Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine

Abstract

In contrast to most crops, Vitis vinifera has benefited little from classical breeding due to its high heterozygosity. Remarkably, the main cultivated grapevine varieties grown today remain largely unchanged from those cultivated centuries ago and have been only marginally improved to cope with evolving environmental constraints. However, climate change and environmental concerns now demand a transition toward knowledge-based viticulture supported by advanced genomic tools. Here, we report haplotype-resolved genome assemblies for two heterozygous V. vinifera cultivars, Chasselas and Ugni Blanc, generated by combining high-fidelity long-read sequencing with high-throughput chromosome conformation capture (Hi-C). Telomere-to-telomere chromosome assemblies enabled the separate reconstruction of both haplotypes for each cultivar and revealed substantial structural variation between homologous chromosomes. Integration of full-length transcript isoforms obtained by Iso-Seq significantly improved genome annotation. Building on these resources, we developed VitExpress, an open and interactive transcriptomic platform providing a genome browser and integrated web tools for expression analysis. VitExpress incorporates more than 3,500 curated Vitis RNA-Seq datasets, whose metadata are standardized using Plant Ontology (PO) and Plant Experimental Conditions Ontology (PECO). This rigorous semantic framework enables reliable cross-project comparisons and underpins the Dual Selection DEG tool, which identifies differentially expressed genes between conditions, even when derived from independent studies. The “Search by Profile” tool further supports hypothesis generation by identifying genes whose expression patterns match user-defined profiles. In addition, ExpressionManager, a dedicated submission portal, allows the community to securely analyze private datasets against the public reference atlas while preserving data confidentiality until publication. By combining high-quality genomic resources with standardized transcriptomic integration and interactive analytics, VitExpress provides a comprehensive framework to accelerate gene discovery and support next-generation grapevine breeding strategies.

References

Djari A, Madignier G, Di Valentin O, Gillet T, Frasse P, Djouhri A, Hu G, Julliard S, Liu M, Zhang Y, Regad F, Pirrello J, Maza E, Bouzayen M. Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for grapevine. Proc Natl Acad Sci U S A. 2024 Jun 4;121(23):e2403750121. doi: 10.1073/pnas.2403750121. Epub 2024 May 28. PMID: 38805269; PMCID: PMC11161759.

Acknowledgements

This work is part of the VitiFunGen project supported by Fondation Jean Poupelain (Cognac, France). O.D.V. was funded by the “EcoleUniversitaire de Recherche (EUR)” TULIP-GS (ANR-18-EURE-0019).