De novo assembling a high-quality genome sequence of Amur grape (Vitis amurensis Rupr.) gives insight into Vitis divergence and sex determination

To date, there is no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding research efforts to improve grape cultivars. This study presents a ∼522 Mb of the Vitis amurensis ( Va ) genome sequence containing 27,635 coding genes. Phylogenetic analysis indicated that V. riparia (Vr) may firstly split from the other two species, Va , V. Vinifera ( Vv ; Pinot Noir: PN40024 and Cabernet Sauvignon). Much divergent gene reservation among three grape duplicated gene sets suggests that the core eudicot common hexaploidy (ECH), 130 million years ago (Mya), has still played a non-negligible role in grape species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va , resulting in a more robust cold resistance gene regulatory network than those in Vv and Vr . In contrast, Va preserved much fewer NBS disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related with sex determination in Va . The content and arrangement order of genes in the putative SDR of female Va were similar to the SDR of female Vv . However, the putative SDR of female Va lost one Flavin-containing monooxygenases (FMO) and contained one extra uncharacterized protein-coding gene. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.