[Arabidopsis] Gramene Release V.19

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[Arabidopsis] Gramene Release V.19

Claire Hebbard

Dear Cereal Researchers,

The Gramene database (http://www.gramene.org) emails its registered users an announcement each time a new release is made. This announcement includes information on new or updated data and software.

Sincerely,
The Gramene Database

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This work is funded by the National Science Foundation (NSF) and the USDA-Agricultural Research Service, and was previously funded by the USDA Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful to numerous collaborators and contributors for help in curation and for sharing their datasets and tools.

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Gramene website features:


Navigation Bar changes:
"Genome Browser" link on the navigation bar replaced with "Genomes".
"CMap" link on the navigation bar replaced with "Maps".
"Protein" link on the navigation bar replaced with "Proteins".
"Ontology" link on the navigation bar replaced with "Ontologies".
"Gene" link on the navigation bar replaced with "Genes".

New and updated tutorials
All tutorials have been updated. Tutorials are available in HTML, PDF or PowerPoint versions to allow for different browser preferences. Many slides have notes pages to improve explanations.
Updated tutorials include Maps, Proteins, Ontologies, Genes, QTL and Literature.
Genomes and BLAST tutorials are two individual tutorials, whereas previously Genome Browser and Blast were a single tutorial.
New tutorials have been developed for Markers, GrameneMart (a tool in the Genomes database), website navigation and an overview of the modules.
Two new exercises have been created to help users conduct an ontology search and a comparison between species.

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Genomes

Mapping to the Oryza sativa (japonica) genome of Rice SAGE tags obtained from MGOS (Magnaporthe Grisea Oryza Sativa Database).

Mapping to the Oryza sativa (japonica) genome of BAC ends of the following species, sequences provided by OMAP project.
Oryza coarctata
Oryza minuta

Mapping to the Oryza sativa (japonica) genome of Maize whole genome shot gun reads from JGI (Joint Genome Institute).

Mapping to the Oryza sativa (japonica) genome of Maize genes/loci sequences being assayed by the Panzea project, most sequences are maize unigenes.

Updated mapping of OMAP BAC ends for the following species.
Oryza alta
Oryza brachyantha

Updated mapping of PUTs (putative unique transcripts) downloaded from PlantGDB.
Oryza sativa
Hordeum vulgare
Sorghum bicolor
Triticum aestivum
Zea mays

Updated mapping of 3' Sorghum EST cluster from LGB(Laboratory of Genomics and Bioinformatics) at University of Georgia. 3' cluster sorghum Milestone version 3.0 replaced the 3' cluster sorghum Milestone version 2.0

Updated mapping of Ryegrass assembly by ViaLactia, the genomic sequences used by the assembly were cloned from a GeneThresher methyl-filtered library.

1307 of the previously unmapped Rice MPSS (Massively Parallel Signature Sequencing) oligo sequences were mapped to the Oryza sativa (japonica) genome.

33 of the previously unmapped Rice Oligos were mapped, these oligos are from NSF Rice Oligonucleotide Array Project

ContigView
The alignment feature query coordinates changed in this release
The alignment block coordinates no longer follow the BLAT output format, where the query coordinates are from the point of view of the reverse strand when the match is on the reverse strand. The query coordinates are always on the forward strand.
All the coordinates are 1-based.
Some track names changed, new names are more accurate, intuitive and consistent.
A new track named "Rice_FSTtransposon" replaced 2 old tracks "Rice_FST_Ds" and "Rice_FST_IS"
Oryza Sativa TE (transponsable element) track added at the bottom of the detail view.
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BLAST

There is now a BLAST tutorial
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Maps
  • In this build (v. 19) we present our initial release of the IRGSP build 4.0 rice genome assembly, to which we have mapped the RFLP markers from rice.
  • We have also added three maps of the recently-released set of Class I SSRs.
  • New BAC end sequence from wild Oryza spp. has been added to the map of the TIGR rice assembly; some other features have also been updated on that map.
  • Nine rice maps been updated with additional QTL and genes.
  • One new QTL map for maize was also added.

New Sequence and Physical Maps New QTL Map Updated Maps
Rice-Gramene IRGSP Assm 2005
Rice-Cornell Class I SSR (TIGR) 2005
Rice-Cornell Class I SSR (IRGSP) 2005
Rice-Cornell Class I SSR (93-11) 2005
Maize Bins QTL 2005

Features Added and Updated
Rice-GR TIGR Assm IRGSP Seq 2005

QTL Added
Rice-IRRI Lemont/Teqing RI RFLP QTL 2001
Rice-JRGP Nipponbare/Kasalath RFLP QTL 2000
Rice-JKU Asominori/IR24 RI RFLP QTL 1996

Genes Added
Rice-Cornell IR64/Azucena SSR 2001
Rice-Cornell BS125/2/BS125/WLO2 RFLP 2001
Rice-IGCN ZhaiYeQing 8/JingXi 17 1998
Rice-IRMI Integrated SSR 2003
Rice-JRGP Nipponbare/Kasalath RFLP 2000
Rice-Hokkaido Morphological 2000

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Markers
The marker database now contains a total of 4,547,608 markers from more than 180 species.
The database has been updated with an additional 13,519 Class I SSRs from rice.
We have added
2,530,661 Genbank dbEST sequences from fifty species of Poaceae as  marker type "EST" 
129,527 NCBI Unigene entries from six Poaceae species and 472,408 TIGR Gene Indexes from eight Poaceae species as marker type; "EST Cluster"; and
91,074 GenBank DNA sequences from Poaceae flagged as mRNA (excluding dbEST) entries from 162 species as marker type "mRNA"

The results table once again shows any number of results, even if more than 1,000 markers result from a query. The search results are returned unsorted, however. Users may still sort the results by clicking on column headings, but sorting a large number (> 1,000) of markers will be slow.

Marker breakdown by species:
Species Markers
Barley (Hordeum spp.)                     535720
Maize (Zea spp.)                          1089433
Oat (Avena spp.)                          8215
Rice (Oryza spp.)                         1475049
Rye (Secale spp.)                         13260
Sorghum (Sorghum spp.)           260634
Sugarcane (Saccharum spp.)               339657
Wheat (Triticum spp. + Aegilops spp.)   787493
Other                                       38147

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Proteins

The Gramene protein database now provides curated information on SP-Trembl entries from family Poaceae (Grasses)

The protein database includes new and updated information on 68,123 gene products drawn from SwissProt (2074) and SP-TREMBL (66,049).

These proteins are annotated using Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro categories. A total of 49,565 gene products are associated with 1,479 Gene Ontology terms.

You can search the protein database for entries by using either the SWISSPROT accession number / SPTrEMBL ID / Protein Sequence Identifier (Protein_ID) / GI number / protein name / gene name / species / cultivar.

The entries for Aegilops, Triticum, Avena and Hordeum link back to GrainGenes database.  Similarly the proteins from maize link back to the MaizeGDB.

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Ontologies
New: The ontology detail page now displays 'External references' and 'Comments' associated with a given ontology term.

Gramene Taxonomy Ontology: NEW
Total number of terms = 2204. A total of 68,122 proteins, 1488 genes, 9871 QTL and 163 mapset associations.

Gene Ontology: Updated
Total number of terms = 19,498. A total of 49,565 proteins and 21,369 Ensembl genes are associated with 1,479 Gene Ontology terms.

Plant Ontology: Updated
Total number of terms = 684. Includes associations to rice genes only

Gramene Plant Growth Stage Ontology: No updates
Total number of terms = 236
The wheat, barley and oat growth stages have the same growth stage ontology.

Trait Ontology: Updated
Total number of terms = 693. A total of 428 genes and 9871 QTL are associated with the trait terms.

Environment Ontology:Updated:
Total number of terms = 490

The Ontology browser now displays the total number of objects (QTL/phenotype gene/EnsEMBL gene/proteins/mapsets) associated with the "term name". For example: genus "Oryza" has following associations:
64,137 data entries 
55,238 proteins from various Oryza species
1488 genes
7302 QTL
109 map sets
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Genes and Alleles

Continually growing, Gramene release 19 presents a reorganized gene detail display page over the last release. Specifically, changes will be noted for allele, germplasm, nucleotide and protein sequences, and the associated features sections. Associated features included all trait (Trait Ontology), growth stage (Plant Ontology), plant anatomy parts (Plant Ontology), and gene ontology terms associated with a particular gene. Links to the Gramene Ontology have been provided as well.

For release 19, there were 151 genes curated and mapped on several rice genetic maps to display as interpolated phenotypes. These map positions were based on closely linked markers. All genes with gene symbols beginning with the letters "A" through "N" and for which information was available are included.

The Gramene Genes Database contains 1,488 genes from rice which have been characterized by phenotype. Among them, 425 genes have been fully annotated with phenotypic descriptions, associations to trait, plant and gene ontologies, map positions, alleles, phenotypic studies, germplasms, sequences, gene products, and related public references.

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QTL

There are 246 newly curated rice QTLs from recent publications that have been added to the database.
Collaborative and integrative efforts between Gramene and MaizeGDB continue, and 1,215 newly imported maize QTLs from MaizeGDB have been integrated into the Gramene QTL database.

Trait Ontology (TO) terms have been integrated with definitions of the associated traits of QTL.
This will also allow the users to browse QTL by searching traits in the Gramene Ontology Database.

The Gramene QTL database includes a total of 9,871 QTL
These QTL were identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice.


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Claire Hebbard
Gramene Outreach Coordinator
G15 Bradfield Hall
Ithaca, NY 14853

Cereals are mankind's most important source of calories. Gramene can assist in research on agriculturally important features in rice, maize, wheat and other grasses.
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