This work is a joint project between EnsemblGenomes at the European Bioinformatics Institute and the group of Doreen Ware at the Cold Spring Harbor Laboratory, who have developed the Gramene database, a resource for plant comparative genomics based on Ensembl technology. A common set of databases are available through EnsemblGenomes and Gramene, and the two groups are collaborating on the integration of content, quality control and the development of new features.

Featured content

• This release of Gramene includes an extensive set of variations for Hordeum vulgare (barley) [1]. Barley serves as a model for adaptation, coping with a range of biotic and abiotic stresses. Here we show variations between the reference sequence and cultivars Barke, Bowman, Igri, Haruna Nijo and a single accession of wild barley (H. spontaneum). Read more...
• A new sequence search service specific to the Triticum aestivum (bread wheat) species has been created. In the absence of a reference genome for wheat, this search service aligns a DNA input sequence against wheat ESTs, publically available in ENA, and has been adapted to link the alignments to the brachypodium genomic locations where the wheat sequences map. The mapping between the wheat EST sequences and the Brachypodium genome relies on pre-computed alignments performed using Exonerate. These alignments can be visualized independently on Brachypodium location view. Click here for example.
• A new variation resource for Brachypodium sylvaticum mapped on Brachypodium distachyon genome provides means for studying genetic diversity of this invasice species, which is often used as model plant for bioenergy feedstock.
• Updated Oryza specific gene trees including 14 Oryza species and a outergroup, Click here for example

References

1. The International Barley Genome Sequencing Consortium (IBSC). A physical, genetical and functional sequence assembly of the barley genome. Nature. 2012.
2. Brenchley R, et. al.. Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature. 2012.

Organelle Annotation

For annotations relating to Organelles, see the organelles page