ArticleG3 (Bethesda, Md.)2023
An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.
Article in G3 (Bethesda, Md.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Esca disease triggers local transcriptomic response and DNA methylation changes in grapevine.Journal of experimental botany · 2026Article
- A dual genome-methylome map of clonal evolution in grapevine.Genome biology · 2026Article
- High-Contiguity Haplotype-Resolved Genome Assembly of the Hexaploid Actinidia valvata Rootstock Sheds Light on Waterlogging Resistance Gene.Plant biotechnology journal · 2026Article
- Transcriptional footprints associated with bud fertility in grapevine development (Vitis vinifera L.).Planta · 2026Article
- Haplotype-resolved T2T gap-free genomes of the winegrape cultivar Cabernet Sauvignon.Scientific data · 2026Article
- Population structure of wild and cultivated grapevines in Armenia.BMC plant biology · 2026Article
- Transcriptional Insights Suggest Altered Ripening Progression and Sugar Regulation in Japanese Indigenous Wine GrapeInternational journal of molecular sciences · 2026Article
- Insect herbivory time-course reveals unique temporal transcriptomic responses in resistant and susceptible grapevines.Frontiers in plant science · 2026Article
- A conserved structural framework accompanies evolutionary divergence and expression specialization in the grapevine SKP1 family.Frontiers in plant science · 2026Article
- Article
- Evolutionary analysis of ascorbate-glutathione cycle genes across green plants with lineage-specific profiling in grapevine (Horticulture research · 2026Article
- Temporal dynamics of photosynthetic inhibition, antioxidant defense, and transcriptomic reprogramming in 'Crimson Seedless' grapevine under saline-alkali stress.Frontiers in plant science · 2026Article
- The grape berry methylome reveals tissue-specific features associated with metabolism in ripening.Horticulture research · 2025Article
- QTL mapping and candidate gene identification of the full flowering date trait in olive trees (Olea Europaea L.).BMC plant biology · 2025Article
- PME10 Is a Pectin Methylesterase Driving PME Activity and Immunity Against Botrytis cinerea in Grapevine (Vitis vinifera L.).Plant biotechnology journal · 2025Article
- Chromosome-level reference genome ofHorticulture research · 2025Article
- Apple DELLA Is Degraded Under Warm Temperature Conditions inPlant direct · 2025Article
- Responding to Stress: Diversity and Resilience of Grapevine in a Changing Climate Under the Perspective of Omics Research.International journal of molecular sciences · 2025Review
- Advances in grape and pathogen genomics toward durable grapevine disease resistance.Journal of experimental botany · 2025Review
- Graft union formation involves interactions among bud signals, carbon availability, dormancy release, wound responses and non-self-communication in grapevine.The Plant journal : for cell and molecular biology · 2025Article
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Authors and funding
17 authors.
Funding
Abstract
The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from 9 selfings of cv. "Helfensteiner" (cross of cv. "Pinot noir" and "Schiava grossa") instead of a single "Pinot noir". These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing toward the eventual elaboration of the grapevine pangenome.
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