Release Notes 41 (May 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 for Amborella trichopoda, Prunus persica (peach), Oryza glumaepatula, O. meridionalis, and O. nivara.
- Updated gene models for Triticum aestivum (bread wheat) v2.1, O. barthii, and O. punctata. The Oryza gene models were updated using the OGE Maker pipeline.
- Updated peptide comparative genomics.
- Updated split genes for 33 plant reference genomes based on the latest Ensembl Compara data.
- Whole-genome alignments within T. aestivum, between its component A, B, and D genomes.
- Calculation of homoeologous genes between the T. aestivum component A, B and D genomes.
- Whole-genome alignments between A. trichopoda and the two following genomes, Oryza sativa Japonica and Arabidopsis thaliana.
- Whole-genome alignments between P. persica and each the three following genomes, O. sativa Japonica, A. thaliana, and V. vinifera.
- Whole-genome alignments between each of the three new rice genomes and O. sativa Japonica, as well as against each other.
- New variation data for Sorghum bicolor based on the SAP panel (Morris et al, 2013).
- ESTs alignments against the peach genome using STAR aligner.
- Wheat ESTs alignment against bread wheat and its wild progenitors, T. urartu, and Aegilops tauschii, using STAR aligner.
- Updated wheat UniGene alignments against bread wheat and its wild progenitors.
- Updated biomart databases.
- Updated genome browser, database schema and API to Ensembl version 75.
- New orthology-based projections of rice pathways to Arabidopsis and Zea mays.
- Five newly curated rice pathways in the Plant Reactome.
Genomes Core
| Species | Assembly | Gene Annotation | |
|---|---|---|---|
| New | |||
| Amborella trichopoda | GCA_000471905.1 (AMTR1.0) | 2014-01-AGD | |
| Prunus persica | Prupe1_0 / GCA_000346465.1 | Prupe1_0 / Peach v1.0 | |
| Oryza meridionalis | GCA_000338895.1 | OGE Maker (Aug 2013) | |
| Oryza glumaepatula | GCA_000576495.1 | OGE Maker (Aug 2013) | |
| Oryza nivara | GCA_000576065.1 | OGE Maker (Aug 2013) | |
| Updated | |||
| Triticum aestivum | IWGSP1 | IWGSP1 (MIPS) | |
| Oryza barthii | GCA_000182155.1 | OGE Maker (Aug 2013) | |
| Oryza punctata | GCA_000573905.1 | OGE Maker (Aug 2013) | |
| 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 brachyantha | GCA_000231095.2 / OGEv1.4b | OGEv1.4 | |
| Oryza glaberrima | GCA_000147395.1 / AGI1.1 (May 2011) | 2011-05-AGI (MIPS) | |
| Oryza sativa japonica | IRGSP-1.0 | MSU 7.0 | |
| Oryza sativa indica | ASM465v1 | 2010-07-BGI | |
| 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 urartu | GCA_000347455.1 | GCA_000347455.1 (ENA, Apr 2013) | |
| Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
| Zea mays (corn) | B73_RefGen_v3 | 5b+ | |
| Leersia perrieri (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
| Oryza granulata (chr3s) | 454.pools.2012Feb | 2012-10-CSHL | |
| Oryza longistaminata (chr3s) | OGE.2012Jul | 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) chr3s | 454.pools.1.1 (Jul 2010) | CSHL | |
| Oryza rufipogon (AA) FPC | OMAP_FPC_2006_JAN | ||
Ensembl Variation
| Updated | Sorghum bicolor |
|---|
| Unchanged | Arabidopsis thaliana |
|---|---|
| Brachypodium sylvaticum | |
| Hordeum vulgare | |
| Oryza glaberrima | |
| Oryza sativa | |
| Triticum aestivum | |
| Vitis vinifera | |
| Zea mays |
Compara
Gene Trees
- The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 51,270 GeneTree families were constructed comprising 1,094,022 individual genes (1,232,442 input proteins) from 33 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
Split gene analysis was done for the 33 fully sequenced plant reference genomes in Gramene release 41. This analysis includes information on 10 new genomes, compared to the last split gene split done in release 38. For a complete list, see Gramene's FTP site. Summary statistics follow.
Split genes by species
| Species | Count |
|---|---|
| Aegilops tauschii | 534 |
| Amborella trichopoda | 739 |
| Arabidopsis lyrata subsp. lyrata | 81 |
| Arabidopsis thaliana | 21 |
| Brachypodium distachyon | 108 |
| Brassica rapa subsp. pekinensis | 107 |
| Chlamydomonas reinhardtii | 45 |
| Cyanidioschyzon merolae | 4 |
| Glycine max | 254 |
| Hordeum vulgare subsp. vulgare | 65 |
| Medicago truncatula | 285 |
| Musa acuminata | 1134 |
| Oryza barthi | 147 |
| Oryza brachyantha | 198 |
| Oryza glaberrima | 357 |
| Oryza glumaepatula | 206 |
| Oryza meridionalis | 125 |
| Oryza nivara | 117 |
| Oryza punctata | 151 |
| Oryza sativa Indica Group | 509 |
| Oryza sativa Japonica Group | 398 |
| Physcomitrella patens subsp. patens | 173 |
| Populus trichocarpa | 1196 |
| Prunus persica | 276 |
| Selaginella moellendorffii | 70 |
| Setaria italica | 171 |
| Solanum lycopersicum | 784 |
| Solanum tuberosum | 412 |
| Sorghum bicolor | 607 |
| Triticum aestivum | 772 |
| Triticum urartu | 447 |
| Vitis vinifera | 440 |
| Zea mays | 564 |
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
No updates in this release. Last update done in release 40 (January 2014).
Mart
New Plant Gene and Plant Variation Marts
Pathway Release Notes
Plant Reactome
- In this release we have implemented orthology-based projections of rice pathways to Arabidopsis and Zea mays.
- Five new rice pathways (listed below) have been added to the Plant Reactome.
| Class | Pathway name |
|---|---|
| Hormones | strigolactone biosynthesis |
| Amines and Polyamines | allantoin degradation I |
| Inorganic Nutrients Metabolism | sulfate activation for sulfonation |
| thiosulfate disproportionation III (rhodanese) | |
| ammonia assimilation cycle |
"Cyc" Pathways
- No updates on this release
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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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