Table of Contents
See also legacy data in Gramene's Archive.
## Genomes Core
Species | Assembly | Gene Annotation | |
---|---|---|---|
Updated | |||
Arabidopsis thaliana | TAIR10 | AraPort11 |
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 | |
Beta vulgaris | RefBeet-1.2.2 | ENA | |
Brachypodium distachyon | Brachy1.0 | Barchy1.2 | |
Brassica napus | AST_PRJEB5043_v1 | ENA | |
Brassica oleracea | GCA_000092065.1 | ENA | |
Brassica rapa | IVFCAASv1 | bra_v1.01_SP2010_01 | |
Chlamydomonas reinhardtii | v3.0 | 2007-11-ENA | |
Chondrus crispus | ASM35022v2 | ENA | |
Cyanidioschyzon merolae | 2008-11-ENA | ASM9120v1 | |
Galdieria sulphuraria | ASM34128v1 | ENA | |
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 | |
Trifolium pratense | Trpr | TGAC | |
Triticum aestivum | TGACv1 | 2014-07-PGSBv2.2 | |
Triticum urartu | GCA_000347455.1 | GCA_000347455.1 (ENA, Apr 2013) | |
Vitis vinifera | IGGP 12x | 2012-07-CRIBI | |
Zea mays (corn) | B73_RefGen_v4 | MAKER-CSHL |
## 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. A total of 61,582 GeneTree families were constructed comprising 1,460,776 individual genes (1,619,230 input proteins) from 44 plant genomes (and 5 non-plant outgroups).
#### Putative Split Genes
Split gene predictions were not updated in this release. Last update was done in release 50 (April 2016), see summary statistics in build 50 release notes and Gramene's FTP site.
### Synteny
Added two pairs of synteny for maize: Setaria italica vs. Zea mays, and Brachypodium distachyon vs. Zea mays.
### WGA and other nucleotide alignments
## Protein Annotation, Go, Xref Protein domain information was updated based on the latest InterProScan analysis.
## Mart
New Plant Gene and Plant Variation Marts
## Plant Reactome
The Plant Reactome has expanded gene homology-based pathway projections to 66 plant species. Newly projected species: Beta vulgaris, Brassica napus, Syncechocystis pcc6803, and Trifolium pratense. Notable updated Compara orthology data has been kindly provided by Ensembl for Triticum aestivum and Zea mays (v4). In addition, we have added nine newly curated pathways and revised two additional curated pathways. Please take a note of the following pathway statistics and status table for more details.
Pathway Curation
Newly curated pathways (O. sativa)
Updated pathways (O. sativa)
Polar auxin transport
Pathway Projection Statistics and Status
*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 | 241^ | 1069 | 1263 | Ensembl Gramene | Uniprot | Curated Reference |
Aegilops tauschii | 200 | 498 | 925 | Ensembl Gramene | Ensembl Gramene | Compara |
Amborella trichopoda | 207 | 530 | 677 | Ensembl Gramene | Ensembl Gramene | Compara |
Arabidopsis lyrata | 205 | 536 | 1064 | Ensembl Gramene | Ensembl Gramene | Compara |
Arabidopsis thaliana | 205 | 539 | 1069 | Ensembl Gramene | TAIR | Compara |
Arachis duranensis | 212 | 542 | 847 | PeanutBase | PeanutBase | Inparanoid |
Arachis ipaensis | 210 | 546 | 862 | PeanutBase | PeanutBase | Inparanoid |
Beta vulgaris | 211 | 553 | 783 | Ensembl Gramene | Ensembl Gramene | Compara |
Brachypodium distachyon | 204 | 562 | 970 | Ensembl Gramene | Ensembl Gramene | Compara |
Brassica napus | 212 | 555 | 3276 | Ensembl Gramene | Ensembl Gramene | Compara |
Brassica oleracea | 204 | 526 | 1613 | Ensembl Gramene | Ensembl Gramene | Compara |
Brassica rapa | 204 | 534 | 1639 | Ensembl Gramene | Ensembl Gramene | Compara |
Cajanus cajan | 213 | 550 | 1103 | LegumeInfo | LegumeInfo | Inparanoid |
Capsicum annuum | 213 | 536 | 1077 | PMID: 24441736 | N/A | Inparanoid |
Chlamydomonas reinhardtii | 145 | 296 | 242 | Ensembl Gramene | Ensembl Gramene | Compara |
Cicer arietinum | 214 | 554 | 1307 | NCBI | NCBI | Inparanoid |
Citrus sinensis | 213 | 552 | 2210 | Phytozome | Phytozome | Inparanoid |
Coffea canephora | 214 | 556 | 994 | PMID:25190796 | N/A | Inparanoid |
Cyanidioschyzon merolae | 123 | 217 | 166 | Ensembl Gramene | Ensembl Gramene | Compara |
Eucalyptus grandis | 206 | 535 | 886 | Phytozome | Phytozome | Inparanoid |
Fragaria vesca | 214 | 536 | 951 | Phytozome | Phytozome | Inparanoid |
Glycine max | 205 | 531 | 1961 | Ensembl Gramene | Ensembl Gramene | Compara |
Gossypium raimondii | 213 | 558 | 1541 | Phytozome | Phytozome | Inparanoid |
Hordeum vulgare | 202 | 500 | 808 | Ensembl Gramene | Ensembl Gramene | Compara |
Jatropha curcas | 203 | 524 | 624 | KDRI (Kazusa) | KDRI (Kazusa) | Inparanoid |
Leersia perrieri | 211 | 560 | 951 | Ensembl Gramene | Ensembl Gramene | Compara |
Malus domestica | 211 | 535 | 1897 | PMID: 20802477 | Phytozome | Inparanoid |
Manihot esculenta | 207 | 534 | 1096 | Phytozome | Phytozome | Inparanoid |
Medicago truncatula | 206 | 528 | 1198 | Ensembl Gramene | Ensembl Gramene | Compara |
Mimulus guttatus | 205 | 537 | 766 | Phytozome | Phytozome | Inparanoid |
Musa acuminata | 204 | 518 | 1260 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza australiensis * | 210 | 518 | 1628 | OMAP/OGE | N/A | Inparanoid |
Oryza barthii | 211 | 570 | 988 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza brachyantha | 211 | 561 | 935 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza glaberrima | 213 | 564 | 1003 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza glumaepatula | 213 | 572 | 1013 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza granulata * | 212 | 534 | 2941 | OMAP/OGE | N/A | Inparanoid |
Oryza kasalath | 173 | 258 | 325 | PMID: 24578372 | N/A | Inparanoid |
Oryza longistaminata * | 210 | 557 | 869 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza meridionalis | 204 | 520 | 869 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza minuta * | 213 | 541 | 1851 | OMAP/OGE | N/A | Inparanoid |
Oryza nivara | 209 | 576 | 1015 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza officinalis * | 211 | 546 | 1616 | OMAP/OGE | N/A | Inparanoid |
Oryza punctata | 209 | 568 | 1002 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza rufipogon | 211 | 578 | 1025 | Ensembl Gramene | Ensembl Gramene | Compara |
Oryza sativa Indica | 214 | 589 | 1083 | Ensembl Gramene | Ensembl Gramene | Compara |
Ostreococcus lucimarinus | 135 | 279 | 230 | Ensembl Gramene | Ensembl Gramene | Compara |
Phaseolus vulgaris | 215 | 558 | 1068 | Phytozome | Phytozome | Inparanoid |
Phoenix dactylifera | 207 | 522 | 1000 | PMID: 23917264 | N/A | Inparanoid |
Physcomitrella patens | 194 | 480 | 986 | Ensembl Gramene | Ensembl Gramene | Compara |
Picea abies | 207 | 501 | 1215 | Congenie | Congenie | Inparanoid |
Pinus taeda | 197 | 456 | 1160 | TreeBase | N/A | Inparanoid |
Populus trichocarpa | 206 | 539 | 1320 | Ensembl Gramene | Ensembl Gramene | Compara |
Prunus persica | 206 | 538 | 888 | Ensembl Gramene | Ensembl Gramene | Compara |
Selaginella moellendorffii | 199 | 498 | 1241 | Ensembl Gramene | Ensembl Gramene | Compara |
Setaria italica | 209 | 566 | 1059 | Ensembl Gramene | Ensembl Gramene | Compara |
Solanum lycopersicum | 208 | 535 | 1069 | Ensembl Gramene | Ensembl Gramene | Compara |
Solanum tuberosum | 205 | 514 | 1023 | Ensembl Gramene | Ensembl Gramene | Compara |
Sorghum bicolor | 210 | 569 | 1025 | Ensembl Gramene | Ensembl Gramene | Compara |
Synechocystis pcc6803 | 148 | 312 | 264 | Jaiswal | MicrobeDB | Inparanoid |
Theobroma cacao | 209 | 543 | 866 | Ensembl Gramene | Ensembl Gramene | Compara |
Trifolium pratense | 208 | 540 | 1006 | Ensembl Gramene | Ensembl Gramene | Compara |
Triticum aestivum | 210 | 571 | 3276 | Ensembl Gramene | Ensembl Gramene | Compara |
Triticum turgidum * | 213 | 553 | 2522 | PMID: 23800085 | N/A | Inparanoid |
Triticum urartu | 205 | 509 | 843 | Ensembl Gramene | Ensembl Gramene | Compara |
Vitis vinifera | 202 | 528 | 928 | Ensembl Gramene | Ensembl Gramene | Compara |
Zea mays | 209 | 563 | 1269 | Ensembl Gramene | MaizeGDB | 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.
## 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 51_85 is set as version 32_85.
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