Vitis vinifera Assembly and Gene Annotation

About Vitis vinifera

Vitis vinifera, the common grape vine, is a species of flowering plant, native to the Mediterranean region, Central Europe, and southwestern Asia, from Morocco and Portugal north to southern Germany and east to northern Iran. As of 2012, there were between 5,000 and 10,000 varieties of Vitis vinifera grapes though only a few are of commercial significance for wine and table grape production.

Picture credit: Creative Commons Attribution-Share Alike 3.0 via Wikimedia Commons (Image source) Taxonomy ID 29760

More information General information about this species can be found in Wikipedia

References

• Shi, X., Cao, S., Wang, X., Huang, S., Wang, Y., Liu, Z., Liu, W., Leng, X., Peng, Y., Wang, N., et al. (2023) The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding. Horticulture Research, Volume 10, Issue 5, uhad061.(https://doi.org/10.1093/hr/uhad061).

Assembly

The assembly presented here has been imported from INSDC and is linked to the assembly accession [GCA_030704535.1].

The total length of the assembly is 494873210 bp contained within 19 scaffolds. The scaffold N50 value is 26899771, the scaffold L50 value is 9. The GC% content of the assembly is 35.0%.

Annotation

The annotation presented is derived from annotation submitted to INSDC with the assembly accession GCA_030704535.1.

The annotation presented is derived from genes imported from the community GFF3 with the assembly accession GCA_030704535.1.

Small RNA features, protein features, BLAST hits and cross-references have been computed by Ensembl-plants.

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.

Links

• International Grape Genome Program
• Genoscope Grape Genome Browser