Genome accessions

Assembly: The PN40024.v4 assembly is based on the Sanger scaffolds of the 12X.2 version that were corrected, extended and completed using 30X PacBio data. The heterozygous regions are better identified (Manuscript in preparation).
 
 
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NEW ANNOTATIONS
 
4.3 Annotation version that includes manually curated genes from the Annot´training School, held in Zaragoza June 2022.
PN40024.v4.3 annotations (gff) => original_PN40024_pseudomolecules.v4.3.BETA.gff3
 
 
4.2 Annotation version that includes manually curated genes from the DAP&CAT Working group meeting, held in Valencia July 2021.
PN40024.v4.2 annotations (gff) => PN40024.v4.2.REF.gff3
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The following download gives access to (click here)

  

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

 
Annotation: The PN40024.v4 annotation is based on a mixed approach, derived from de novo annotation and reciprocal matching with the previous structural annotation version. In an effort to preserve VCOST.v3 gene IDs where possible (e.g. in cases where chromosome numbers are unchanged) a reciprocal best-hits strategy between VCOST.v3 and PN40024.v4.1 annotations was carried out. This allowed the transfer of 67.27% of VCOST.v3 gene IDs. In general, the new de novo annotation performed better than the previous annotation in terms of BUSCO stats. INTEGRAPE will soon offer a Training School for gene model manual curation using several tools such as WebApollo, JBrowser and the Gene Tree tool made available by the Gramene Database (Dr. Doreen Ware).
 

NEW => Blast sequence server: http://138.102.159.70:4567/

NEW => Apollo for manual curation: http://138.102.159.70:8080/apollo/annotator/index (request an account by email to Amandine Velt and/or Camille Rustenholz)

NEW => Jbrowse (under construction): http://138.102.159.70/jbrowse/

 
Provider
Camille Rustenholz / Amandine Velt (Assembly-Annotation)

Bianca Frommer (Annotation)

Primary contact | camille.rustenholz (at) inrae.fr | amandine.velt (at) inrae.fr

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

Provider
Jerome Grimplet
Primary contact | jgrimplet (at) cita-aragon.es

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.

Provider
Dario Cantu
Primary contact | dacantu (at) ucdavis.edu 

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.

Website: http://vitis.gramene.org

Provider:

Doreen Ware

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

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