Release Notes 40 (Jan 2014)
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Genomes Release Notes
- Updated gene models for Oryza sativa japonica from RAP-DB.
- Gene models for Triticum aestivum (bread wheat) chromosome survey sequences from MIPS.
- DNA-DNA alignments between bread wheat and Oryza sativa, as well as Brachypodium distachyon.
- DNA-DNA alignments between Hordeum vulgare (barley) and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).
- Additional RNA-Seq data were aligned to bread wheat as well as to its wild progenitors.
- Wheat UniGene clusters sequences were also aligned to bread wheat as well as to its wild progenitors.
- Updated gene-trees to include bread wheat gene models.
- Updated (TREP) repeat analysis for wheat and barley genomes.
- Updated functional domain (InterPro) and ontology (InterPro2GO) annotation.
- Updated biomart databases.
- Updated genome browser, database schema and API to Ensembl version 74.
Genomes Core
| Species | Assembly | Gene Annotation | |
|---|---|---|---|
| Updated | |||
| Oryza sativa japonica | IRGSP-1.0 / MSU 7.0 | IRGSP-1.0 / MSU 7.0 | |
| Unchanged | |||
| Aegilops tauschii | ASM34733v1 | GCA_000347335.1 | |
| Arabidopsis lyrata | Araly1.0 | Araly1.0 | |
| Arabidopsis thaliana | TAIR10 | TAIR10 | |
| Brachypodium distachyon | Brachy1.0 | Barchy1.2 | |
| 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 | |
| Medicago truncatula | MedtrA17_3.5 | 2011-11-EnsemblPlants | |
| Musa acuminata (banana) | MA1 | 2012-08-Cirad | |
| Oryza barthii | OGE.2012Jul | 2012-10-CSHL | |
| Oryza brachyantha | OGEv1.4b | OGEv1.4 | |
| Oryza glaberrima | AGI1.1 (May 2011) | 2011-05-AGI | |
| Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
| Oryza punctata | Mar 2013 | CSHL Mar 2013 | |
| Physcomitrella patens | ASM242v1 | 2011-03-Phypa1.6 | |
| 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 | |
| Triticum aestivum | IWGSP1 | IWGSP1 | |
| Triticum urartu | ASM34745v1 | GCA_000347455.1 | |
| Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
| Zea mays (corn) | B73_RefGen_v3 | 5b+ | |
| Leersia perrieri (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
| Oryza glumaepatula (chr3s) | 454.pools.2012Feb | 2012-04-CSHL | |
| Oryza granulata (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
| Oryza longistaminata (chr3s) | OGE.2012Jul | 2012-10-CSHL | |
| Oryza meridionalis (chr3s) | 454.pools.2012Feb | 2012-04-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 nivara (AA) chr3s | 454.pools.1.1 (Jul 2010) | CSHL | |
| Oryza officinallis (CC) chr3s | BAC.Sanger.1.1 (May 2011) | CSHL v3.1 | |
| Oryza rufipogon (AA) chr3s | 454.pools.1.1 (Jul 2010) | CSHL | |
| Oryza rufipogon (AA) FPC | OMAP_FPC_2006_JAN | ||
Ensembl Variation
| Unchanged | Arabidopsis thaliana |
|---|---|
| Brachypodium sylvaticum | |
| Hordeum vulgare | |
| Oryza glaberrima | |
| Oryza sativa | Sorghum bicolor |
| Triticum aestivum | |
| Vitis vinifera | |
| Zea mays |
Compara
Gene Trees
- The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 43,812 GeneTree families were constructed comprising 894,376 individual genes (1,017,959 input proteins) from 31 genomes, of which 5 are 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
No new split gene annotations were identified for this release. Last update was done in release 38 (August 2013). For a complete list, see Gramene's FTP site. Summary statistics follow.
Split genes by species
| Species | Count |
|---|---|
| Arabidopsis lyrata subsp. lyrata | 172 |
| Arabidopsis thaliana | 34 |
| Brachypodium distachyon | 150 |
| Brassica rapa subsp. pekinensis | 150 |
| Chlamydomonas reinhardtii | 96 |
| Cyanidioschyzon merolae | 8 |
| Glycine max | 404 |
| Hordeum vulgare subsp. vulgare | 56 |
| Musa acuminata | 1558 |
| Oryza barthi | 1 |
| Oryza brachyantha | 334 |
| Oryza glaberrima | 436 |
| Oryza sativa Indica Group | 730 |
| Oryza sativa Japonica Group | 628 |
| Physcomitrella patens subsp. patens | 248 |
| Populus trichocarpa | 2076 |
| Selaginella moellendorffii | 172 |
| Setaria italica | 362 |
| Solanum lycopersicum | 1138 |
| Solanum tuberosum | 648 |
| Sorghum bicolor | 1036 |
| Vitis vinifera | 876 |
| Zea mays | 1160 |
Synteny
No new synteny data was generated for this release. Last update was done in release 39 (October 2013).
WGA and other nucleotide alignments
DNA-DNA alignments between bread wheat and Oryza sativa, bread wheat and Brachypodium distachyon, and barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).
RNA-Seq data aligned to bread wheat, as well as to its wild progenitors.
Wheat UniGene clusters sequences aligned to bread wheat, as well as to its wild progenitors.
Protein Annotation, Go, Xref
Updated functional domain (InterPro) and ontology (InterPro2GO) annotation.
Mart
New Plant Gene and Plant Variation Marts
Pathways
"Cyc" Pathways Release Notes (version 3.7)
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MaizeCyc was updated to Version 2.2 with 37 updated GO annotations, evidence codes and publication references.
NOTE: BioPAX level 2 and 3 generated with the pathway tools software have a discrepant number of pathways. For more details, please see the note in the MaizeCyc 2.2 FTP directory.
Plant Reactome
32 new rice pathways have been added to the Plant Reactome, including the signaling pathway for the plant hormone ethylene. 8 pathways have been updated.
Modified pathways
| ABA biosynthesis and signalling pathway |
| Calvin cycle |
| TCA cycle |
| oleoresin sesquiterpene volatiles biosynthesis |
| oleoresin monoterpene volatiles biosynthesis |
| carotenoid biosynthesis |
| monoterpene biosynthesis |
| polyisoprenoid biosynthesis |
New pathways
| Ethylene biosynthesis and signaling |
| Oryzalexin S biosynthesis |
| S-adenosyl-L-methionine cycle |
| S-methylmethionine cycle |
| UDP-L-arabinose biosynthesis I |
| UDP-L-arabinose biosynthesis II |
| alanine biosynthesis II |
| alanine biosynthesis III |
| arginine biosynthesis I |
| arginine biosynthesis II |
| aspartate biosynthesis I |
| beta-alanine biosynthesis I |
| beta-alanine biosynthesis III |
| cysteine biosynthesis I |
| fructan biosynthesis |
| fructan degradation |
| galactose degradation II |
| geranylgeranyl diphosphate biosynthesis II |
| histidine biosynthesis I |
| methionine biosynthesis II |
| methionine salvage pathway |
| mevalonate pathway |
| momilactone biosynthesis |
| oryzalexin A-F biosynthesis |
| phytyl-pp biosynthesis |
| putrescine biosynthesis I |
| putrescine biosynthesis II |
| putrescine biosynthesis III |
| spermidine biosynthesis |
| spermine biosynthesis |
| sucrose biosynthesis |
| tetrapyrrole biosynthesis I |
Ontologies Release Notes
No updates in this release (except for updated InterPro2GO annotations under 'Protein Annotation, Go, Xref' section above). 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