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, 25 (12), 4777-88

The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared With the Reference Genome

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The High Polyphenol Content of Grapevine Cultivar Tannat Berries Is Conferred Primarily by Genes That Are Not Shared With the Reference Genome

Cecilia Da Silva et al. Plant Cell.

Erratum in

  • CORRECTION
    Plant Cell 29 (4), 913. PMID 28341805.

Abstract

The grapevine (Vitis vinifera) cultivar Tannat is cultivated mainly in Uruguay for the production of high-quality red wines. Tannat berries have unusually high levels of polyphenolic compounds, producing wines with an intense purple color and remarkable antioxidant properties. We investigated the genetic basis of these important characteristics by sequencing the genome of the Uruguayan Tannat clone UY11 using Illumina technology, followed by a mixture of de novo assembly and iterative mapping onto the PN40024 reference genome. RNA sequencing data for genome reannotation were processed using a combination of reference-guided annotation and de novo transcript assembly, allowing 5901 previously unannotated or unassembled genes to be defined and resulting in the discovery of 1873 genes that were not shared with PN40024. Expression analysis showed that these cultivar-specific genes contributed substantially (up to 81.24%) to the overall expression of enzymes involved in the synthesis of phenolic and polyphenolic compounds that contribute to the unique characteristics of the Tannat berries. The characterization of the Tannat genome therefore indicated that the grapevine reference genome lacks many genes that appear to be relevant for the varietal phenotype.

Figures

Figure 1.
Figure 1.
Variation in the Tannat Genome. (A) Classification of SNPs, indels, and unbalanced substitutions based on the V. vinifera PN40024 genome and annotation. UTR, untranslated region. (B) Distribution of lengths of deletions and insertion.
Figure 2.
Figure 2.
Schematic Diagram of Metabolic Pathways Involved in Polyphenol Biosynthesis. For each enzyme, the number of known genes (blue box), novel genes (yellow box), and varietal genes in Tannat (red box) is reported. FS, flavone synthase; IFS, 2-hydroxyisoflavanone synthase; LDOX, leucocyanidin oxygenase; ANR, anthocyanidin reductase.
Figure 3.
Figure 3.
Analysis of Gene Expression in Tannat Berries. (A) Hierarchical clustering of RNA-Seq read counts (Log2 FPKM) in three tissues of Tannat berries. (B) Venn diagram showing numbers of commonly and uniquely differentially expressed known genes in pairwise comparisons of whole berry at 1 wpf (WB1), seeds at 7 wpf (SE7), and skin at 7 wpf (SK7). (C) Venn diagram showing numbers of commonly and uniquely differentially expressed novel genes in pairwise comparisons among WB1, SE7, and SK7 samples. (D) Venn diagram showing numbers of commonly and uniquely differentially expressed varietal genes in pairwise comparisons among WB1, SE7, and SK7 samples.
Figure 4.
Figure 4.
Comparison of Gene Expression in Different Tannat Berry Tissues. (A) to (F) Expression profiles of CHS (A), F3H (B), DFR (C), LAR (D), FLS (E), and MybPA1 (F) in whole berries at 1 wpf, skin at 7 wpf, and seeds at 7 wpf. (G) Scatterplot of RNA-Seq expression values in seeds and skin at 7 wpf. Selected genes involved in polyphenol biosynthesis are shown in color as indicated.
Figure 5.
Figure 5.
Family Expansion and Expression Contribution of Genes Related to Polyphenol Biosynthesis. (A) Percentage contribution of known, novel, and varietal genes to the overall expression of gene families encoding enzymes in the phenylpropanoid and flavonoid biosynthesis pathways. (B) Percentage of known, novel, and varietal genes in gene families encoding enzymes in the phenilpropanoid and flavonoid biosynthesis pathways.
Figure 6.
Figure 6.
Categorization of the 1873 Genes Not Shared with PN40024. Number of genes found in common among Tannat, Corvina, and Pinot Noir (ENTAV 115).

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