De novoassembling a high-quality genome sequence of Amur grape (Vitis amurensisRupr.) gives insight intoVitisdivergence and sex determination

Abstract

AbstractTo 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 theVitis amurensis(Va) genome sequence containing 27,635 coding genes. Phylogenetic analysis indicated thatV. 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 inVa, resulting in a more robust cold resistance gene regulatory network than those inVvandVr. In contrast,Vapreserved 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 duringVaberry development. A selective sweep analysis revealed a hypotheticalVasex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related with sex determination inVa. The content and arrangement order of genes in the putative SDR of femaleVawere similar to the SDR of femaleVv. However, the putative SDR of femaleValost one Flavin-containing monooxygenases (FMO) and contained one extra uncharacterized protein-coding gene. These findings will improve the understanding ofVitisbiology and contribute to the improvement of grape breeding.