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toggle section  Version 39 - October 2013

Gramene Release 39 - October 2013

Gramene Database:


Genomes Release Notes

top ]
  • Added complete genome reference sequence for Triticum aestivum (bread wheat).
  • Updated Oryza sativa japonica to the first merged IRGSP v1.0 (MSU7) assembly.
  • Updated Oryza glaberrima variation data.
  • Projected O. sativa variations to the new assembly.
  • Updated peptide comparative genomics.
  • Updated whole genome alignments for O. sativa against all other species.
  • Updated synteny data for O. sativa against all other Liliopsida genomes.
  • Updated synteny data for Zea mays against Sorghum bicolor.
  • Updated probe alignments projected to the new O. sativa assembly.
  • Updated BioMarts.
  • Updated genome browser, database schema and API to Ensembl version 73.

Genomes Core

  Species Assembly Gene Annotation
New
Triticum aestivum IWGSP1 IWGSP1
 
Updated
Oryza sativa japonica IRGSP-1.0 / MSU 7.0 IRGSP-1.0 / MSU 7.0
 
Unchanged
Aegilops tauschii ASM34733v1 GCA_000347335.1
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
Glycine max (soybean) Glyma1.0 Glyma1.1
Hordeum vulgare (barley) 030312v2 IBSC_1.0
Medicago truncatula MedtrA17_3.5 2011-11-EnsemblPlants
Musa acuminata (banana) MA1 2012-08-Cirad
Oryza barthii OGE.2012Jul 2012-10-CSHL
Oryza brachyantha OGEv1.4b OGEv1.4
Oryza glaberrima AGI1.1 (May 2011) 2011-05-AGI
Oryza sativa indica ASM465v1 2010-07-BGI
Oryza punctata Mar 2013 CSHL Mar 2013
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
Solanum tuberosum (potato) 3.0 SolTub_3.0
Sorghum bicolor Sorbi1 2007-12-JGI
Triticum urartu ASM34745v1 GCA_000347455.1
Vitis vinifera IGGP 12x 2012-07-CRIBI
Zea mays (corn) B73_RefGen_v3 5b+
Leersia perrieri (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza glumaepatula (chr3s) 454.pools.2012Feb 2012-04-CSHL
Oryza granulata (chr3s) 454.pools.2012Feb 2012-10-CSHL
Oryza longistaminata (chr3s) OGE.2012Jul 2012-10-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 rufipogon (AA) chr3s 454.pools.1.1 (Jul 2010) CSHL
Oryza rufipogon (AA) FPC OMAP_FPC_2006_JAN

Ensembl Variation


Updated Oryza glaberrima
Oryza sativa
Unchanged Arabidopsis thaliana
Brachypodium sylvaticum
Hordeum vulgare
Sorghum bicolor
Triticum aestivum
Vitis vinifera
Zea mays

Functional Genomics

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

Compara

  • Gene Tree

    • The EnsemblCompara GeneTree database was updated. A total of 40,594 GeneTree families were constructed comprising 791,918 individual genes (910,023 input proteins) from 30 genomes, of which 5 are non-plant outgroups.
    • The OGE Compara tree was not updated. 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 gene model.
  • Potential gene annotation artifacts

  • No new split gene annotations were identified for this release. Last update was done in release 38 (August 2013). For a complete list, see Gramene's FTP site. Summary statistics follow.

    Split genes by species

    SpeciesCount
    Arabidopsis lyrata subsp. lyrata172
    Arabidopsis thaliana34
    Brachypodium distachyon150
    Brassica rapa subsp. pekinensis150
    Chlamydomonas reinhardtii96
    Cyanidioschyzon merolae8
    Glycine max404
    Hordeum vulgare subsp. vulgare56
    Musa acuminata1558
    Oryza barthi1
    Oryza brachyantha334
    Oryza glaberrima436
    Oryza sativa Indica Group730
    Oryza sativa Japonica Group628
    Physcomitrella patens subsp. patens248
    Populus trichocarpa2076
    Selaginella moellendorffii172
    Setaria italica362
    Solanum lycopersicum1138
    Solanum tuberosum648
    Sorghum bicolor1036
    Vitis vinifera876
    Zea mays1160
  • Synteny

    No updates in this release. Last update done in release 36b (March 2013).
  • WGA

    New whole-genome barley alignments to B. distachyon and O. sativa (rice).

Protein Annotation, Go, Xref

No updates in this release. Last updated done in release 36 (December 2012).

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

top ]

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 3.6)

top ]
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 2.1)
ClassCount
Pathways428
Enzymatic Reactions2,132
Transport Reactions106
Polypeptides39,655
Enzymes8,887
Transporters305
Compounds1,453
SorghumCyc Summary (version 1.1)
ClassCount
Pathways302
Enzymatic Reactions1,838
Transport Reactions9
Polypeptides36,347
Enzymes10,636
Transporters269
Compounds1,356


Diversity Release Notes

top ]

Data sets

Unchanged:

    Arabidopsis, B. sylvaticum, H. vulgare, O. glaberiima, O. sativa spp, V. vinifera and Z. mays.

Software

Tassel

No updates in this release. Last update done in release 35 (June 2012). TASSEL 4.0 coming up on Gramene. Meanwhile, available from the TASSEL webpage.

SNP query

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

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 ]

Analysis of the bread wheat genome using whole-genome shotgun sequencing. Brenchley R, Spannagl M, Pfeifer M, Barker GL, D'Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo N, Luo MC, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KF, Edwards KJ, Bevan MW, Hall N. (2012). Nature 491(7426):705-10.


Website

top ]

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.

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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