Release Notes 44 (January 2015)

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Website

See also legacy data in the Gramene's Archive.

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Genomes Release Notes

  • New assembly for bread wheat

    1. A new chromosome-scale pseudomolecule assembly using existing IWGSC CSS contigs incorporating POPSEQ data from IPK and processed by TGAC.
    2. New 3B chromosome and gene-model annotations from the IWGSC.
    3. All sequence features, including the MIPS gene set v2.2, and sequence alignments, were projected to the new pseudomolecule assembly.

  • New marker and variation data for barley

    1. New POPSEQ marker and variation data from IPK.
    2. New variation identifiers from the transPLANT variation archive.

  • New & updated pathways (Cyc Pathway DBs & Plant Reactome)

    1. Cyc databases were moved to a website powered by the iPlant collaborative. The Pathway tools software was updated to version 18.0 and Cyc databases were updated if a newer version was available.
    2. Plant Reactome pathways for 33 new species based on orthology projections from curated pathways in rice.

  • New data

    1. New marker data from KeyGene for Brassica rapa.
    2. New whole genome alignment data for B. oleracea against B. rapa.

  • Updated data

    1. Updated to Ensembl 78 software.
    2. Updated gene, sequence and variation BioMarts.

Genomes Core

  Species Assembly Gene Annotation
Updated
Triticum aestivum IWGSP1 IWGSP1 (MIPS)
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) SL2.40 ITAG2.3
Solanum tuberosum (potato) 3.0 SolTub_3.0
Sorghum bicolor Sorbi1 2007-12-JGI
Theobroma cacao (cocoa) GCA_000403535.1 ENA
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 Hordeum vulgare
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 updated. The new database includes a total of 56,107 GeneTree families comprising 1,243,311 individual genes (1,394,771 input proteins) from 38 plant genomes (and 5 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 genome assembly.

Potential gene annotation artifacts

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

Split genes by species

These predictions were last generated for Gramene build 42 (September 2014).

SpeciesCount
Aegilops tauschii 721
Amborella trichopoda980
Arabidopsis lyrata subsp. lyrata183
Arabidopsis thaliana39
Brachypodium distachyon145
Brassica oleracea var. oleracea909
Brassica rapa subsp. pekinensis151
Chlamydomonas reinhardtii137
Cyanidioschyzon merolae28
Glycine max384
Hordeum vulgare subsp. vulgare121
Medicago truncatula496
Musa acuminata1583
Oryza barthi341
Oryza brachyantha316
Oryza glaberrima571
Oryza glumaepatula372
Oryza meridionalis267
Oryza nivara300
Oryza punctata240
Oryza rufipogon287
Oryza sativa Indica Group833
Oryza sativa Japonica Group702
Physcomitrella patens subsp. patens281
Populus trichocarpa1628
Prunus persica423
Selaginella moellendorffii227
Setaria italica323
Solanum lycopersicum1188
Solanum tuberosum632
Sorghum bicolor949
Theobroma cacao103
Triticum aestivum1074
Triticum urartu665
Vitis vinifera695
Zea mays838

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 updates in this release. Last update done in release 42 (Sept 2014).

Protein Annotation, Go, Xref

No updates in this release. Last update done in release 43 (Dec 2014).

Mart

New Plant Gene and Plant Variation Marts

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Pathway Release Notes

"Cyc" Pathways

  • BioCyc-based pathway databases were upgraded to Pathway Tools ver. 18.0 and are now available from a virtual server hosted at iPlant.

Updated 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 new 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

In addition, this release includes 16 newly curated and 1 updated rice pathways:

  • New
    • Asparagine Biosynthesis I
    • Asparagine biosynthesis III
    • Beta alanine biosynthesis II
    • Citrulline Biosynthesis
    • Citrulline Nitric Oxide cycle
    • PRPP biosynthesis
    • Trehalose biosynthesis I
    • Xylan biosynthesis
    • Xyloglucan biosynthesis
    • xylogalacturonan biosynthesis
    • Asaparagine degradation
    • Lysine degradation
    • Trehalose degradation II
    • Arginine degradation VI
    • Brassinosteroid signaling
    • Strigolactone signaling
  • Updated
    • Strigolactone biosynthesis
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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.

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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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