Gramene Release 19 October 2005

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), Gramene navigation, and a module overview.
- Two new exercises have been created to help users conduct an ontology search< and to help users make comparisons between species.

Gramene Database:

Database statistics can be accessed here.
Genomes: This build brings many updated and new mappings to the database. Also notable are changes in the ContigView, changes to make track names more intuitive and consistent, and a new Oryza Sativa TE (transponsable element) track added at the bottom of the detail view. (More info)
Maps: In this build, we present our initial release of the IRGSP build 4.0 rice genome assembly, have added RFLP markers from rice, added three maps of the recently-released set of Class I SSRs, updated the TIGR rice assembly; updated 9 rice maps with genes and QTL, and added a QTL map for maize. (More info)
Markers: The database has been updated with an additional 13,519 Class I SSRs from rice; 2,530,661 Genbank dbEST sequences from fifty species of Poaceae as marker type "EST"; 129,527 NCBI Unigene entries from six Poaceae species; 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". (More info)
Proteins: The protein database includes new and updated information on 68,123 gene products drawn from SwissProt (2,074) 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. (More info)
Ontologies: The Gene (GO), Plant (PO and GRO), Trait (TO), Environment (EO) and taxonomy (GR_tax) ontologies were updated with their most recent version, including the addition of new terms and annotations. The ontology detail page displays were updated to show external references and comments associated with a given ontology term. e.g. NADP-malic enzyme C4 photosynthesis (GO:0009762) has references linking to PubMed (PMID:11788762) and Pathway (MetaCyc:PWY-241). (More info)
Genes: This release presents a reorganized gene detail display page, and additional curated and mapped genes.(More info)
QTL: For release 19, there are newly curated rice QTLs from recent publications and newly imported maize QTLs from MaizeGDB; Trait Ontology (TO) terms have also been integrated (More info)

Genomes Release Notes

New Genomes Data

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

New Genomes Features

ContigView

The alignment feature query coordinates changed in this release

The alignemnt 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.

BLAST Release Notes

There is now a BLAST tutorial.

Maps Release Notes

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

Markers Release Notes

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

Proteins Release Notes

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. e.g. Protochlorophyllide reductase from Wheat. Similarly the proteins from maize link back to the MaizeGDB.
A more detailed protein database statistics report can be found here.

Ontologies Release Notes

New: The ontology detail page now displays 'External references' and 'Comments' associated with a given ontology term. e.g. NADP-malic enzyme C4 photosynthesis (GO:0009762) has references linking to PubMed (PMID:11788762) and Pathway (MetaCyc:PWY-241).
Ontologies: For more details on different types of ontologies please visit the ontology home

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

Genes and Alleles Release Notes

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.

QTL Release Notes

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.