Release Notes 45 (April 2015)
Website
See also legacy data in the Gramene's Archive.
Genomes Release Notes
Updated genomes
- Medicago truncatula latest assembly and gene set.
- Oryza meridionalis latest assembly and gene set.
New data
- Split gene predictions for 39 plant genomes.
- Whole genome alignments between Triticeae genomes using ATAC between:
- The Triticum aestivum (bread wheat) component genomes (A, B and D - Ensembl Plants stats),
- T. urartu against the bread wheat A genome (Ensembl Plants stats),
- Aegilops tauschii against the bread wheat D genome (Ensembl Plants stats),
- T. urartu against A. tauschii (Ensembl Plants stats), and
- Hordeum vulgare (barley) against T. aestivum (Ensembl Plants stats), T. urartu (Ensembl Plants stats), and A. tauschii (Ensembl Plants stats).
- Whole genome alignments using LASTZ between:
- Brassica oleracea and Arabidopsis thaliana (Ensembl Plants stats).
- M. truncatula and Glycine max, Arabidopsis thaliana, Vitis vinifera and Oryza sativa group Japonica (Ensembl Plants stats).
- Enabled the assembly converter tool to allow conversion of tomato 2.50 onto 2.40 coordinates.
- Synteny regions for bread wheat against O. sativa Japonica.
- Two new RNA-Seq studies aligned to barley (read more).
- New RNA-Seq studies (leaf, root and panicle) for OGE genomes, including O. barthii, O. brachyantha, O. glaberrima, O. glumaepatula, O. meridionalis, O. nivara, O. punctata, O. rufipogon, O. sativa Japonica, and Leersia perrieri.
- New genome browser tracks for Zea mays (read more).
- New browser tracks for Sorghum bicolor (read more).
- New links to gene annotations from AraPort and Expression ATLAS (see for example, pad4).
Updated data
- Updated to Ensembl 79 software.
- Updated gene, sequence and variation BioMarts.
- Updated BLAST software from Ensembl.
- Peptide comparative genomics data across all species.
- Projection of manual GO annotation from Arabidopsis thaliana to 1:1 orthologues in all other plant species.
- Projection of manually assigned gene names and descriptions from Arabidopsis thaliana to 1:1 orthologues in all other dicotyledons species.
- Renamed the unordered barley chromosomes.
Genomes Core
| Species | Assembly | Gene Annotation | |
|---|---|---|---|
| Updated | |||
| Medicago truncatula | MedtrA17_3.5 | 2011-11-EnsemblPlants | |
| Oryza meridionalis | GCA_000338895.1 | OGE Maker (Aug 2013) | 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 | |
| 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 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) | SL2.40 | 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+ | |
| Oryza granulata (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
| Oryza minuta (BB) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
| Oryza minuta (CC) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
| Oryza officinallis (CC) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
| Oryza rufipogon (AA) FPC | OMAP_FPC_2006_JAN |
Ensembl Variation
| New | Hordeum vulgare |
|---|
| Unchanged | Arabidopsis thaliana |
|---|---|
| Brachypodium sylvaticum | |
| Oryza glaberrima | |
| Oryza sativa | |
| Solanum lycopersicum | |
| Sorghum bicolor | |
| Triticum aestivum | |
| Vitis vinifera | |
| Zea mays |
Compara
Gene Trees
The EnsemblCompara GeneTree database was updated. The new database includes a total of 56,582 GeneTree families comprising 1,275,735 individual genes (1,429,007 input proteins) from 39 plant genomes (and 5 non-plant outgroups).
The OGE Compara tree was not updated. 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.
Potential gene annotation artifacts
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 |
Synteny
No new synteny data was generated for this release. Last update was done in release 39 (October 2013).
WGA and other nucleotide alignments
No updates in this release. Last update done in release 42 (Sept 2014).
Protein Annotation, Go, Xref
No updates in this release. Last update done in release 43 (Dec 2014).
Mart
New Plant Gene and Plant Variation Marts
Pathway Release Notes
"Cyc" Pathways
- BioCyc-based pathway databases on Pathway Tools ver. 18.0 are available from a virtual server hosted at iPlant.
Summary tables for the Cyc pathway databases created by Gramene.
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Plant Reactome
Plant Reactome pathways for 33 species, including maize, wheat, soybean, Arabidopsis, banana, Brassicas, and numerous wild species related to rice. These pathways were annotated based on orthology projections from curated pathways in rice.
Projection Statistics
| Species | Pathways | Reactions | Gene Products |
| Oryza sativa japonica (curated reference) | 238 | 1056 | 935 |
| Aegilops tauschii | 177 | 461 | 731 |
| Arabidopsis thaliana | 184 | 493 | 832 |
| Brachypodium distachyon | 181 | 507 | 745 |
| Brassica rapa | 183 | 492 | 1283 |
| Glycine max | 181 | 483 | 1494 |
| Hordeum vulgare | 177 | 448 | 627 |
| Leersia perrieri | 186 | 506 | 731 |
| Medicago truncatula | 171 | 410 | 643 |
| Musa acuminata | 179 | 477 | 1019 |
| Oryza australiensis | 174 | 444 | 734 |
| Oryza barthii | 186 | 517 | 769 |
| Oryza brachyantha | 186 | 509 | 741 |
| Oryza glaberrima | 188 | 513 | 769 |
| Oryza glumaepatula | 187 | 520 | 770 |
| Oryza granulata | 175 | 450 | 789 |
| Oryza kasalath | 123 | 205 | 165 |
| Oryza longistaminata | 179 | 475 | 622 |
| Oryza meridionalis | 180 | 475 | 682 |
| Oryza minuta | 172 | 447 | 556 |
| Oryza nivara | 185 | 521 | 773 |
| Oryza officinalis | 178 | 434 | 474 |
| Oryza punctata | 184 | 508 | 765 |
| Oryza rufipogon | 186 | 514 | 779 |
| Oryza sativa Indica | 189 | 534 | 836 |
| Populus trichocarpa | 182 | 484 | 1045 |
| Prunus persica | 184 | 494 | 713 |
| Setaria italica | 185 | 511 | 833 |
| Solanum lycopersicum | 183 | 491 | 873 |
| Solanum tuberosum | 180 | 469 | 844 |
| Sorghum bicolor | 186 | 514 | 802 |
| Triticum aestivum | 185 | 512 | 1841 |
| Triticum urartu | 180 | 470 | 672 |
| Zea mays | 184 | 506 | 950 |
A new Plant Reactome release is anticipated for the late April 2015.
Ontologies Release Notes
No updates in this release. Last update done in release 31 (May 2010). Below is a summary of the ontologies data.
| Prefix | Term Type | Count |
|---|---|---|
| EO | plant_environment_ontology | 500 |
| GO | biological_process | 24767 |
| GO | cellular_component | 3194 |
| GO | molecular_function | 10376 |
| GRO | cereal_plant_growth_stage | 235 |
| GR_tax | gramene_taxonomy | 58550 |
| PO | plant_anatomy | 1295 |
| PO | plant_structure_development_stage | 324 |
| TO | plant_trait_ontology | 1290 |
See also the detailed Ontology Module statistics report (build 39, Oct. 2013).
Infrastructure
Web Services
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.
Public MySQL Server
Gramene provides direct MySQL access to our core Ensembl databases for each of our sequenced genomes as well our databases for markers, sequences, genes, QTL and ontologies. To connect, use the following:
mysql -hgramenedb.gramene.org -pgramene
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