Anis Djari, Guillaume Madignier, Olivia Di Valentin, Thibault Gillet, Pierre Frasse, Amel Djouhri, Guojian Hu, Sebastien Julliard,              Ming Chun Liu, Yang Zhang, Farid Regad, Julien Pirrello, Elie Maza, and Mondher Bouzayen

PNAS; May 28, 2024; 121 (23) e2403750121

Significance

In contrast to most crops, Vitis vinifera benefited little from classical breeding due to their heterozygosis. Strikingly, the main cultivated grape varieties that we see today have remained the same as they were centuries ago; they have been poorly enriched with traits to adapt to changing environment. However, climate change and concerns about environment call for major changes in viticulture that require transitioning to knowledge-based concepts and advanced genomics tools. We report here the generation of haplotype-resolved genome assemblies for two grapevine cultivars and the setup of VitExpress, an open interactive transcriptomic platform, providing genome browser and integrated web tools for expression profiling and gene correlation studies. These community resources and tools are anticipated to foster advances in several areas of grapevine research.

Abstract

Haplotype-resolved genome assemblies were produced for Chasselas and Ugni Blanc, two heterozygous Vitis vinifera cultivars by combining high-fidelity long-read sequencing and high‐throughput chromosome conformation capture (Hi-C). The telomere-to-telomere full coverage of the chromosomes allowed us to assemble separately the two haplo-genomes of both cultivars and revealed structural variations between the two haplotypes of a given cultivar. The deletions/insertions, inversions, translocations, and duplications provide insight into the evolutionary history and parental relationship among grape varieties. Integration of de novo single long-read sequencing of full-length transcript isoforms (Iso-Seq) yielded a highly improved genome annotation. Given its higher contiguity, and the robustness of the IsoSeq-based annotation, the Chasselas assembly meets the standard to become the annotated reference genome for V. vinifera. Building on these resources, we developed VitExpress, an open interactive transcriptomic platform, that provides a genome browser and integrated web tools for expression profiling, and a set of statistical tools (StatTools) for the identification of highly correlated genes. Implementation of the correlation finder tool for MybA1, a major regulator of the anthocyanin pathway, identified candidate genes associated with anthocyanin metabolism, whose expression patterns were experimentally validated as discriminating between black and white grapes. These resources and innovative tools for mining genome-related data are anticipated to foster advances in several areas of grapevine research.

See https://www.pnas.org/doi/10.1073/pnas.2403750121

Fig. 3: MybA1-correlated genes. (A) Expression pattern of MybA1 (Vv02g11300) and UFGT (Vv16g02100) as determined by VitExpress using 213 berry samples corresponding to 150 black and 63 white grape berries. (B) Heatmap clustering using Pearson correlation of MybA1 and UFGT expression showing their expression in black and white grape varieties. (C) Correlation circles displaying the 10 genes whose expression pattern is the most highly correlated with MybA1 (blue color). The shorter the distance with regard to MybA1, the higher is the correlation. (D) Heatmap clustering using Pearson correlation between the expression of MybA1 and the 7 most highly correlated genes (correlation coefficient ≥ 0.75). The average expression level of a given gene in white and black varieties is indicated by the black numbers. (E) Putative Myb-binding sites in the promoter region of genes displaying highly correlated expression to MybA1 as revealed by in silico search using VitExpress. (F) Relative expression assessed by qRT-PCR of MybA1 and the 7 most highly correlated genes in Gamay red callus producing anthocyanin and in white calli, Muscat and Syrah both deficient in anthocyanin pigment biosynthesis. Expression in the white calli is calculated relatively to that of red Gamay callus. P value: **P < 0.01 and ***P < 0.001. The MybA1-correlated genes are the following: Vv02g11300 MybA1; Vv01g15680 Anthocyanin-O-methyltransferase; Vv16g11110 anthoMATE; Vv08g12510 Solute carrier family 35 member F2; Vv06g12460 Flavonoid 3′,5′-hydroxylase2-like; Vv16g02100 UDP-glucose: flavonoid 3-O-glucosyltransferase; Vv04g09160 Glutathione S-transferase; Vv01g15670 Flavonoid 3′,5′-methyltransferase-like; Vv02g04950 Leucoanthocyanidin dioxygenase; Vv03g08520 Serine carboxypeptidase-like 13 and Vv06g03290 Phenylalanine ammonia-lyase.