Population comparative genomics reveals gene gain and loss during grapevine domestication. Researchers analyzed 17 grapevine genomes, including domesticated and wild progenitors, to identify changes in gene content during domestication. Only 7% of gene families were shared among 16 Vitis genomes, while 8% were specific to each accession, indicating significant variation in grapevine genomes. Domesticated grapevines showed increased genes related to asexual reproduction, while wild progenitors had more genes related to pollination, suggesting a shift from sexual to clonal propagation. Domesticated accessions had fewer disease resistance genes than wild progenitors. Structural variations (SVs) occurred frequently in aroma and disease resistance genes, indicating rapid diversification during domestication. The study provides insights and resources for grapevine research and breeding. Comparative genomic analyses showed that domesticated grapevines had more genes related to fruit development and carbohydrate metabolism, while wild populations had more genes related to defense and seed development. The study also identified resistance gene analogues and their distribution in grapevine populations. The results highlight the importance of studying gene content changes during domestication and their impact on agronomic traits and resistance. The study used long-read sequencing and assembly to analyze genome diversity and gene content changes, revealing the role of SVs in grapevine domestication. The findings suggest that domestication has significantly impacted grapevine genetics, leading to the development of beneficial traits. The study provides a reference for grapevine genetics, genomics, and breeding.Population comparative genomics reveals gene gain and loss during grapevine domestication. Researchers analyzed 17 grapevine genomes, including domesticated and wild progenitors, to identify changes in gene content during domestication. Only 7% of gene families were shared among 16 Vitis genomes, while 8% were specific to each accession, indicating significant variation in grapevine genomes. Domesticated grapevines showed increased genes related to asexual reproduction, while wild progenitors had more genes related to pollination, suggesting a shift from sexual to clonal propagation. Domesticated accessions had fewer disease resistance genes than wild progenitors. Structural variations (SVs) occurred frequently in aroma and disease resistance genes, indicating rapid diversification during domestication. The study provides insights and resources for grapevine research and breeding. Comparative genomic analyses showed that domesticated grapevines had more genes related to fruit development and carbohydrate metabolism, while wild populations had more genes related to defense and seed development. The study also identified resistance gene analogues and their distribution in grapevine populations. The results highlight the importance of studying gene content changes during domestication and their impact on agronomic traits and resistance. The study used long-read sequencing and assembly to analyze genome diversity and gene content changes, revealing the role of SVs in grapevine domestication. The findings suggest that domestication has significantly impacted grapevine genetics, leading to the development of beneficial traits. The study provides a reference for grapevine genetics, genomics, and breeding.