![[Home Page]](/images/icons/gramene_logo180new.jpg "[Home Page]"){kind=icon}
Gramene Release 20 March 2006
This release includes:.
Gramene website features:
- The new layout of the website has been successful with users. Remember that the Gramene logo is your link to the Gramene Home Page, and the species pages can be accessed through the images on the footer. New users may find it useful to use the Site Map (listed under "help" to review the website layout.
- FAQ's have changed format, and can now be searched through a link at the bottom left of the page. To submit a question to the FAQ, send a question via the "feedback" link at the top of every page, or use the Gramene Mailing list. This page will be simplified eventually, but for now users should simply select the module they have a question for, or use the search option at the bottom left of the page.
- New species page for Wheat. There has also been some restructuring of the species pages, with a new species Home and links to a general cereal introduction and statistics.
Gramene Database:
- Genomes: This build brings the addition of more rice SSRs and rice QTL to the browser. More Maize BACs have been loaded in the Maize Genome browser and all the datasets have been remapped to these updated BACs. (More info)
- Maps: For a list of all the new maps see ... (More info)
- Markers: The markers database has been updated with an additional 1,745,793 markers. It now contains a total of 6,293,401 markers from more than 180 species. (More info)
- Proteins: The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. (More info)
- Ontologies: Various ontologies and their associations were updated. (More info)
- Genes: This build offers the option to restrict a search by a single field. Maize GDB genes have also been added to the genes database. (More info)
- QTL: For release 20 rice QTL have been added to the genome browser, and 276 QTL have been added to the QTL database.(More info)
Genomes Release Notes
New Genomes Data
- Mapping to the Oryza sativa (japonica) genome of 14589 rice SSR tags obtained from gramene markers database.
- Mapping to the Oryza sativa (japonica) genome of 5416 rice QTLs anchored by boundry markers
- updated 504 full-length Zea mays clones deposited with GenBank as of 26-Jan-2006 in Maize Accessioned BAC Browser
- Mapping to the full-length Zea mays clones of the 61 sets of sequences that are mapped to rice TIGR v3 assembly. These 61 datasets include many datasets that are already mapped to Maize clones and many new datasets that are mapped to Maize clones for the 1st times. For a complete list, see "in silicon mapping summary". Some of these new sequence sets are
- Maize_BACends: 104007 out of 472700 sequences was mapped
- Maize_wgs_JGI: 222255 out of 1124441 sequences was mapped
- Maize_ArrayGenes_NSF58K: 2910 out of 57452 sequences was mapped.
New Genomes Features
- Zea mays accessioned clones ContigView
- The alignment feature coordinates representation changed in this release, and is consistant with the coordinates representation in rice genome browser
- 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.
- Track names changed to be consistant with Oryza sativa genome browser
BLAST Release Notes
The following databases have been added;
- Maize - cDNAs (FGENESH gene models)
- Maize - Peptides (FGENESH gene models)
- Maize - Clones (GenBank)
The following databases have been updated;
- All species - UniProtKB (SPTr) Peptides
Maps Release Notes
In this build, we present one new genetic map each from barley and rice and a new rice QTL map. Additional QTL have also been added to four existing rice QTL maps. Nearly 3,000 maize genes have been positioned on the maize bin map. The map of the rice TIGR assembly has been updated to reflect all the latest features mapped to the rice genome, which should synchronize the CMap and versions of the map.
New Genetic Maps New QTL Map Updated Maps
- Barley-Barley consensus 2003
- Rice-CIAT SSR 2006
- Rice-CNHAU Zhenshan97/ H94 DH SSR QTL 2005
- QTL Added
- Rice-TKU Asominori/IR24 RI RFLP QTL 1996
- Rice-TTU IR58821/IR52561 RI AFLP QTL 2002
- Rice-NDSU EM93-1//EM93-1/SS18-2 BC1 SSR QTL 2004
- Rice-CNHZAU Zhenshan97/Minghui63 RI QTL 2002
- Features Added and Updated
- Rice-GR TIGR Assm IRGSP Seq 2005
- Maize Bins
Markers Release Notes
The markers database has been updated with an additional 1,745,793 markers, most notably 1,099,874 genomic survey sequences from maize and related species. It now contains a total of 6,293,401 markers from more than 180 species.
Marker breakdown by species:
Species Markers Barley (Hordeum spp.) 535720 Maize (Zea spp.) 2622201 Oat (Avena spp.) 8215 Rice (Oryza spp.) 1651823 Rye (Secale spp.) 13262 Sorghum (Sorghum spp.) 312845 Sugarcane (Saccharum spp.) 339657 Wheat (Triticum spp. + Aegilops spp.) 798051 Other 38154
Proteins Release Notes
The Gramene protein database provides curated information on SP-Trembl entries from family Poaceae (Grasses). The annotations include Pfam, Prosite, TMHMM (for transmembrane domains), TargetP and Predotar (plastid, mitochrondrial and secretory pathway targeting) and Interpro assignments. Various ontologies such as Gene Ontology (GO), Plant Ontologies (PO+GRO) and Environment Ontology (EO) are used to provide functional characteristics.
In this release we have:
- Total number of proteins: 76,512
- Proteins from SWISS-PROT: 2,304
- Proteins from TrEMBL: 74,208
Ontologies Release Notes
- Ontologies: Various ontologies and their associations were updated. For more details on different types of ontologies please visit the ontology home
- The ontologies provided are:
- Gene Ontology:
- Plant Ontology:
- Gramene Plant Growth Stage Ontology:
- Trait Ontology:
- Gramene Taxonomy Ontology:
- Environment Ontology: The Environment Ontology now provides associations to genes, proteins and EST libraries from rice
Genes and Alleles Release Notes
Continually growing, Gramene release 20 presents a reorganized gene search interface over the last release. In addition to the generic search, the users can use keyword to search the Genes database. The search can be restricted to any one field, such as gene symbol, gene name, chromosome number, ontology terms (trait ontology, plant structure, growth stage, gene ontology, environment ontology), GenBank accession and Gramene protein accession. If necessary, the users also can do a search in all these fields.
As a collaboration and integration effort between Gramene and MaizeGDB, 6,676 newly imported maize genes from MaizeGDB have been integrated into the Gramene Genes database. Together with 1,525 rice genetically identified genes, the total number of genes in the Genes database has reached 8,201.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database includes a total of 10,147 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice.
A significant improvement in this release is the integration of rice QTL to the rice genome. Following the protocol developed in our database, 5,416 rice QTL with directly associated markers on the genome have been anchored to the rice genome. This will allow users to access a specific genome region corresponding to a QTL or to browse QTL by searching for traits on the rice genome browser.
In addition, 276 newly curated rice QTLs from the recent publications have been add to the database. A more detailed QTL database statistics report can be found here.
