12X.2 version of the grapevine reference genome sequence from The French-Italian Public Consortium (PN40024)

The sequence of the contigs and scaffolds are unchanged compared to the 12X.0 version. The chromosome assembly has been improved and is published in a data paper:

12X.2 Assembly and its structural annotation (VCost.v3): 

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

With two associated datasets:

https://doi.org/10.15454/1.4962347083032307E12

https://doi.org/10.15454/1.5009072354498936E12

 

• VV_12X_embl_102_WGS_contigs : CAAP03000001-CAAP03014665 [14665 entries] at EMBL (release 102)

• VV_12X_embl_102_Scaffolds : FN594950-FN597014 [2065 entries] at EMBL (release 102)

The agp file describing this assembly can be found in the following archive .

An archive containing the fasta file of the 12X.2 Vitis vinifera genome assembly is available for download : here

 

12X.0 "golden path" files for chromosome assembly (2009_12_04)

• Scaffolds anchored on the 19 chromosomes : chr.agp (18.03 kB)

• The chromosome Unknown (scaffolds not anchored) : chrUn.agp (179.38 kB)

• Description of the chr.agp file: here

• Length of the chromosomes : chr.lg (549 B)

• Scaffolds list (2059 scaffolds > 2 kb) : scaffolds.lg (38.53 kB)

 

12X.0 version of the grapevine reference genome sequence from The French-Italian Public Consortium (PN40024)

• VV_12X_embl_102_WGS_contigs : CAAP03000001-CAAP03014665 [14665 entries] at EMBL (release 102)

• VV_12X_embl_102_Scaffolds : FN594950-FN597014 [2065 entries] at EMBL (release 102)

• VV_chr12x (chromosomes) : FN597015-FN597047 [33 entries] at EMBL (release 102)

 

8X version of the of the grapevine reference genome sequence from The French-Italian Public Consortium (PN40024)

• VV_8X_embl_98_WGS_contigs : CAAP02000001-CAAP02019577 [19577 entries] SUPPRESSED at EMBL

• VV_8X_embl_98_Scaffolds : CU459218-CU462731 [3514 entries] SUPPRESSED at EMBL

• VV_chr8x (chromosomes) : CU462738-CU462756 [19 entries] SUPPRESSED at EMBL

 

Vitis vinifera WGS Pinot Noir clone ENTAV 115

• VV_clone_entav_115 (contigs)

 

Assembly summary

12X.2 assembly

• Contigs : 14,642
• Scaffolds : 2,059 (> 2kb)
• Mapped scaffolds : 366 (coverage of the genome : 95%)

12X.0 assembly

• Contigs : 14,642
• Scaffolds : 2,059 (> 2kb)
• Mapped scaffolds : 211 (coverage of the genome : 91.2%)

8X assembly

• Contigs : 19,577
• Scaffolds : 3,514
• Mapped ultracontigs : 191 (coverage of the genome : 68.9%)