Release Notes 48 (November 2015)


See also legacy data in the Gramene's Archive.

Genomes Release Notes

  • New data

    • New ATLAS gene expression annotations. See an example Gene summary page
    • New pairwise alignment between Solanum tuberosum and S. lycopersicum (build 2.50)
    • New pairwise alignments between Theobroma cacao and:
      • Arabidopsis thaliana, and
      • Oryza sativa, and
      • Vitis vinifera
    • Extensive new pairwise alignments between the 12 OGE species, covering nearly 50 pairs of species, e.g.
      • O. barthii vs. O. rufipogon,
      • O. meridionalis vs. O. sativa, and
      • O. barthii vs. Leersia perrieri
    • Updated repeat identification across all plant species using RepBase (release 20140131) and PGSB-REdat (release 9.3p)
  • Updated data

    1. Updated to Ensembl 82 software
    2. Updated BioMarts
    3. Updated protein domain information based on latest InterProScan
    4. Updated pairwise alignments between Hordeum vulgare and:
      • Aegilops tauschii,
      • Brachypodium distachyon, and
      • O. sativa

Genomes Core

  Species Assembly Gene Annotation
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

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 56,387 GeneTree families were constructed comprising 1,280,368 individual genes (1,432,406 input proteins) from 39 plant genomes (and 5 non-plant outgroups).

  • The OGE Compara tree was not updated at 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

Updated whole genome alignments for S. lycopersicum vs A. thaliana, O. sativa Japonica, and V. vinifera.

Protein Annotation, Go, Xref

UniProtKB cross-references were updated across all species.


New Plant Gene and Plant Variation Marts

Pathway Release Notes

"Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at iPlant.

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 -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 48_82 is set as version 29_82.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "" with the password "gramene," e.g.:

mysql -pgramene