Release Notes 47 (August 2015)

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Website

See also legacy data in the Gramene's Archive.

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Genomes Release Notes

  • No new nor updated genomic data since build 46 (June 2015).

Genomes Core

  Species Assembly Gene Annotation
Unchanged
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 TAIR10
Brachypodium distachyon Brachy1.0 Barchy1.2
Brassica oleracea GCA_000092065.1 ENA
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
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 Sorbi1 2007-12-JGI
Theobroma cacao (cocoa) GCA_000403535.1 ENA
Triticum aestivum IWGSP1 IWGSP1 (MIPS)
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+

Ensembl Variation

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

Compara

Gene Trees

  • The EnsemblCompara GeneTree database was not updated in this release. Last update was done in release 46 (June 2015).

  • The OGE Compara tree was not updated at oge.gramene.org. 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 predictions were not updated in this release. Last update was done in release 45 (April 2015). See summary statistics in release 45 and Gramene's FTP site.

Synteny

No new synteny data was generated for this release. Last update was done in release 39 (October 2013).

WGA and other nucleotide alignments

Whole genome alignments were not updated in this release. Last update was done in release 46 (June 2015).

Protein Annotation, Go, Xref

UniProtKB cross-references were not updated in this release. Last update was done in release 46 (June 2015).

Mart

No new data in the Plant Gene and Plant Variation Marts in this release. Data was last updated in release 46 (June 2015).

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Pathway Release Notes

"Cyc" Pathways

  • BioCyc-based pathway databases on Pathway Tools ver. 18.0 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.

Plant Reactome

The Plant Reactome web site (http://plantreactome.gramene.org) is now running version 3 of the Reactome software platform. Notable new features include:

  • Data analysis tools

    • Diagram overlay visualization of gene lists, Uniprot IDs, 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

  • Redesigned Pathway Browser user interface

  • Updated web site design built on Wordpress

Projection Statistics

The latest (projection statistics)[http://plantreactome.gramene.org/stats.html] are available from the Plant Reactome website.

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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.

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Infrastructure

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 -hgramenedb.gramene.org -pgramene

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