The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

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 [1][2][3] . 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 4-10 . 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 11 . 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.All grapevine varieties are highly heterozygous; preliminary data showed that there was as much as 13% sequence divergence between alleles, which would hinder reliable contig assembly when a wholegenome shotgun strategy was used for sequencing. Our consortium therefore selected the grapevine PN40024 genotype for sequencing. This line, originally derived from Pinot Noir, has been bred close to full homozygosity (estimated at about 93%) by successive selfings, permitting a high-quality whole-genome shotgun assembly.A total of 6.2 million end-reads were produced by our consortium, representing an 8.4-fold coverage of the genome. Within the assembly, performed with Arachne 12 , 316 supercontigs represent putative allelic haplotypes that constitute 11.6 million bases (Mb). These values are in good fit with the 7% residual heterozygosity of PN40024 assessed by using genetic markers. When considering only one of the haplotypes in each heterozygous region, the assembly (Table 1a) consists of 19,577 contigs (N 50 5 65.9 kilobases (kb), where N 50 corresponds to the size of the shorter supercontig or contig in a subset representing half of the assembly size) and 3,514 supercontigs (N 50 5 2.07 Mb) totalling 487 Mb. This value is close to the 475 Mb previously reported for the grapevine genome size 13 .Using a set of 409 molecular markers from the reference grapevine map 14 , 69% of the assembled 487 Mb, arranged into 45 ultracontigs

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

“…Difficulties with SSR markers development have been already reported in plants (Tero et al 2006) as well as animal species (Zhang 2004;McInerney et al 2011) , and linked to the presence of repetitive DNA and/or transposable elements. This might be also the case in our study, since most of the SSR gaps were located in low gene density regions of the grapevine genome (Online Resource 2), which had been found substantially complementary to high density of repetitive/transposable elements (Jaillon et al 2007). …”

“…Following domestication, thousands of cultivars derived from spontaneous or controlled crosses, but also from somatic variation (Torregrosa et al 2011), have been selected and spread by vegetative propagation throughout the world, from temperate to tropical climates (Bouquet 2011). The highly heterozygous diploid genome of grapevine has a polyploid origin (Jaillon et al 2007). Its relatively small size (475 Mbp and 2n=38 chromosomes; Lodhi and Reisch 1995) has facilitated a significant progress in grapevine genomics, being the publication of the genome sequence in 2007 the most important one (Velasco et al 2007;Jaillon et al 2007).…”

“…The highly heterozygous diploid genome of grapevine has a polyploid origin (Jaillon et al 2007). Its relatively small size (475 Mbp and 2n=38 chromosomes; Lodhi and Reisch 1995) has facilitated a significant progress in grapevine genomics, being the publication of the genome sequence in 2007 the most important one (Velasco et al 2007;Jaillon et al 2007). The availability of the grapevine genome sequence combined with the advent of cheaper and high throughput single nucleotide polymorphism (SNP) genotyping strategies (Gupta et al 2008;Davey et al 2011) were expected to shift the tools of genetic studies in grapevine.…”

Polyploidy-associated genome modifications during land plant evolution

“…Picea abies is the first gymnosperm species with a full genome sequence, completed in 2013 [28]. Angiosperms are by far the largest group of land plants, with more than 300 000 living species, of which at least 33 have sequenced genomes (as in Phytozome v9.1), notably Arabidopsis [29], Populus [30], grape [31], Oryza [32], Sorghum [33], banana [34] and many more, with many additional genome sequences in progress. These genome sequences from species across land plant phylogeny provide critical resources to study genome evolution and associated innovations of plant form and function.…”

Evolution of floral diversity: genomics, genes andgamma

“…polyploidy) in the origin and subsequent diversification of flowering plants [31][32][33][34][35][36][37]. For example, an ancient polyploidy event has been inferred for the common ancestor of all angiosperms [38,39], three sequential polyploidy events in the monocots pre-date the radiation of the grasses [40,41] and ancient hexaploidy characterizes most eudicots [42][43][44][45]. Additional WGDs have been identified among many relatively younger branches of the flowering plant evolutionary tree, mostly among the eudicots [46], many of which coincide closely with the Cretaceous/Tertiary (K/T) boundary about 65 Ma [32].…”