Annotations of the 12X.2 genome assembly

12X.2 Assembly and its structural annotation (VCost.v3): https://doi.org/10.15454/1.5009072354498936E12

This data set supports the paper:

Canaguier A, Grimplet J, Scalabrin S, Di Gaspero G, Mohellibi N, Choisne N, Rombauts S, Ruztenholtz C, Morgante M, Quesneville H, Adam-Blondon A-F (2017) A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genomic Data, 2017, https://doi.org/10.1016/j.gdata.2017.09.002

You can download here the dataset that comprises the 12X.v2 grapevine reference genome assembly and its VCost.v3 gene annotation in Genbank format. The VCost.v3 gene annotation is also available in gff3 format.

The correspondance between the former V1 and the VCost.v3 annotations is available here:

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Note that 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).

You can also find below the CDS sequences and the proteins sequences generated from this gff3:

• cds sequences
• proteins sequences

Other structural annotations:

The following gff3 files contain annotations performed on the 12X.0 genome assembly that have been transposed on the 12X.2 assembly with an algorithm that uses the shift observed for each scaffold between both assemblies (for more details about this program  see ). The features located between 2 scaffolds have been transposed only when these scaffolds have the same order and orientation in both assemblies.

• CRIBI structural annotation (V1)
• CRIBI structural annotation (V2.1)  
• Genoscope structural annotation
• NCBI functionnal annotation
• CRIBI functionnal annotation (V1)  Note that the annotations located on chromosome chr00 are not available for the moment.
• STS CHS gene family annotations
• TPS (terpene synthase) gene family annotations (last version corrected on October 2016) 

• Transposable Elements annotation of 12X.v2 grapevine reference genome assembly with the REPET package  https://urgi.versailles.inra.fr/Tools/REPET ): 
  • a fasta file of 2473 consensus library obtained with TEdenovo pipeline and manually curated.
  • a gff3 file corresponding to the genome copies annotation of this library by using TEannot pipeline.

• Evidences of Caulimoviridae called 'Florendovirus' have been described in several plant genomes including grapevine ( Florian Maumus et al .):  download the gff3 file

The data set is provided in support of the data paper:

Canaguier A, Grimplet J, Di Gaspero G, Scalabrin S, Duchêne E, Choisne N, Mohellibi N, Guichard C, Rombauts S, Le Clainche I, Bérard A, Chauveau A, Bounon R, Ruztenholtz C, Morgante M, Le Paslier M-C, Brunel D, Adam-Blondon A-F . A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3). Genomic Data, https://doi.org/10.1016/j.gdata.2017.09.002

Annotation of the florendovirus sequences on the 12X.0 genome assembly

The florendovirus sequences have been detected in the 12X.0 genome assembly: 

V1 annotation of the 12X.0 genome assembly (CRIBI)   

  V1 annotation files is divided in V1_NR (no repetitive genes) and V1_RO (repetitive genes, like genes family)

• chrAll.jigsawgaze_NR.gff.gz (6.78 MB)
• chrAll.jigsawgaze_RO.gff.gz (452.93 kB)

• V1_JigsawGazeNR_mRNA.fa.gz (11.48 MB)
• V1_JigsawGazeRO_mRNA.fa.gz (1.16 MB)

• V1_JigsawGazeNR.prot.fa.gz (5.92 MB)
• V1_JigsawGazeRO.prot.fa.gz (469.29 kB)

 V1 structural and functional annotation at CRIBI (Universita degli Studi di Padova)

V0 annotation of the 12X.0 genome assembly (Genoscope)

  V0 annotation summary

• Annotated genes : 26,346
• Annotated transcripts : 26,346
• Average number of coding exons per gene : 5.95
• Median gene size (bp) : 3,572
• Average CDS size (bp) : 1,137
• Median exon size (bp) : 122

  V0 annotation files

• Vitis_vinifera_annotation.gff.gz (3.21 MB)
• Vitis_vinifera_mRNA.fa.gz (8.39 MB)
• Vitis_vinifera_peptide.fa.gz (5.35 MB)

• repeats files :
   
  •   RepeatMasker.gff3.bz2 (11.60 MB)
  •   TRF.gff3.bz2 (2.26 MB)