Release Notes 46 (June 2015)

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Website

See also legacy data in the Gramene's Archive.

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Genomes Release Notes

  • Updated genomes

    Solanum lycopersicum assembly updated to v2.50.

  • New data

    • New Wheat HapMap variation data and updated genotypes from CerealsDB
    • New probe data for barley

  • Updated data

    1. Updated to Ensembl 80 software
    2. Updated gene, sequence and variation BioMarts
    3. Updated whole genome alignments: S. lycopersicum vs Arabidopsis thaliana, Oryza sativa Japonica, and Vitis vinifera
    4. Peptide comparative genomics data across all species
    5. Updated cross-references to UniProtKB across all species

Genomes Core

  Species Assembly Gene Annotation
Updated
Solanum lycopersicum (tomato) SL2.50 ITAG2.3
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 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+
Oryza granulata (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza minuta (BB) chr3s BAC.Sanger.1.1 (May 2011) CSHL v3.1
Oryza minuta (CC) chr3s BAC.Sanger.1.1 (May 2011) CSHL v3.1
Oryza officinallis (CC) chr3s BAC.Sanger.1.1 (May 2011) CSHL v3.1
Oryza rufipogon (AA) FPC OMAP_FPC_2006_JAN

Ensembl Variation

New & Updated/th> Triticum aestivum
Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Oryza glaberrima
Oryza sativa
Solanum lycopersicum
Sorghum bicolor
Vitis vinifera
Zea mays

Compara

Gene Trees

  • The EnsemblCompara GeneTree database was updated. The new database includes a total of 56,387 GeneTree families were constructed comprising 1,280,368 individual genes (1,432,406 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

For a complete list, see Gramene's FTP site. Summary statistics follow.

Split genes by species

SpeciesCount
Aegilops tauschii 740
Amborella trichopoda994
Arabidopsis lyrata subsp. lyrata180
Arabidopsis thaliana37
Brachypodium distachyon158
Brassica oleracea var. oleracea911
Brassica rapa subsp. pekinensis151
Chlamydomonas reinhardtii141
Cyanidioschyzon merolae8
Glycine max390
Hordeum vulgare subsp. vulgare108
Leersia_perrieri189
Medicago truncatula394
Musa acuminata1624
Oryza barthi338
Oryza brachyantha302
Oryza glaberrima518
Oryza glumaepatula394
Oryza longistaminata291
Oryza meridionalis272
Oryza nivara310
Oryza punctata282
Oryza rufipogon300
Oryza sativa Indica Group796
Oryza sativa Japonica Group636
Ostreococcus_lucimarinus_CCE990126
Physcomitrella patens subsp. patens276
Populus trichocarpa1651
Prunus persica448
Selaginella moellendorffii215
Setaria italica332
Solanum lycopersicum1216
Solanum tuberosum653
Sorghum bicolor953
Theobroma cacao113
Triticum aestivum1234
Triticum urartu674
Vitis vinifera725
Zea mays844

Synteny

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

WGA and other nucleotide alignments

Updated whole genome alignments for S. lycopersicum vs A. thaliana, O. sativa Japonica, and V. vinifera.

Protein Annotation, Go, Xref

UniProtKB cross-references were updated across all species.

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. 18.0 are available from a virtual server hosted at iPlant.

Summary tables for the Cyc pathway databases created by Gramene.

RiceCyc Summary (version 3.3)
ClassCount
Pathways306
Enzymatic Reactions2,103
Transport Reactions87
Polypeptides47894
Enzymes6,040
Transporters603
Compounds1543
BrachyCyc Summary (version 2.0)
ClassCount
Pathways320
Enzymatic Reactions2,057
Transport Reactions87
Polypeptides26,633
Enzymes7,723
Transporters950
Compounds1641
MaizeCyc Summary (version 2.2)
ClassCount
Pathways424
Enzymatic Reactions2,132
Transport Reactions106
Polypeptides39,655
Enzymes8,887
Transporters305
Compounds1,453
SorghumCyc Summary (version 1.1)
ClassCount
Pathways292
Enzymatic Reactions1,838
Transport Reactions9
Polypeptides36,347
Enzymes10,636
Transporters269
Compounds1,356

Plant Reactome

Plant Reactome pathways for 33 species, including maize, wheat, soybean, Arabidopsis, banana, Brassicas, and numerous wild species related to rice. These pathways were annotated based on orthology projections from curated pathways in rice.

Projection Statistics

SpeciesPathwaysReactionsGene Products
Oryza sativa japonica (curated reference)2381056935
Aegilops tauschii177461731
Arabidopsis thaliana184493832
Brachypodium distachyon181507745
Brassica rapa1834921283
Glycine max1814831494
Hordeum vulgare177448627
Leersia perrieri186506731
Medicago truncatula171410643
Musa acuminata1794771019
Oryza australiensis174444734
Oryza barthii186517769
Oryza brachyantha186509741
Oryza glaberrima188513769
Oryza glumaepatula187520770
Oryza granulata175450789
Oryza kasalath123205165
Oryza longistaminata179475622
Oryza meridionalis180475682
Oryza minuta172447556
Oryza nivara185521773
Oryza officinalis178434474
Oryza punctata184508765
Oryza rufipogon186514779
Oryza sativa Indica189534836
Populus trichocarpa1824841045
Prunus persica184494713
Setaria italica185511833
Solanum lycopersicum183491873
Solanum tuberosum180469844
Sorghum bicolor186514802
Triticum aestivum1855121841
Triticum urartu180470672
Zea mays184506950
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Ontologies Release Notes

No updates in this release. Last update done in release 31 (May 2010). Below is a summary of the ontologies data.

Prefix Term Type Count
EO plant_environment_ontology 500
GO biological_process 24767
GO cellular_component 3194
GO molecular_function 10376
GRO cereal_plant_growth_stage 235
GR_tax gramene_taxonomy 58550
PO plant_anatomy 1295
PO plant_structure_development_stage 324
TO plant_trait_ontology 1290

See also the detailed Ontology Module statistics report (build 39, Oct. 2013).

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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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