Release Notes 50 (April 2016)
Website
See also legacy data in the Gramene's Archive.
Genomes Release Notes
New data
- New variation data for rice
- New Plant Reactome cross references added to all species
- New ncRNA alignments across all plant species
- New track hubs for more than 900 public RNA-Seq studies, totaling more than 16,000 tracks across 35 plant species
Updated data
- Updated putative split gene annotation artifacts
- Updated protein domain information based on latest InterProScan
- Updated BioMarts
- Updated to Ensembl 84 software
New features
- Searches within ensembl.gramene.org are now being served by our new search API hosted at data.gramene.org
- New HMMER tool for fast protein sequence search using Hidden Markov Models
Genomes Core
| 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+ |
Ensembl Variation
| Updated | Oryza sativa japonica |
|---|
| Unchanged | Arabidopsis thaliana |
|---|---|
| Brachypodium sylvaticum | |
| Oryza glaberrima | |
| Oryza glumaepatula | |
| Oryza sativa | |
| Sorghum bicolor | |
| Solanum lycopersicum | |
| Triticum aestivum | |
| Vitis vinifera | |
| Zea mays |
Compara
Gene Trees
The EnsemblCompara GeneTree database was updated. The new database includes a total of 55,519 GeneTree families were constructed comprising 1,280,352 individual genes (1,432,395 input proteins) from 39 plant genomes (and 5 non-plant outgroups).
Last update to the OGE Compara tree at oge.gramene.org (build on the MSU6 genome assembly) was done in release 38 (August 2013).
Putative Split Genes
The putative gene annotation artifacts (also known as contiguous gene split models) based on the latest Ensembl Compara Gene Tree database were updated in the current release. Brief statistics for each species is given below.
| Species | Count |
| Aegilops_tauschii | 463 |
| Amborella_trichopoda | 654 |
| Arabidopsis_lyrata_subsp._lyrata | 102 |
| Arabidopsis_thaliana | 13 |
| Brachypodium_distachyon | 105 |
| Brassica_oleracea_var._oleracea | 624 |
| Brassica_rapa_subsp._pekinensis | 94 |
| Chlamydomonas_reinhardtii | 62 |
| Cyanidioschyzon_merolae_strain_10D | 4 |
| Glycine_max | 257 |
| Hordeum_vulgare_subsp._vulgare | 91 |
| Leersia_perrieri | 157 |
| Medicago_truncatula | 267 |
| Musa_acuminata_subsp._malaccensis | 889 |
| Oryza_barthii | 208 |
| Oryza_brachyantha | 229 |
| Oryza_glaberrima | 432 |
| Oryza_glumipatula | 242 |
| Oryza_longistaminata | 213 |
| Oryza_meridionalis | 157 |
| Oryza_nivara | 185 |
| Oryza_punctata | 160 |
| Oryza_rufipogon | 179 |
| Oryza_sativa_Indica_Group | 558 |
| Oryza_sativa_Japonica_Group | 558 |
| Ostreococcus_lucimarinus_CCE9901 | 14 |
| Physcomitrella_patens | 149 |
| Populus_trichocarpa | 1100 |
| Prunus_persica | 307 |
| Selaginella_moellendorffii | 121 |
| Setaria_italica | 230 |
| Solanum_lycopersicum | 816 |
| Solanum_tuberosum | 458 |
| Sorghum_bicolor | 706 |
| Theobroma_cacao | 84 |
| Triticum_aestivum | 979 |
| Triticum_urartu | 357 |
| Vitis_vinifera | 465 |
| Zea_mays | 603 |
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 new alignments for this release. Last update was done in release 48 (November 2015).
Protein Annotation, Go, Xref
Protein domain information was updated based on the latest InterProScan analysis.
Mart
New Plant Gene and Plant Variation Marts
Pathway Release Notes
Plant Reactome
The Plant Reactome has expanded gene homology-based pathway projections to 62 plant species. Notable newly projected species: Eucalyptus grandis, Jatropha curcas, Manihot esculenta, and Mimulus guttatus. In addition, we have added six newly curated pathways. Please take a note of the following pathway statistics and status table for more details.
Newly projected species
- Eucalyptus grandis
- Jatropha curcas
- Manihot esculenta
- Mimulus guttatus
Newly curated pathways
- O. sativa choline biosynthesis I
- O. sativa choline biosynthesis III
- O. sativa cardiolipin biosynthesis
- O. sativa glycine betaine biosynthesis III (plants)
- O. sativa suberin biosynthesis
- O. sativa polar auxin transport
Reinstated pathway
- O. sativa Auxin signaling
Pathway Projections
Planteome Inparanoid data was kindly provided by the Planteome project. When available, the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources.
Projection Statistics
*data from sequenced transcriptomes
^ projections currently exclude cell-cycle pathways and annotations
| Species | Pathways | Reactions | Gene Products | Sequence source | Outgoing Link | Homology method |
|---|---|---|---|---|---|---|
| Oryza sativa japonica | 222^ | 1025 | 1173 | Ensembl Gramene | Uniprot | Curated Reference |
| Aegilops tauschii | 182 | 472 | 841 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Amborella trichopoda | 189 | 499 | 617 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Arabidopsis lyrata | 187 | 506 | 942 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Arabidopsis thaliana | 187 | 508 | 944 | Ensembl Gramene | TAIR | Ensembl Compara |
| Arachis duranensis | 196 | 518 | 788 | PeanutBase | PeanutBase | Planteome Inparanoid |
| Arachis ipaensis | 194 | 522 | 801 | PeanutBase | PeanutBase | Planteome Inparanoid |
| Brachypodium distachyon | 186 | 527 | 873 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Brassica oleracea | 186 | 497 | 1417 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Brassica rapa | 186 | 504 | 1443 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Cajanus cajan | 197 | 525 | 1009 | LegumeInfo | LegumeInfo | Planteome Inparanoid |
| Capsicum annuum | 198 | 511 | 1004 | PMID: 24441736 | N/A | Planteome Inparanoid |
| Chlamydomonas reinhardtii | 141 | 287 | 233 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Cicer arietinum | 198 | 528 | 1192 | NCBI | NCBI | Planteome Inparanoid |
| Citrus sinensis | 197 | 528 | 2026 | Phytozome | Phytozome | Planteome Inparanoid |
| Coffea canephora | 198 | 530 | 926 | PMID:25190796 | N/A | Planteome Inparanoid |
| Cyanidioschyzon merolae | 116 | 208 | 158 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Eucalyptus grandis | 190 | 510 | 825 | Phytozome | Phytozome | Planteome Inparanoid |
| Fragaria vesca | 198 | 514 | 888 | Phytozome | Phytozome | Planteome Inparanoid |
| Glycine max | 187 | 499 | 1730 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Gossypium raimondii | 197 | 532 | 1405 | Phytozome | Phytozome | Planteome Inparanoid |
| Hordeum vulgare | 184 | 469 | 734 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Jatropha curcas | 187 | 499 | 575 | KDRI (Kazusa) | KDRI (Kazusa) | Planteome Inparanoid |
| Leersia perrieri | 193 | 525 | 861 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Malus domestica | 196 | 511 | 1771 | PMID: 20802477 | Phytozome | Planteome Inparanoid |
| Manihot esculenta | 191 | 510 | 1014 | Phytozome | Phytozome | Planteome Inparanoid |
| Medicago truncatula | 188 | 497 | 1064 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Mimulus guttatus | 189 | 512 | 703 | Phytozome | Phytozome | Planteome Inparanoid |
| Musa acuminata | 186 | 490 | 1141 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza australiensis * | 194 | 494 | 1485 | OMAP/OGE | N/A | Planteome Inparanoid |
| Oryza barthii | 193 | 536 | 900 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza brachyantha | 193 | 528 | 850 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza glaberrima | 195 | 533 | 910 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza glumaepatula | 195 | 537 | 918 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza granulata * | 196 | 510 | 2565 | OMAP/OGE | N/A | Planteome Inparanoid |
| Oryza kasalath | 157 | 249 | 298 | PMID: 24578372 | N/A | Planteome Inparanoid |
| Oryza longistaminata * | 192 | 523 | 790 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza meridionalis | 186 | 487 | 789 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza minuta * | 197 | 516 | 1691 | OMAP/OGE | N/A | Planteome Inparanoid |
| Oryza nivara | 191 | 542 | 916 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza officinalis * | 195 | 524 | 1465 | OMAP/OGE | N/A | Planteome Inparanoid |
| Oryza punctata | 191 | 534 | 904 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza rufipogon | 193 | 544 | 923 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Oryza sativa Indica | 196 | 555 | 984 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Ostreococcus lucimarinus | 131 | 270 | 220 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Phaseolus vulgaris | 199 | 534 | 977 | Phytozome | Phytozome | Planteome Inparanoid |
| Phoenix dactylifera | 191 | 497 | 922 | PMID: 23917264 | N/A | Planteome Inparanoid |
| Physcomitrella patens | 176 | 454 | 904 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Picea abies | 191 | 477 | 1119 | Congenie | Congenie | Planteome Inparanoid |
| Pinus taeda | 181 | 434 | 1088 | TreeBase | N/A | Planteome Inparanoid |
| Populus trichocarpa | 188 | 508 | 1181 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Prunus persica | 188 | 507 | 797 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Selaginella moellendorffii | 181 | 472 | 1108 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Setaria italica | 191 | 531 | 962 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Solanum lycopersicum | 190 | 504 | 960 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Solanum tuberosum | 187 | 486 | 933 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Sorghum bicolor | 192 | 536 | 929 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Theobroma cacao | 191 | 511 | 775 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Triticum aestivum | 193 | 531 | 2159 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Triticum turgidum * | 197 | 528 | 2388 | PMID: 23800085 | N/A | Planteome Inparanoid |
| Triticum urartu | 187 | 481 | 768 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Vitis vinifera | 184 | 496 | 835 | Ensembl Gramene | Ensembl Gramene | Ensembl Compara |
| Zea mays | 191 | 528 | 1102 | Ensembl Gramene | MaizeGDB | Ensembl Compara |
NOTE: The pathway counts for both reference and projected species include a few organizational “container” names, such as “Hormone biosyntheses” and “Metabolism”. Additionally, the bulk of the projected pathways occur in the areas of metabolic and regulatory function, whereas the rice reference data set has additional pathways related to cell cycle functions. We are not currently using these additional pathways as a source for orthology projection.
"Cyc" Pathways
BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse.
Summary tables for the Cyc pathway databases created by Gramene can be seen in release 46 notes.
Ontologies Release 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.
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
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 50_84 is set as version 31_84.
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
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