Gramene Release 36 - December 2012

Gramene Database:

Genomes Release Notes

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Genomes Core

  Species Assembly Gene Annotation
New
Hordeum vulgare (barley) 030312v2 IBSC_1.0
Musa acuminata (banana) MA1 2012-08-Cirad
Solanum tuberosum (potato) 3.0 SolTub_3.0
Oryza barthii (WGS) OGE.2012Jul 2012-10-CSHL
Leersia perrieri (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza granulata (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza longistaminata (chr3s) OGE.2012Jul 2012-10-CSHL
 
Updated
Glycine max (soybean) Glyma1.0 Glyma1.1
Vitis vinifera IGGP 12x 2012-07-CRIBI
 
Unchanged
Arabidopsis lyrata Araly1.0 Araly1.0
Arabidopsis thaliana TAIR10 TAIR10
Brachypodium distachyon Brachy1.0 Barchy1.2
Brassica rapa IVFCAASv1 bra_v1.01_SP2010_01
Chlamydomonas reinhardtii v3.0 2007-11-ENA
Cyanidioschyzon merolae 2008-11-ENA ASM9120v1
Oryza brachyantha OGEv1.4b OGEv1.4
Oryza glaberrima AGI1.1 (May 2011) 2011-05-AGI
Oryza sativa indica ASM465v1 2010-07-BGI
Oryza sativa japonica MSU 6.0 MSU 6.0
Physcomitrella patens ASM242v1 2011-03-Phypa1.6
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) SL2.40 ITAG2.3
Sorghum bicolor Sorbi1 2007-12-JGI
Zea mays (corn) B73 RefGen AGPv2 5a.53
Oryza barthii (AA) chr3s 454.pools.1.1 (Mar 2009) CSHL
Oryza brachyantha (FF) chr3s 454.pools.1.1 (Jul 2010) CSHL
Oryza glumaepatula (chr3s) 454.pools.2012Feb 2012-04-CSHL
Oryza meridionalis (chr3s) 454.pools.2012Feb 2012-04-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 nivara (AA) chr3s 454.pools.1.1 (Jul 2010) CSHL
Oryza officinallis (CC) chr3s BAC.Sanger.1.1 (May 2011) CSHL v3.1
Oryza punctata (BB) chr3s BAC.Sanger.1.1 (May 2011) CSHL v2.1
Oryza rufipogon (AA) chr3s 454.pools.1.1 (Jul 2010) CSHL
Oryza rufipogon (AA) FPC OMAP_FPC_2006_JAN

Ensembl Variation

Updated Sorghum bicolor
Zea mays

Unchanged Arabidopsis thaliana
Oryza glaberrima
Oryza sativa
Triticum aestivum
Vitis vinifera

Functional Genomics

No updates in this release. Last update done in release 34 (October 2011).

Compara

Protein Annotation, Go, Xref

  • Protein feature annotations were updated using InterProScan on the following genomes:

    • Mart

    Maps and Markers Release Notes

    [     top ] No updates in this release. Last updated done in release 33 (April 2011). Gramene's comparative maps database hosts 215 map sets from genetic, physical, bin, sequence, cytogenetic, and QTL studies.

    See also the detailed Map Module statistics report.

    Marker breakdown by type

    Marker Type Count
    AFLP 8,149
    Breakpoint Interval 303
    Centromere 57
    Chromosomal Segment 10
    Clone 3,549,765
    Cytological Structure 8
    DArT 1,158
    Deletion 333
    EST 18,974,596
    EST Cluster 4,633,006/td>
    FISH Probe 37
    FPC 17,479
    Gene 8,916
    Gene Candidate 17
    Gene Family 3
    Gene Prediction 354,564
    Gene Primer 19
    Genomic DNA 1,827,315
    GSS 9,459,811
    Insertion 308
    ISBP 691
    Lapsed Locus 4
    Maize Bin 114
    Microarray Probe 260,656
    mRNA 953,688
    Oligo 2,396,466
    OVERGO 23,921
    Point 332
    Primer 76,036
    Probed Site 5,220
    Pseudogene 1
    QTL 11,625
    RAPD 175
    Restriction Fragment 5
    RFLP 18,754
    SNP 2,942
    SSR 24,389
    STS 3,290
    Telomere 20
    Transposable Element 4
    Undefined 1,391

    Marker breakdown by species

    SpeciesCount
    Hordeum713,300
    Zea7,604,538
    Avena71,594
    Oryza6,739,198
    Secale15,058
    Sorghum1,513,436
    Saccharum44,2434
    Triticum1,432,375

    See also the detailed Marker Module statistics report.

    Proteins Release Notes

     [ top ] No updates in this release. Last update done in release 31 (May 2010).

    The Gramene protein database provides a heterogeneous set of functional annotations from sources such as SWISS-PROT and TrEMBL, and which include Pfam, Prosite, and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO), Trait Ontology (TO) and Environment Ontology (EO) are used to attribute functional characteristics.

    See also the detailed Protein Module statistics report.

    Ontologies Release Notes

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    Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. 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.

    Genes and Alleles Release Notes

     [ top ] No updates in this release. Last update done in release 31 (May 2010).

    A more detailed genes database statistics report can be found here.

    QTL Release Notes

     [ top ] No updates in this release. Last update done in release 27 (April 2008).

    A more detailed QTL database statistics report can be found here.

    Pathways Release Notes (version 3.5)

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    Pathway databases are available dynamically via the Gramene's pathway server and those created and maintained by Gramene are also available for bulk download from Gramene's FTP site.

    MaizeCyc has been updated to version 2.0.2

    RiceCyc Summary (version 3.3)
    ClassCount
    Pathways316
    Enzymatic Reactions2,103
    Transport Reactions87
    Polypeptides47,894
    Enzymes6,040
    Transporters603
    Compounds1,543
    BrachyCyc Summary (version 2.0)
    ClassCount
    Pathways327
    Enzymatic Reactions2,057
    Transport Reactions87
    Polypeptides26,633
    Enzymes7,723
    Transporters950
    Compounds1,641
    MaizeCyc Summary (version 2.0.2)
    ClassCount
    Pathways392
    Enzymatic Reactions2,110
    Transport Reactions68
    Polypeptides39,655
    Enzymes8,889
    Transporters291
    Compounds1,468
    SorghumCyc Summary (version 1.1)
    ClassCount
    Pathways302
    Enzymatic Reactions1,838
    Transport Reactions9
    Polypeptides36,347
    Enzymes10,636
    Transporters269
    Compounds1,356

    Diversity Release Notes

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    Data sets

    New:

    Updated:

    Unchanged:

    Software

    Tassel

    No updates in this release. Last update done in release 35 (June 2012).

    SNP query

    No updates in this release. Last update done in release 34 (October 2011). See also the TASSEL webpage.

    Association Viewer

    Explore Atwell GWAS data in our Association Viewer (beta).

    Click here for database summary.

    Germplasm

     [ top ] No updates in this release. Last update done in release 34 (October 2011).

    Literature

     [ top ] New papers by Wurtzel et al.

    Website

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    Distributed Annotation System

    Gramene provides a DAS server for our own markers and sequences database as well as our Ensembl databases. These can use by the Ensembl genome browser as well as outside applications with a need to display sequences annotations on our various genome assemblies. Substantial improvements to the architecture should improve performance and usability considerably.

    Our DAS resources make use of FastBit for the retrieval engine. We offer DAS tracks for sixteen species. See our DAS sources.

    Diversity via GDPC/TASSEL

    The TASSEL program via Genomic Diversity and Phenotype Connection (GDPC) can connect to Gramene's genetic diversity databases for rice, maize, and arabidopsis for detailed analysis by the user.

    Web Services

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

    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