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Updated: Oct 25, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
Chromosome-level phylogenomics and genome evolution of the grape family
Xiangfeng Wang1,2,3, Jie Sun1, Jingxuan Wang1
1Shandong Key Laboratory of Precision Molecular Crop Design and Breeding, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, China.
Abstract:
Grapevines (Vitis) are pivotal fruit crops for human nutrition and civilization. The evolutionary history of grapevines in the grape family (Vitaceae) remains mysterious, requiring family-wide and whole-genome phylogenomic insights. Here we conduct evolutionary genomic analyses of Vitaceae by generating chromosome-level genome assemblies, placing Ampelopsis closer to Parthenocissus and Vitis. Karyotype evolution analysis delineates major chromosome rearrangements, highlighting overall conservation within Vitis but extensive reorganization for Tetrastigma and Cissus. Pan-3D genome analysis reveals that structural variants contribute to A/B compartment and topologically associated domain variation, exhibiting structural variant clearance at topologically associated domain boundaries. We show that Helitron transposons drive expansion and regulate expression of nucleotide-binding leucine-rich repeat disease resistance genes in Vitis, and discover a nucleotide-binding leucine-rich repeat gene VbRpv35 from wild grape Vitis bellula, whose heterologous expression enhances downy mildew resistance in Vitis vinifera. Together, we provide phylogenomic insight into grapevine genome evolution and valuable resources for improving grapevines and understanding angiosperm evolution.
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