Release Notes 41 (May 2014)


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

Genomes Release Notes

  • New genomes for Amborella trichopoda, Prunus persica (peach), Oryza glumaepatula, O. meridionalis, and O. nivara.
  • Updated gene models for Triticum aestivum (bread wheat) v2.1, O. barthii, and O. punctata. The Oryza gene models were updated using the OGE Maker pipeline.
  • Updated peptide comparative genomics.
  • Updated split genes for 33 plant reference genomes based on the latest Ensembl Compara data.
  • Whole-genome alignments within T. aestivum, between its component A, B, and D genomes.
  • Calculation of homoeologous genes between the T. aestivum component A, B and D genomes.
  • Whole-genome alignments between A. trichopoda and the two following genomes, Oryza sativa Japonica and Arabidopsis thaliana.
  • Whole-genome alignments between P. persica and each the three following genomes, O. sativa Japonica, A. thaliana, and V. vinifera.
  • Whole-genome alignments between each of the three new rice genomes and O. sativa Japonica, as well as against each other.
  • New variation data for Sorghum bicolor based on the SAP panel (Morris et al, 2013).
  • ESTs alignments against the peach genome using STAR aligner.
  • Wheat ESTs alignment against bread wheat and its wild progenitors, T. urartu, and Aegilops tauschii, using STAR aligner.
  • Updated wheat UniGene alignments against bread wheat and its wild progenitors.
  • Updated biomart databases.
  • Updated genome browser, database schema and API to Ensembl version 75.
  • New orthology-based projections of rice pathways to Arabidopsis and Zea mays.
  • Five newly curated rice pathways in the Plant Reactome.

Genomes Core

  Species Assembly Gene Annotation
Amborella trichopoda GCA_000471905.1 (AMTR1.0) 2014-01-AGD
Prunus persica Prupe1_0 / GCA_000346465.1 Prupe1_0 / Peach v1.0
Oryza meridionalis GCA_000338895.1 OGE Maker (Aug 2013)
Oryza glumaepatula GCA_000576495.1 OGE Maker (Aug 2013)
Oryza nivara GCA_000576065.1 OGE Maker (Aug 2013)
Triticum aestivum IWGSP1 IWGSP1 (MIPS)
Oryza barthii GCA_000182155.1 OGE Maker (Aug 2013)
Oryza punctata GCA_000573905.1 OGE Maker (Aug 2013)
Aegilops tauschii ASM34733v1 GCA_000347335.1
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
Hordeum vulgare (barley) 030312v2 IBSC_1.0
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 sativa japonica IRGSP-1.0 MSU 7.0
Oryza sativa indica ASM465v1 2010-07-BGI
Physcomitrella patens ASM242v1 2011-03-Phypa1.6
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
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+
Leersia perrieri (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza granulata (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza longistaminata (chr3s) OGE.2012Jul 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) chr3s 454.pools.1.1 (Jul 2010) CSHL
Oryza rufipogon (AA) FPC OMAP_FPC_2006_JAN

Ensembl Variation

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


Gene Trees

  • The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 51,270 GeneTree families were constructed comprising 1,094,022 individual genes (1,232,442 input proteins) from 33 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 33 fully sequenced plant reference genomes in Gramene release 41. This analysis includes information on 10 new genomes, compared to the last split gene split done in release 38. For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

Aegilops tauschii 534
Amborella trichopoda739
Arabidopsis lyrata subsp. lyrata81
Arabidopsis thaliana21
Brachypodium distachyon108
Brassica rapa subsp. pekinensis107
Chlamydomonas reinhardtii45
Cyanidioschyzon merolae4
Glycine max254
Hordeum vulgare subsp. vulgare65
Medicago truncatula285
Musa acuminata1134
Oryza barthi147
Oryza brachyantha198
Oryza glaberrima357
Oryza glumaepatula206
Oryza meridionalis125
Oryza nivara117
Oryza punctata151
Oryza sativa Indica Group509
Oryza sativa Japonica Group398
Physcomitrella patens subsp. patens173
Populus trichocarpa1196
Prunus persica276
Selaginella moellendorffii70
Setaria italica171
Solanum lycopersicum784
Solanum tuberosum412
Sorghum bicolor607
Triticum aestivum772
Triticum urartu447
Vitis vinifera440
Zea mays564


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

  • In this release we have implemented orthology-based projections of rice pathways to Arabidopsis and Zea mays.
  • Five new rice pathways (listed below) have been added to the Plant Reactome.
ClassPathway name
Hormonesstrigolactone biosynthesis
Amines and Polyaminesallantoin degradation I
Inorganic Nutrients Metabolismsulfate activation for sulfonation
thiosulfate disproportionation III (rhodanese)
ammonia assimilation cycle

"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