reference genome was covered by all genome assemblies, and these regions contained 64% of annotated genes in the reference. These genes that were present in all ten genomes were defined as core genes.   The core genome is significantly correlated with many genome features (Figure 2). The core genome was positively correlated with gene density (\(\rho\) = -0.75, P <1E-13 in Spearmans correlation test )and negatively correlated with density of transposable elements (TEs), in particular the most abundant TE family, Gypsy (Supplementary figure 1) (\(\rho\) = 0.76, P <1E-13 in Spearmans correlation test).