Release Notes 54 (July 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



  Species Assembly Gene Annotation
Hordeum vulgare (barley)


  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
Sorghum bicolor V2 20016-08-JGI    
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 Ar 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.



Arabidopsis thaliana

Brachypodium sylvaticum
Hordeum vulgare
Oryza glaberrima
Oryza glumaepatula
Oryza sativa Indica
Oryza sativa Japonica
Sorghum bicolor
Solanum lycopersicum
Triticum aestivum
Vitis vinifera
Zea mays


Gene Trees

  • The EnsemblCompara GeneTree database was updated to include updated barley, sorghum, corn and wheat. A total of 62,367 GeneTree families were constructed comprising 1,469,948 individual genes (1,631,582 input proteins) from 44 plant genomes (and 5 non-plant outgroups).

Putative Split Genes

  • No updates in this release. Last update done in release 53 (May 2017). The latest split gene predictions are available in the 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 has released several new data files, available for download, that articulate the relationships between gene products, pathways, and reactions, and external reference sources such as ChEBI, Ensembl, NCBI, and UniProt. Both identifiers and web links within the site are available. Visit the Download section of the Plant Reactome web site to learn more.

* Pathway Projection Statistics and Status

  • Last update release 52 (November 2016). See pathway 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 offers 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 54_89 is set as version 36_89 at Ensembl.