Release Notes 42 (September 2014)


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

Genomes Release Notes

  • New genomes

    1. Ostreococcus lucimarinus (a green alga)
    2. Leersia perrieri (a wild grass)
    3. Oryza rufipogon (brownbeard rice)
    4. Oryza longistaminata (a wild rice)
    5. Theobroma cacao (cocoa)
    6. Brassica oleracea (the brassica C genome)
  • Updated genomes

    1. Updated assembly and gene build for O. barthii (wild rice)
    2. Chloroplast genomes added to the triticeae genomes: Hordeum vulgare (barley), Aegilops tauschii (Tausch's goatgrass), Triticum aestivum (bread wheat) and Triticum urartu (an einkorn wheat)
    3. Mitochondrial genome added to Triticum aestivum (bread wheat)
  • New & updated pathways (Plant Reactome)

    1. New auxin signaling pathway in rice
    2. Updated 9 amino acid pathways by incorporating recent literature and genes & compartment re-assignments.
      • arginine biosynthesis I
      • arginine biosynthesis II
      • glutamate biosynthesis I
      • glutamate biosynthesis V
      • glutamine biosynthesis I
      • alanine biosynthesis II
      • alanine biosynthesis III
      • glutamate biosynthesis IV
      • lysine biosynthesis VI
    3. New & updated orthology-based projections of rice pathways to 17 of the 39 completely sequenced plant genomes hosted by Gramene
  • New data

    1. Split gene predictions for 37 plant genomes
    2. ncRNA annotation for Triticum aestivum (bread wheat)
    3. Probes from the Affymetrix barley genome array aligned to Hordeum vulgare (barley)
    4. Zea mays (maize) variation data based on Panzea release 2.7
    5. Sorghum bicolor (sorghum) variation data from Mace et al (2013)
    6. Triticum aestivum (bread wheat) variation data from Axiom, iSelect and KASP array sets
    7. Two transcriptome datasets from diploid einkorn wheat (Triticum monococcum cv DV92 and G3116), generated by Jaiswal's Lab, have been aligned to barley, bread wheat and Triticum urartu genomes using STAR
    8. TriFLDB full-length cDNA sequences aligned to bread wheat genome
    9. Whole genome alignments for bread wheat against barley
  • Updated data

    1. Updated gene-trees across 37 species (Ostreococcus lucimarinus and Oryza longistaminata were not included in gene tree construction in the present release)
    2. Updated gene, sequence and variation BioMarts
    3. Updated GO term and gene name projection from Arabidopsis thaliana to all dicots

Genomes Core

  Species Assembly Gene Annotation
Brassica oleracea GCA_000092065.1 ENA
Leersia perrieri GCA_000325765.3 OGE
Oryza longistaminata v0117-2013Aug OGE
Oryza rufipogon PRJEB4137 OGE
Ostreococcus lucimarinus v2.0 GCA_000092065.1 JGI
Theobroma cacao (cocoa) GCA_000403535.1 ENA
Oryza barthii GCA_000182155.1 OGE Maker (Aug 2013)
Hordeum vulgare (barley) 030312v2 IBSC_1.0
Aegilops tauschii ASM34733v1 GCA_000347335.1
Triticum aestivum IWGSP1 IWGSP1 (MIPS)
Triticum urartu GCA_000347455.1 GCA_000347455.1 (ENA, Apr 2013)
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 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
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Musa acuminata (banana) MA1 2012-08-Cirad
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 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 sativa japonica IRGSP-1.0 MSU 7.0
Oryza sativa indica ASM465v1 2010-07-BGI
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
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

Updated Sorghum bicolor
Triticum aestivum
Zea mays
Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Hordeum vulgare
Oryza glaberrima
Oryza sativa
Vitis vinifera


Gene Trees

  • The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 56,134 GeneTree families were constructed 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

Split gene analysis was done for the 38 fully sequenced plant reference genomes in Gramene release 42. This analysis includes information on 5 new genomes, compared to the last split gene split done in release 41. 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

  1. DNA-DNA alignments between bread wheat and Oryza sativa, bread wheat and Brachypodium distachyon, and barley and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).

  2. RNA-Seq data aligned to bread wheat, as well as to its wild progenitors.

  3. Wheat UniGene clusters sequences aligned to bread wheat, as well as to its wild progenitors.

Protein Annotation, Go, Xref

No updates in this release. Last update done in release 40 (January 2014).


New Plant Gene and Plant Variation Marts

Pathway Release Notes

Plant Reactome

  • A new pathway on auxin signaling in rice has been released.

  • The following amino acid pathways have been revised by incorporating recent literature and genes & compartment re-assignments: arginine biosynthesis I, arginine biosynthesis II, glutamate biosynthesis I, glutamate biosynthesis V, glutamine biosynthesis I, alanine biosynthesis II, alanine biosynthesis III, glutamate biosynthesis IV and lysine biosynthesis VI. Lysine biosynthesis VI is the new featured pathway on the Plant Reactome homepage.

  • In this release we have also implemented orthology-based projections of rice pathways to 17 other species.

Projection Statistics

SpeciesPathwaysReactionsGene Products
Oryza sativa (curated reference)194*583867
Aegilops tauschii159418705
Arabidopsis thaliana167469761
Brachypodium distachyon160456700
Brassica rapa1664641178
Glycine max1674641476
Hordeum vulgare158408586
Medicago truncatula156406635
Musa acuminata162436966
Populus trichocarpa168467996
Prunus persica168468693
Setaria italica166467780
Solanum lycopersicum167465793
Solanum tuberosum164447781
Sorghum bicolor167471759
Triticum aestivum1684701772
Triticum urartu162434658
Zea mays162450834

"Cyc" Pathways

  • No updates on this release
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

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