See also legacy data in the Gramene's Archive.
New data
Updated data
Species | Assembly | Gene Annotation | Unchanged |
---|---|---|---|
Aegilops tauschii | ASM34733v1 | GCA_000347335.1 | |
Amborella trichopoda | GCA_000471905.1 (AMTR1.0) | 2014-01-AGD | |
Arabidopsis lyrata | Araly1.0 | Araly1.0 | |
Arabidopsis thaliana | TAIR10 | TAIR10 | |
Brachypodium distachyon | Brachy1.0 | Barchy1.2 | |
Brassica oleracea | GCA_000092065.1 | ENA | |
Brassica rapa | IVFCAASv1 | bra_v1.01_SP2010_01 | |
Chlamydomonas reinhardtii | v3.0 | 2007-11-ENA | |
Cyanidioschyzon merolae | 2008-11-ENA | ASM9120v1 | |
Glycine max (soybean) | Glyma1.0 | Glyma1.1 | |
Hordeum vulgare (barley) | 030312v2 | IBSC_1.0 | |
Leersia perrieri | GCA_000325765.3 | OGE | |
Medicago truncatula | MedtrA17_3.5 | 2011-11-EnsemblPlants | |
Musa acuminata (banana) | MA1 | 2012-08-Cirad | |
Oryza barthii | GCA_000182155.1 | OGE Maker (Aug 2013) | |
Oryza brachyantha | GCA_000231095.2 / OGEv1.4b | OGEv1.4 | |
Oryza glaberrima | GCA_000147395.1 / AGI1.1 (May 2011) | 2011-05-AGI (MIPS) | |
Oryza glumaepatula | GCA_000576495.1 | OGE Maker (Aug 2013) | |
Oryza longistaminata | v0117-2013Aug | OGE | |
Oryza meridionalis | GCA_000338895.1 | OGE Maker (Aug 2013) | |
Oryza nivara | GCA_000576065.1 | OGE Maker (Aug 2013) | |
Oryza punctata | GCA_000573905.1 | OGE Maker (Aug 2013) | |
Oryza rufipogon | PRJEB4137 | OGE | |
Oryza sativa japonica | IRGSP-1.0 | MSU 7.0 | |
Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
Ostreococcus lucimarinus | v2.0 GCA_000092065.1 | JGI | |
Physcomitrella patens | ASM242v1 | 2011-03-Phypa1.6 | |
Prunus persica | Prupe1_0 / GCA_000346465.1 | Prupe1_0 / Peach v1.0 | |
Populus trichocarpa | JGI 2.0 | 2010-01-JGI | |
Selaginella moellendorffii | v1.0 | 2011-05-ENA | |
Setaria italica (foxtail millet) | JGIv2.0 | JGIv2.1 | |
Solanum lycopersicum (tomato) | SL2.50 | ITAG2.3 | |
Solanum tuberosum (potato) | 3.0 | SolTub_3.0 | |
Sorghum bicolor | Sorbi1 | 2007-12-JGI | |
Theobroma cacao (cocoa) | GCA_000403535.1 | ENA | |
Triticum aestivum | IWGSP1 | IWGSP1 (MIPS) | |
Triticum urartu | GCA_000347455.1 | GCA_000347455.1 (ENA, Apr 2013) | |
Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
Zea mays (corn) | B73_RefGen_v3 | 5b+ |
Unchanged | Arabidopsis thaliana |
---|---|
Brachypodium sylvaticum | |
Oryza glaberrima | |
Oryza sativa | |
Solanum lycopersicum | |
Sorghum bicolor | |
Triticum aestivum | |
Vitis vinifera | |
Zea mays |
The EnsemblCompara GeneTree database was updated. The new database includes a total of 56,387 GeneTree families were constructed comprising 1,280,368 individual genes (1,432,406 input proteins) from 39 plant genomes (and 5 non-plant outgroups).
The OGE Compara tree was not updated at oge.gramene.org. Last update was done in release 38 (August 2013). Note: The OGE Compara tree was pulled out from the website since they were build on the obsolete MSU6 genome assembly.
For a complete list, see Gramene's FTP site. Summary statistics follow.
Split genes by species
Species | Count |
---|---|
Aegilops tauschii | 740 |
Amborella trichopoda | 994 |
Arabidopsis lyrata subsp. lyrata | 180 |
Arabidopsis thaliana | 37 |
Brachypodium distachyon | 158 |
Brassica oleracea var. oleracea | 911 |
Brassica rapa subsp. pekinensis | 151 |
Chlamydomonas reinhardtii | 141 |
Cyanidioschyzon merolae | 8 |
Glycine max | 390 |
Hordeum vulgare subsp. vulgare | 108 |
Leersia_perrieri | 189 |
Medicago truncatula | 394 |
Musa acuminata | 1624 |
Oryza barthi | 338 |
Oryza brachyantha | 302 |
Oryza glaberrima | 518 |
Oryza glumaepatula | 394 |
Oryza longistaminata | 291 |
Oryza meridionalis | 272 |
Oryza nivara | 310 |
Oryza punctata | 282 |
Oryza rufipogon | 300 |
Oryza sativa Indica Group | 796 |
Oryza sativa Japonica Group | 636 |
Ostreococcus_lucimarinus_CCE9901 | 26 |
Physcomitrella patens subsp. patens | 276 |
Populus trichocarpa | 1651 |
Prunus persica | 448 |
Selaginella moellendorffii | 215 |
Setaria italica | 332 |
Solanum lycopersicum | 1216 |
Solanum tuberosum | 653 |
Sorghum bicolor | 953 |
Theobroma cacao | 113 |
Triticum aestivum | 1234 |
Triticum urartu | 674 |
Vitis vinifera | 725 |
Zea mays | 844 |
No new synteny data was generated for this release. Last update was done in release 39 (October 2013).
Updated whole genome alignments for S. lycopersicum vs A. thaliana, O. sativa Japonica, and V. vinifera.
UniProtKB cross-references were updated across all species.
New Plant Gene and Plant Variation Marts
Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.
No updates in this release. Last update done in release 31 (May 2010). A summary of ontologies data was last provided in release 46.
Gramene's web services page documents many ways to directly connect to and analyze our databases.
Programmatic access to Gramene is now available through the RESTful Ensembl API.
Our partner Ensembl Genomes offer a public, read-only MySQL server with copies of the species-specific and comparative genomic databases that we use. To use this with the mysql command-line client:
$ mysql -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous
Please note that the versioning scheme used at this public database differs from ours; Gramene's release 48_82 is set as version 29_82.
Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:
mysql -hgramenedb.gramene.org -pgramene