Release Notes 40 (Jan 2014)


You'll notice we have a new look. You can find all the old stuff at Gramene's Archive.

Genomes Release Notes

  • Updated gene models for Oryza sativa japonica from RAP-DB.
  • Gene models for Triticum aestivum (bread wheat) chromosome survey sequences from MIPS.
  • DNA-DNA alignments between bread wheat and Oryza sativa, as well as Brachypodium distachyon.
  • DNA-DNA alignments between Hordeum vulgare (barley) and the wild wheat progenitors (Triticum urartu and Aegilops tauschii).
  • Additional RNA-Seq data were aligned to bread wheat as well as to its wild progenitors.
  • Wheat UniGene clusters sequences were also aligned to bread wheat as well as to its wild progenitors.
  • Updated gene-trees to include bread wheat gene models.
  • Updated (TREP) repeat analysis for wheat and barley genomes.
  • Updated functional domain (InterPro) and ontology (InterPro2GO) annotation.
  • Updated biomart databases.
  • Updated genome browser, database schema and API to Ensembl version 74.

Genomes Core

  Species Assembly Gene Annotation
Oryza sativa japonica IRGSP-1.0 / MSU 7.0 IRGSP-1.0 / MSU 7.0
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 barthii OGE.2012Jul 2012-10-CSHL
Oryza brachyantha OGEv1.4b OGEv1.4
Oryza glaberrima AGI1.1 (May 2011) 2011-05-AGI
Oryza sativa indica ASM465v1 2010-07-BGI
Oryza punctata Mar 2013 CSHL Mar 2013
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 aestivum IWGSP1 IWGSP1
Triticum urartu ASM34745v1 GCA_000347455.1
Vitis vinifera IGGP 12x 2012-07-CRIBI
Zea mays (corn) B73_RefGen_v3 5b+
Leersia perrieri (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza glumaepatula (chr3s) 454.pools.2012Feb 2012-04-CSHL
Oryza granulata (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza longistaminata (chr3s) OGE.2012Jul 2012-10-CSHL
Oryza meridionalis (chr3s) 454.pools.2012Feb 2012-04-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 nivara (AA) chr3s 454.pools.1.1 (Jul 2010) CSHL
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

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


Gene Trees

  • The EnsemblCompara GeneTree database was updated to include bread wheat gene models. A total of 43,812 GeneTree families were constructed comprising 894,376 individual genes (1,017,959 input proteins) from 31 genomes, of which 5 are 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

No new split gene annotations were identified for this release. Last update was done in release 38 (August 2013). For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

Arabidopsis lyrata subsp. lyrata172
Arabidopsis thaliana34
Brachypodium distachyon150
Brassica rapa subsp. pekinensis150
Chlamydomonas reinhardtii96
Cyanidioschyzon merolae8
Glycine max404
Hordeum vulgare subsp. vulgare56
Musa acuminata1558
Oryza barthi1
Oryza brachyantha334
Oryza glaberrima436
Oryza sativa Indica Group730
Oryza sativa Japonica Group628
Physcomitrella patens subsp. patens248
Populus trichocarpa2076
Selaginella moellendorffii172
Setaria italica362
Solanum lycopersicum1138
Solanum tuberosum648
Sorghum bicolor1036
Vitis vinifera876
Zea mays1160


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

Updated functional domain (InterPro) and ontology (InterPro2GO) annotation.


New Plant Gene and Plant Variation Marts


"Cyc" Pathways Release Notes (version 3.7)

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

MaizeCyc was updated to Version 2.2 with 37 updated GO annotations, evidence codes and publication references.

NOTE: BioPAX level 2 and 3 generated with the pathway tools software have a discrepant number of pathways. For more details, please see the note in the MaizeCyc 2.2 FTP directory.

Plant Reactome

32 new rice pathways have been added to the Plant Reactome, including the signaling pathway for the plant hormone ethylene. 8 pathways have been updated.

Modified pathways

ABA biosynthesis and signalling pathway
Calvin cycle
TCA cycle
oleoresin sesquiterpene volatiles biosynthesis
oleoresin monoterpene volatiles biosynthesis
carotenoid biosynthesis
monoterpene biosynthesis
polyisoprenoid biosynthesis

New pathways

Ethylene biosynthesis and signaling
Oryzalexin S biosynthesis
S-adenosyl-L-methionine cycle
S-methylmethionine cycle
UDP-L-arabinose biosynthesis I
UDP-L-arabinose biosynthesis II
alanine biosynthesis II
alanine biosynthesis III
arginine biosynthesis I
arginine biosynthesis II
aspartate biosynthesis I
beta-alanine biosynthesis I
beta-alanine biosynthesis III
cysteine biosynthesis I
fructan biosynthesis
fructan degradation
galactose degradation II
geranylgeranyl diphosphate biosynthesis II
histidine biosynthesis I
methionine biosynthesis II
methionine salvage pathway
mevalonate pathway
momilactone biosynthesis
oryzalexin A-F biosynthesis
phytyl-pp biosynthesis
putrescine biosynthesis I
putrescine biosynthesis II
putrescine biosynthesis III
spermidine biosynthesis
spermine biosynthesis
sucrose biosynthesis
tetrapyrrole biosynthesis I

Ontologies Release Notes

No updates in this release (except for updated InterPro2GO annotations under 'Protein Annotation, Go, Xref' section above). 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