Release Notes 49 (January 2016)

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Website

See also legacy data in the Gramene's Archive.

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Genomes Release Notes

  • New data

    • New EMS-derived mutation data for Sorghum bicolor (see for example, a premature STOP codon introduced in Sb03g028120)
    • New variation data for Oryza glumaepatula

  • Updated data

    1. Updated Oryza longistaminata assembly and annotations
    2. Updated protein domain information based on latest InterProScan
    3. Updated Compara gene trees
    4. Updated BioMarts
    5. Updated to Ensembl 83 software

  • New features

    • SIFT scores added for barley variation (see example; also available in the Variant Effect Predictor)

Genomes Core

  Species Assembly Gene Annotation
Updated
Oryza longistaminata v0117-2013Aug OGE
  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 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

New Sorghum bicolor (EMS-induced mutations)
Oryza glumaepatula

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

Compara

Gene Trees

  • The EnsemblCompara GeneTree database was updated. The new database includes a total of 55,519 GeneTree families were constructed comprising 1,280,352 individual genes (1,432,395 input proteins) from 39 plant genomes (and 5 non-plant outgroups).

  • 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 48 (November 2015), see . See summary statistics in build 48 release notes 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

No new alignments for this release. Last update was done in release 48 (November 2015).

Protein Annotation, Go, Xref

Protein domain information was updated based on the latest InterProScan analysis.

Mart

New Plant Gene and Plant Variation Marts

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Pathway Release Notes

"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.

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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

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 -hmysql-eg-publicsql.ebi.ac.uk -P4157 -uanonymous

Please note that the versioning scheme used at this public database differs from ours; Gramene's release 49_83 is set as version 30_83.

Gramene currently a legacy public, read-only MySQL server for release 40 of our databases. You can connect to the host "gramenedb.gramene.org" with the password "gramene," e.g.:

mysql -hgramenedb.gramene.org -pgramene

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