Release Notes 53 (May 2017)

Table of Contents


In this release we have moved the gramene homepage to our integrated search interface. Blog content and other static pages have been moved to so they can be displayed within the new interface.

See also legacy data in Gramene's Archive.

#Genomes Release Notes

  • Updated genomes
  • New data
  • Updated data
    • Updated genebuild (including new gene descriptions) for Zea mays (B73 maize RefGen_V4)
    • Reincorporated Japonica rice SSR/RFLP and QTLs from Gramene's archives remapped to IRGSPv1
    • Updated protein features from InterPro
    • Updated peptide comparative genomics
    • Updated gene and variation BioMarts
  • Updated software



  Species Assembly Gene Annotation
Sorghum bicolor V2 20016-08-JGI    
Zea mays (corn) B73_RefGen_v4 2017-CSHL-MAKER
  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 AraPort11    
Beta vulgaris RefBeet-1.2.2 ENA
Brachypodium distachyon Brachy1.0 Barchy1.2
Brassica napus AST_PRJEB5043_v1 ENA
Brassica oleracea GCA_000092065.1 ENA
Brassica rapa IVFCAASv1 bra_v1.01_SP2010_01
Chlamydomonas reinhardtii v3.0 2007-11-ENA
Chondrus crispus ASM35022v2 ENA
Cyanidioschyzon merolae 2008-11-ENA ASM9120v1
Galdieria sulphuraria ASM34128v1 ENA
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
Theobroma cacao (cocoa) GCA_000403535.1 ENA
Trifolium pratense Trpr TGAC
Triticum aestivum TGACv1 2014-07-PGSBv2.2
Triticum urartu GCA_000347455.1 GCA_000347455.1 (ENA, Apr 2013)
Vitis vinifera IGGP 12x 2012-07-CRIBI
Zea mays (corn) B73_RefGen_v4 MAKER-CSHL


Genetic and Structural Variation

New and updated genetic variation data for Japonica rice was incorporated to the Oryza sativa Japonica genome browser. Legacy rice SSR/RFLP markers and QTLs from Gramene's archives, as well as QTLs from the Q-TARO database were remapped to IRGSPv1 coordinates by the KeyGene coorporation.



Oryza sativa Japonica

Triticum aestivum

Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Hordeum vulgare
Oryza glaberrima
Oryza glumaepatula
Oryza sativa Indica
Sorghum bicolor
Solanum lycopersicum
Vitis vinifera
Zea mays


Gene Trees

  • The EnsemblCompara GeneTree database was updated to include updated barley, sorghum, corn and wheat. A total of 61,696 GeneTree families were constructed comprising 1,457,923 individual genes (1,618,436 input proteins) from 44 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

  • Split gene predictions were updated in this release and are available from Gramene's FTP site.


  • No updates in this release. Last update done in release 52 (November 2016).

WGA and other nucleotide alignments

  • No updates in this release. Last update done in release 52 (November 2016).

Protein Annotation, Go, Xref Protein domain information was updated based on the latest InterProScan analysis.


# Pathways

Plant Reactome software platform

The Plant Reactome underwent a major software, user interface and functionality upgrade: 

  • Upgraded to the Reactome v3.3 platform, which includes a new Neo4j graph database and a new Fireworks hierarchical graph display of pathways
  • Improved visualization of uploaded Omics data, capabilities to import gene-gene interaction data from external resources for overlaying on pathway diagram and including them in analysis, and comparative pathway analysis between the reference and projected species.
  • Supports display of gene expression profiles in the context of pathways accessed remotely from the EMBL-EBI gene expression ATLAS.
  • Added ContentService and AnalysisService data APIs that allow direct RESTful access to Plant Reactome data.
  • Implemented DiagramJs and FireworksJs graphical widget APIs for users to embed interactive pathway navigation in their web sites.
  • Implemented a revised Solr Search data index and search results layout.
  • All data objects carry stable IDs for cross-referencing.
  • Plant Reactome data and diagrams are now integrated with Gramene’s new search interface mentioned above.

The Plant Reactome database was built in collaboration with the Human Reactome project.

Pathway Curation

  • Revision made to set the top-level pathways as Cellular Processes, Circadian Rhythm, Metabolism & Regulation, Response to Stress, and Inflorescence Development (for Fireworks utility).

Pathway Projection Statistics and Status

  • Last update release 52 (November 2016). See release 52 notes for a table of pathway projection counts, data source and methods.

"Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 19.0 are available from a virtual server hosted at CyVerse. Summary tables for the Cyc pathway databases created by Gramene is available 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.

# Infrastructure

Web Services: Gramene's web services page documents many ways to directly connect to and analyze our databases.

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 53_88 is set as version 35_88.

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