Genome Reconstruction and Functional Characterization Of Vitis vinifera cv. Tannat, The Red Wine Variety With The Highest Polyphenol Content

Vitis vinifera cv. Tannat originated from southwestern France largely cultivated in Uruguay to produce high quality red wines.

Tannat has a very high polyphenol content which provides an intense purple color and a remarkable antioxidant property. To characterize the genetic components of Tannat that may be responsible for these unique phenotypic characteristics, we sequenced the Uruguayan clone UY11 by Illumina technology. As the grapevine reference genome was generated by the sequencing of a predominantly homozygous clone (PN40024), relying on it for genome comparison may underestimate the genetic differences with Tannat. Therefore, the Tannat genome (134X coverage) was reconstructed with the IMR/DENOM pipeline, which is based on de novo assembly and iterative mapping on the reference genome.

The gene annotation was carried out by reference-guided transcriptome assembly and de novo assembly of RNA-Seq data. This led to the finding of 4,728 novel genes in the reconstructed genome. Moreover, we estimated 1,125 novel genes not present neither in the Tannat and Pinot Noir genome assemblies, but matching unassembled raw reads of Tannat and Pinot Noir. We also detected 2,615 genes matched by unassembled Tannat reads but not by Pinot reads, that we therefore considered private of the Tannat genome. Ten percent of these private genes are related to the phenylalanine and phenylpropanoid biosynthesis.

These findings reveal that Tannat has many private genes related to its unique characteristic, and strongly support the hypothesis that the phenotypic diversity found among grape varieties is due to a set of private genes in each variety.