Pseudomolecules of the 19 chromosomes + chrUn => PN40024.v4.REF.fasta
Allelic version of the heterozygous regions => PN40024.v4.ALT.heterozyguous_regions.fasta
PN40024.v4.1 annotations (gff and fasta) => REF_annotations/
PN40024.v4.1 annotations (gff and fasta) of the allelic version of the heterozygous regions => ALT_annotations/
Functional annotations generated with Blast2GO => Blast2GO_results_PN40024_september_2021/
Stats and infos => Blast2GO_results_PN40024_september_2021/PN40024.v4.1.REF.b2g.pdf
Functional annotation file (full info) => Blast2GO_results_PN40024_september_2021/PN40024.v4.1.REF.b2g.tsv
Functional annotation file (condensed info) => Blast2GO_results_PN40024_september_2021/PN40024.v4.1.REF.b2g.annot
NEW => Blast sequence server: http://220.127.116.11:4567/
NEW => Apollo for manual curation: http://18.104.22.168:8080/apollo/annotator/index (request an account by email to Amandine Velt and/or Camille Rustenholz)
NEW => Jbrowse (under construction): http://22.214.171.124/jbrowse/
Bianca Frommer (Annotation)
Assembly: The 12X.v2 chromosome assembly is based on the scaffolds of the grapevine reference genome build (FN594950-FN597014, EMBL release 102; Vitis vinifera cv. PN40024). Click here for more info: 12X.2 Genome assembly
Here you can also find: structural annotation (VCost.v3) or the 12X.0-V1 annotation transposed on 12X.2. More details on Annotation: 12X.2 V.COST Annotations.
NEW ⇒ Updated Annotation file (includes genes from the INTEGRAPEv2.0 catalogue): VCost.v3_INTEGRAPEv2.gff3
Other wine grape cultivar and Vitis species assemblies/annotations (GrapeGenomics – University of California Davis)
Genomes of different cultivars, subspecies and species of the Vitis genus are hosted at www.grapegenomics.com, and include several chromosome-scale phased assemblies. The repository is actively maintained by the CantuLab at University of California Davis. The PN40024 reference assembly (12X.2) and its different annotations (V1+V2+V.cost) are also hosted here.
The Vitis pangenome browser is a Gramene portal focused on Vitis vinifera genomes. The site hosts genome assemblies, gene annotations and phylogenetic analyses for each of the hosted grapevine genomes and a selection of reference plant model organisms from Gramene.
Primary contact | feedback (at) gramene.org
USDA-ARS and Cold Spring Harbor Laboratory
Database which provided several ways to access to the grape genomic data: as a blast search page, a genome browser and a direct link to download the data. Gene V1 annotations originally performed on the 12X.0 genome assembly have now been transposed on the PN40024 12X.2 Assembly (available in the 12X.2 Assembly at URGI).
Credits & Support
ELIXIR-ITA-PADOVA | Institute