Release Notes 45 (April 2015)


See also legacy data in the Gramene's Archive.

Genomes Release Notes

  • Updated genomes

    1. Medicago truncatula latest assembly and gene set.
    2. Oryza meridionalis latest assembly and gene set.
  • New data

    • Split gene predictions for 39 plant genomes.
    • Whole genome alignments between Triticeae genomes using ATAC between:
    1. The Triticum aestivum (bread wheat) component genomes (A, B and D - Ensembl Plants stats),
    2. T. urartu against the bread wheat A genome (Ensembl Plants stats),
    3. Aegilops tauschii against the bread wheat D genome (Ensembl Plants stats),
    4. T. urartu against A. tauschii (Ensembl Plants stats), and
    5. Hordeum vulgare (barley) against T. aestivum (Ensembl Plants stats), T. urartu (Ensembl Plants stats), and A. tauschii (Ensembl Plants stats).
    • Whole genome alignments using LASTZ between:
    1. Brassica oleracea and Arabidopsis thaliana (Ensembl Plants stats).
    2. M. truncatula and Glycine max, Arabidopsis thaliana, Vitis vinifera and Oryza sativa group Japonica (Ensembl Plants stats).
    • Enabled the assembly converter tool to allow conversion of tomato 2.50 onto 2.40 coordinates.
    • Synteny regions for bread wheat against O. sativa Japonica.
    • Two new RNA-Seq studies aligned to barley (read more).
    • New RNA-Seq studies (leaf, root and panicle) for OGE genomes, including O. barthii, O. brachyantha, O. glaberrima, O. glumaepatula, O. meridionalis, O. nivara, O. punctata, O. rufipogon, O. sativa Japonica, and Leersia perrieri.
    • New genome browser tracks for Zea mays (read more).
    • New browser tracks for Sorghum bicolor (read more).
    • New links to gene annotations from AraPort and Expression ATLAS (see for example, pad4).
  • Updated data

    1. Updated to Ensembl 79 software.
    2. Updated gene, sequence and variation BioMarts.
    3. Updated BLAST software from Ensembl.
    4. Peptide comparative genomics data across all species.
    5. Projection of manual GO annotation from Arabidopsis thaliana to 1:1 orthologues in all other plant species.
    6. Projection of manually assigned gene names and descriptions from Arabidopsis thaliana to 1:1 orthologues in all other dicotyledons species.
    7. Renamed the unordered barley chromosomes.

Genomes Core

  Species Assembly Gene Annotation
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Oryza meridionalis GCA_000338895.1 OGE Maker (Aug 2013)
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
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 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 Hordeum vulgare
Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Oryza glaberrima
Oryza sativa
Solanum lycopersicum
Sorghum bicolor
Triticum aestivum
Vitis vinifera
Zea mays


Gene Trees

  • The EnsemblCompara GeneTree database was updated. The new database includes a total of 56,582 GeneTree families comprising 1,275,735 individual genes (1,429,007 input proteins) from 39 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

Aegilops tauschii 740
Amborella trichopoda994
Arabidopsis lyrata subsp. lyrata180
Arabidopsis thaliana37
Brachypodium distachyon158
Brassica oleracea var. oleracea911
Brassica rapa subsp. pekinensis151
Chlamydomonas reinhardtii141
Cyanidioschyzon merolae8
Glycine max390
Hordeum vulgare subsp. vulgare108
Medicago truncatula394
Musa acuminata1624
Oryza barthi338
Oryza brachyantha302
Oryza glaberrima518
Oryza glumaepatula394
Oryza longistaminata291
Oryza meridionalis272
Oryza nivara310
Oryza punctata282
Oryza rufipogon300
Oryza sativa Indica Group796
Oryza sativa Japonica Group636
Physcomitrella patens subsp. patens276
Populus trichocarpa1651
Prunus persica448
Selaginella moellendorffii215
Setaria italica332
Solanum lycopersicum1216
Solanum tuberosum653
Sorghum bicolor953
Theobroma cacao113
Triticum aestivum1234
Triticum urartu674
Vitis vinifera725
Zea mays844


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

No updates in this release. Last update done in release 43 (Dec 2014).


New Plant Gene and Plant Variation Marts

Pathway Release Notes

"Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 18.0 are available from a virtual server hosted at iPlant.

Summary tables for the Cyc pathway databases created by Gramene.

RiceCyc Summary (version 3.3)
Enzymatic Reactions2,103
Transport Reactions87
BrachyCyc Summary (version 2.0)
Enzymatic Reactions2,057
Transport Reactions87
MaizeCyc Summary (version 2.2)
Enzymatic Reactions2,132
Transport Reactions106
SorghumCyc Summary (version 1.1)
Enzymatic Reactions1,838
Transport Reactions9

Plant Reactome

Plant Reactome pathways for 33 species, including maize, wheat, soybean, Arabidopsis, banana, Brassicas, and numerous wild species related to rice. These pathways were annotated based on orthology projections from curated pathways in rice.

Projection Statistics

SpeciesPathwaysReactionsGene Products
Oryza sativa japonica (curated reference)2381056935
Aegilops tauschii177461731
Arabidopsis thaliana184493832
Brachypodium distachyon181507745
Brassica rapa1834921283
Glycine max1814831494
Hordeum vulgare177448627
Leersia perrieri186506731
Medicago truncatula171410643
Musa acuminata1794771019
Oryza australiensis174444734
Oryza barthii186517769
Oryza brachyantha186509741
Oryza glaberrima188513769
Oryza glumaepatula187520770
Oryza granulata175450789
Oryza kasalath123205165
Oryza longistaminata179475622
Oryza meridionalis180475682
Oryza minuta172447556
Oryza nivara185521773
Oryza officinalis178434474
Oryza punctata184508765
Oryza rufipogon186514779
Oryza sativa Indica189534836
Populus trichocarpa1824841045
Prunus persica184494713
Setaria italica185511833
Solanum lycopersicum183491873
Solanum tuberosum180469844
Sorghum bicolor186514802
Triticum aestivum1855121841
Triticum urartu180470672
Zea mays184506950

A new Plant Reactome release is anticipated for the late April 2015.

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 (build 39, Oct. 2013).


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 -pgramene