Release Notes 43 (December 2014)
Website
Although we have a new look, you can still find all the old stuff at Gramene's Archive.
Genomes Release Notes
New genomes
No new genomes in this release.
Updated genomes
Updated assembly for Hordeum vulgare (barley) based on POPSEQ data from IPK.
New & updated pathways (Plant Reactome & Cyc Pathway DBs)
- Plant Reactome updates coming up! Check back in January 2015.
- BioCyc-based pathway databases are now available from a virtual server hosted at iPlant. Pathway tools (ptools) software on this platform was updated to version 18.0. The pathway server on Gramene continues to exist in ptools ver 17.0, which is no longer supported by SRI ptools developers, and therefore will be eventually deprecated from the Gramene server.
New data
- New Triticum aestivum (bread wheat) inter-homoeologous variation (IHV) data.
- SIFT scores added to existing and new IHV data for bread wheat.
- New Solanum lycopersicum (tomato) variation data based on the 150 Tomato Genomes ReSequencing Project.
Updated data
- All barley sequence features have been projected to new chromosomal assembly coordinates.
- Updated domain annotation of protein coding genes for all species using InterPro version 48.0 and InterProScan version 5 .
- Updated gene, sequence and variation BioMarts.
Genomes Core
| Species | Assembly | Gene Annotation | Updated |
|---|---|---|---|
| Hordeum vulgare (barley) | 030312v2 | IBSC_1.0 | 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 | |
| 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) | SL2.40 | 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 | Solanum lycopersicum |
|---|
| Unchanged | Arabidopsis thaliana |
|---|---|
| Brachypodium sylvaticum | |
| Hordeum vulgare | |
| Oryza glaberrima | |
| Oryza sativa | |
| Sorghum bicolor | |
| Triticum aestivum | |
| Vitis vinifera | |
| Zea mays |
In addition, inter-homoeologous variation data was generated for Triticum aestivum (bread wheat), and SIFT scores were added to the existing and new IHV) bread wheat data.
Compara
Gene Trees
The EnsemblCompara GeneTree database was not updated. The last update (b42, Sept 2014) included a total of 56,134 GeneTree families comprising 1,242,576 individual genes (1,394,452 input proteins) from 38 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 | 721 |
| Amborella trichopoda | 980 |
| Arabidopsis lyrata subsp. lyrata | 183 |
| Arabidopsis thaliana | 39 |
| Brachypodium distachyon | 145 |
| Brassica oleracea var. oleracea | 909 |
| Brassica rapa subsp. pekinensis | 151 |
| Chlamydomonas reinhardtii | 137 |
| Cyanidioschyzon merolae | 28 |
| Glycine max | 384 |
| Hordeum vulgare subsp. vulgare | 121 |
| Medicago truncatula | 496 |
| Musa acuminata | 1583 |
| Oryza barthi | 341 |
| Oryza brachyantha | 316 |
| Oryza glaberrima | 571 |
| Oryza glumaepatula | 372 |
| Oryza meridionalis | 267 |
| Oryza nivara | 300 |
| Oryza punctata | 240 |
| Oryza rufipogon | 287 |
| Oryza sativa Indica Group | 833 |
| Oryza sativa Japonica Group | 702 |
| Physcomitrella patens subsp. patens | 281 |
| Populus trichocarpa | 1628 |
| Prunus persica | 423 |
| Selaginella moellendorffii | 227 |
| Setaria italica | 323 |
| Solanum lycopersicum | 1188 |
| Solanum tuberosum | 632 |
| Sorghum bicolor | 949 |
| Theobroma cacao | 103 |
| Triticum aestivum | 1074 |
| Triticum urartu | 665 |
| Vitis vinifera | 695 |
| Zea mays | 838 |
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
Domain annotation of protein coding genes was updated for all species using InterPro version 48.0 and InterProScan version 5.
Mart
New Plant Gene and Plant Variation Marts
Pathway Release Notes
"Cyc" Pathways
- BioCyc-based pathway databases were upgraded to Pathway Tools ver. 18.0 and are now available from a virtual server hosted at iPlant.
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Updated summary tables for the Cyc pathway databases created by Gramene.
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.
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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