Release Notes 48b (November 2015)


See also legacy data in the Gramene's Archive.

Genomes Release Notes

Same as in release #48

Pathway Release Notes

Plant Reactome

The Plant Reactome database has expanded gene homology-based pathway projections to 58 plant species (previous Gramene release 47 included pathway projections for 33 plant species). Notable newly projected species include wild ancestors of peanut, common bean (Phaseolus), chickpea, pigeonpea, cacao, Brassica oleracea, capsicum pepper, sweet orange, coffee, cotton, grape, date palm, Triticum turgidum (wheat BB), basal angiosperm Amborella, the gymnosperms Norway spruce and Loblolly pine, lower plants Physcomitrella and Selaginella, and green algae Chlamydomonas. In addition, we have added two new hormone signaling pathways and revised three previously curated pathways. Please take a note of the following pathway statistics and status table for more details.

The Plant Reactome database continues to provide the following features:

  • Tutorial for users via our YouTube Channel
  • Data analysis tools
    • Diagram overlay visualization of gene lists, Uniprot IDs (O. sativa japonica only), compound identifiers, and/or -omics expression data
    • Inter-species pathway comparison
  • Advanced search features built on the Apache Solr platform
  • RESTful API for programmatic access to Plant Reactome data

  • Newly curated hormone signaling pathways

    • O. sativa Salicylic acid signaling
    • O. sativa Jasmonic acid signaling
  • Updated pathways

    • O. sativa Salicylic acid biosynthesis
    • O. sativa Brassinosteroid signaling
    • O. sativa Strigolactone signaling
  • Pathway Projection Statistics and Status (update/new)


  • *data from sequenced transcriptomes
  • ^ projections currently exclude cell-cycle pathways and annotations
  • Planteome Inparanoid data was kindly provided by the Planteome project
  • When available the outgoing links from gene product IDs mapped to reactions are always hyperlinked to respective entries in collaborator databases/online resources
  • The latest projection statistics are also available from the Plant Reactome website.
SpeciesPathwaysReactionsGene ProductsSequence sourceOutgoing LinkHomology methodStatus
Oryza sativa japonica241^1069955Ensembl GrameneUniprotCurated ReferenceUpdated
Aegilops tauschii178458731Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Amborella trichopoda185483554Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Arabidopsis lyrata183485826Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Arabidopsis thaliana183489818Ensembl GrameneTAIREnsembl ComparaUpdated
Arachis duranensis191512738PeanutBasePeanutBasePlanteome InparanoidNew
Arachis ipaensis189516748PeanutBasePeanutBasePlanteome InparanoidNew
Brachypodium distachyon182505738Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Brassica oleracea1824761231Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Brassica rapa1824851242Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Cajanus cajan192519942LegumeInfoLegumeInfoPlanteome InparanoidNew
Capsicum annuum193505937PMID: 24441736N/APlanteome InparanoidNew
Chlamydomonas reinhardtii138287224Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Cicer arietinum1935221091NCBINCBIPlanteome InparanoidNew
Citrus sinensis1935221920PhytozomePhytozomePlanteome InparanoidNew
Coffea canephora193524873PMID:25190796N/APlanteome InparanoidNew
Cyanidioschyzon merolae116214157Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Fragaria vesca193508846PhytozomePhytozomePlanteome InparanoidNew
Glycine max1834811511Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Gossypium raimondii1925261305PhytozomePhytozomePlanteome InparanoidNew
Hordeum vulgare180450630Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Leersia perrieri189503718Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Malus domestica1905041667PMID: 20802477PhytozomePlanteome InparanoidNew
Medicago trunculata184479949Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Musa acuminata182472958Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza australiensis *1894881357OMAP/OGEN/APlanteome InparanoidUpdated
Oryza barthii189514749Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza brachyantha189505708Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza glaberrima191514762Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza glumaepatula191516758Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza granulata *1915042372OMAP/OGEN/APlanteome InparanoidUpdated
Oryza kasalath154247287PMID: 24578372N/APlanteome InparanoidUpdated
Oryza longistaminata *1935121146OMAP/OGEN/APlanteome InparanoidUpdated
Oryza meridionalis183468652Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza minuta *1925101594OMAP/OGEN/APlanteome InparanoidUpdated
Oryza nivara187522762Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza officinalis *1905181363OMAP/OGEN/APlanteome InparanoidUpdated
Oryza punctata187513754Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza rufipogon189522770Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Oryza sativa indica192531814Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Ostreococcus lucimarinus129272214Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Phaseolus vulgaris194528909PhytozomePhytozomePlanteome InparanoidNew
Phoenix dactylifera187493860PMID: 23917264N/APlanteome InparanoidNew
Physcomitrella patens171434829Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Picea abies1874741067CongenieCongeniePlanteome InparanoidUpdated
Pinus taeda1764301046TreeBaseN/APlanteome InparanoidUpdated
Populus trichocarpa1844891030Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Prunus persica184488713Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Selaginella moellendorffii1774601031Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Setaria italica187509826Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Solanum lycopersicum186487860Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Solanum tuberosum183467828Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Sorghum bicolor188514791Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Theobroma cacao187491689Ensembl GrameneEnsembl GrameneEnsembl ComparaNew
Triticum aestivum1885111862Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Triticum turgidum *1925222268PMID: 23800085N/APlanteome InparanoidNew
Triticum urartu183466664Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Vitis vinifera180476732Ensembl GrameneEnsembl GrameneEnsembl ComparaUpdated
Zea mays186506925Ensembl GrameneMaizeGDBEnsembl ComparaUpdated

"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