Population comparative genomic analyses unveil gene gain and loss during grapevine domestication.

Plant domestication shapes gene contents between the cultivars and their wild progenitors. Previously, short-reads and small variants (SNPs, indels and microsatellites) were mostly used to study grapevine (Vitis vinifera) domestication processes. Due to the lack of population-level assemblies for both the crop and its wild progenitors, capturing gene gain and loss caused by large structural variants remains a challenge. Here, we applied comparative genomic analyses to discover gene gain and loss during grapevine domestication using long-read assemblies of representative population samples for both domesticated grapevines (V. vinifera ssp. vinifera) and their wild progenitors (V. vinifera ssp. sylvestris). Only ∼7% of gene families were shared by 16 Vitis genomes while ∼8% of gene families were specific to each accession, suggesting dramatic variations of gene contents in grapevine genomes. Compared to wild progenitors, the domesticated accessions possessed more genes involved in asexual reproduction, while the wild progenitors harbored more genes related to pollination, revealing the transition from sexual reproduction to clonal propagation during domestication processes. Moreover, the domesticated accessions harbored fewer disease-resistance genes than wild progenitors. The structural variants occurred frequently in aroma and disease-resistance related genes between domesticated grapevines and wild progenitors, indicating the rapid diversification of these genes during domestication. Our study provides insights and resources for biological studies and breeding programs in grapevine.