Release Notes 43 (December 2014)


Although we have a new look, you can still find all the old stuff at Gramene's Archive.

Genomes Release Notes

  • New genomes

    No new genomes in this release.

  • Updated genomes

    Updated assembly for Hordeum vulgare (barley) based on POPSEQ data from IPK.

  • New & updated pathways (Plant Reactome & Cyc Pathway DBs)

    1. Plant Reactome updates coming up! Check back in January 2015.
    2. BioCyc-based pathway databases are now available from a virtual server hosted at iPlant. Pathway tools (ptools) software on this platform was updated to version 18.0. The pathway server on Gramene continues to exist in ptools ver 17.0, which is no longer supported by SRI ptools developers, and therefore will be eventually deprecated from the Gramene server.
  • New data

    1. New Triticum aestivum (bread wheat) inter-homoeologous variation (IHV) data.
    2. SIFT scores added to existing and new IHV data for bread wheat.
    3. New Solanum lycopersicum (tomato) variation data based on the 150 Tomato Genomes ReSequencing Project.
  • Updated data

    1. All barley sequence features have been projected to new chromosomal assembly coordinates.
    2. Updated domain annotation of protein coding genes for all species using InterPro version 48.0 and InterProScan version 5 .
    3. Updated gene, sequence and variation BioMarts.

Genomes Core

  Species Assembly Gene Annotation
Hordeum vulgare (barley) 030312v2 IBSC_1.0
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
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) SL2.40 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 Solanum lycopersicum
Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Hordeum vulgare
Oryza glaberrima
Oryza sativa
Sorghum bicolor
Triticum aestivum
Vitis vinifera
Zea mays

In addition, inter-homoeologous variation data was generated for Triticum aestivum (bread wheat), and SIFT scores were added to the existing and new IHV) bread wheat data.


Gene Trees

  • The EnsemblCompara GeneTree database was not updated. The last update (b42, Sept 2014) included a total of 56,134 GeneTree families comprising 1,242,576 individual genes (1,394,452 input proteins) from 38 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 721
Amborella trichopoda980
Arabidopsis lyrata subsp. lyrata183
Arabidopsis thaliana39
Brachypodium distachyon145
Brassica oleracea var. oleracea909
Brassica rapa subsp. pekinensis151
Chlamydomonas reinhardtii137
Cyanidioschyzon merolae28
Glycine max384
Hordeum vulgare subsp. vulgare121
Medicago truncatula496
Musa acuminata1583
Oryza barthi341
Oryza brachyantha316
Oryza glaberrima571
Oryza glumaepatula372
Oryza meridionalis267
Oryza nivara300
Oryza punctata240
Oryza rufipogon287
Oryza sativa Indica Group833
Oryza sativa Japonica Group702
Physcomitrella patens subsp. patens281
Populus trichocarpa1628
Prunus persica423
Selaginella moellendorffii227
Setaria italica323
Solanum lycopersicum1188
Solanum tuberosum632
Sorghum bicolor949
Theobroma cacao103
Triticum aestivum1074
Triticum urartu665
Vitis vinifera695
Zea mays838


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

Domain annotation of protein coding genes was updated for all species using InterPro version 48.0 and InterProScan version 5.


New Plant Gene and Plant Variation Marts

Pathway Release Notes

"Cyc" Pathways

  • BioCyc-based pathway databases were upgraded to Pathway Tools ver. 18.0 and are now available from a virtual server hosted at iPlant.
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

Updated summary tables for the Cyc pathway databases created by Gramene.

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.


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