Haplotype-resolved genome assembly and implementation of VitExpress, an open interactive transcriptomic platform for
Anis Djari1, Guillaume Madignier1,2, Olivia Di Valentin1
1Laboratoire de Recherche en Sciences Végétales-Génomique et Biotechnologie des Fruits-UMR5546, Université de Toulouse, CNRS, Université Paul Sabatier, Institut Polytechnique de Toulouse, Auzeville Tolosan 31326, France.
Summary
High-fidelity genome sequencing of grapevines (Vitis vinifera) produced haplotype-resolved assemblies. These assemblies reveal structural variations and improve genome annotation, establishing a new reference genome for grapevine research.
Area of Science:
- Genomics
- Plant Science
- Bioinformatics
Background:
- Grapevine (Vitis vinifera) genome research has been limited by heterozygous cultivar complexity.
- Accurate genome assemblies are crucial for understanding genetic variation and evolutionary history.
Purpose of the Study:
- To generate haplotype-resolved genome assemblies for two Vitis vinifera cultivars (Chasselas and Ugni Blanc).
- To reveal structural variations within cultivars and improve genome annotation.
- To develop novel bioinformatics tools for grapevine research.
Main Methods:
- Combining high-fidelity long-read sequencing with chromosome conformation capture (Hi-C) for telomere-to-telomere genome assembly.
- Utilizing Iso-Seq (full-length transcript isoform sequencing) for enhanced genome annotation.
- Developing the VitExpress platform with genome browsing and expression profiling tools.
Main Results:
- Successfully assembled separate haplo-genomes for Chasselas and Ugni Blanc, revealing structural variations like deletions, inversions, and translocations.
- The Chasselas assembly achieved high contiguity and robust annotation, meeting standards for a reference genome.
- Identified candidate genes involved in anthocyanin metabolism using expression profiling and correlation analysis.
Conclusions:
- The developed haplotype-resolved assemblies and annotation provide a robust reference for Vitis vinifera.
- New bioinformatics tools (VitExpress, StatTools) facilitate advanced analysis of grapevine transcriptomic data.
- These resources will accelerate research in grapevine genetics, evolution, and breeding.
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