Genus-wide core-genome for Vitis
As the explosion of the genomic data in the past decade, it has been noted that a single genome is insufficient to capture genetic variance of one species. Multiple genomes provide a comprehensive understanding of complex structural variations, lineage specific genes and large effect variations within one species . In this study, we constructed a pan-genome for the whole Vitis genus, which diverged approxinately 20 million years ago. Different from the pan-genome that constructed for one specie or close related specie, we expect the core genome for the Vitis genus is smaller than that in one species due to the elevated genetic distance between the samples we collected. For example, In soybean, 80% genes are present in all seven accessions \cite{Li2014}. In rice , 61% of genes are present in 90% of total 62 collections\cite{Zhao2018}. In maize, it has been reported that only 50% percent of genome are in syntenic blockes between B73 and Mo17 \cite{Sun2018}. In the most distant related speices in Vitis genus we examine (between V. rupestris and V.vinifera), about 29% of the genome are collinear with the reference genome PN40024. However, we found that the core genome in the Vitis genus is enriched in gene region and is overlapped with about 70% of genes in the PN40024 genome.