Vitis vinifera (12X)

Vitis vinifera Assembly and Gene Annotation

About Vitis vinifera

Vitis vinifera (grape) is the most widely cultivated and economically important grape species used for both eating and wine. It has a diploid genome with haploid chromosome number of 19, and an estimated genome size of ~500 Mb.

Assembly

This release is based on a 12x whole genome shotgun sequence assembly and the V1 annotation of the Vitis vinifera genome. These data were prepared by a French-Italian Public Consortium for Grapevine Genome Characterisation under the auspices of the International Grape Genome Program (IGGP). Further details of the sequencing and assembly are available from Genoscope.

Annotation

Protein-coding genes were predicted by combining ab initio models, V. vinifera complementary DNA alignments, and alignments of proteins and genomic DNA from other species. The integration of the data was performed with GAZE.

Repeats were annotated with the Ensembl Genomes repeat feature pipeline. There are: 1,106,465 Low complexity (Dust) features, covering 63 Mb (13.0% of the genome); 282,465 RepeatMasker features (with the nrTEplants library), covering 225 Mb (46.4% of the genome); 130,283 RepeatMasker features (with the REdat library), covering 61 Mb (12.5% of the genome); 357303 Tandem repeats (TRF) features, covering 39 Mb (8.0% of the genome).

Regulation

Oligo probes from the GeneChip Vitis vinifera Genome Array have been aligned using the standard Ensembl mapping procedure.

Variation

Single nucleotide polymorphisms were identified by re-sequencing a collection of grape cultivars and wild Vitis species from the USDA germplasm collection.

References

  1. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C et al. 2007. Nature. 449:463-467.
  2. GAZE: a generic framework for the integration of gene-prediction data by dynamic programming.
    Howe KL, Chothia T, Durbin R. 2002. Genome Res. 9:1418-27.
  3. Rapid genomic characterization of the genus vitis.
    Myles S, Chia JM, Hurwitz B, Simon C, Zhong GY, Buckler E, Ware D.
    1. PLoS ONE. 5:e8219.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

Assembly12X, INSDC Assembly GCA_000003745.2, Nov 2011
Database version104.3
Golden Path Length486,265,422
Genebuild byCRIBI
Genebuild methodImport
Data sourceGenoscope

Gene counts

Coding genes29,971
Non coding genes690
Small non coding genes672
Long non coding genes18
Gene transcripts30,661

Other

Short Variants457,245

About this species