The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

TLDR

Early plant genome analyses revealed unexpected ancient duplications that shaped evolution, and the grapevine—chosen for its cultural significance—provides a non‑recently duplicated reference for studying ancestral genomic organization. We assembled a high‑quality draft of the highly homozygous Vitis vinifera genome, the first fruit‑crop and second woody plant genome sequenced to date. The grapevine genome shows extensive aromatic gene family expansions, derives its haploid content from three ancestral genomes—a pattern shared by dicots but not rice—and clarifies the timing of past whole‑genome duplications in flowering plants.

Abstract

The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on the basis of their genetics. These polyploidization events may have had important consequences in plant evolution, in particular for species radiation and adaptation and for the modulation of functional capacities. Here we report a high-quality draft of the genome sequence of grapevine (Vitis vinifera) obtained from a highly homozygous genotype. The draft sequence of the grapevine genome is the fourth one produced so far for flowering plants, the second for a woody species and the first for a fruit crop (cultivated for both fruit and beverage). Grapevine was selected because of its important place in the cultural heritage of humanity beginning during the Neolithic period. Several large expansions of gene families with roles in aromatic features are observed. The grapevine genome has not undergone recent genome duplication, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This analysis reveals the contribution of three ancestral genomes to the grapevine haploid content. This ancestral arrangement is common to many dicotyledonous plants but is absent from the genome of rice, which is a monocotyledon. Furthermore, we explain the chronology of previously described whole-genome duplication events in the evolution of flowering plants.