Gramene Release 23 November 2006
This release includes:.
Gramene website features:
- Species pages A link to the species pages has been placed on the navigation bar at the top of page. These pages have been broken down into more but smaller pages, and the consistency of format between the species has been improved. Now you can navigate between species from any species page, not just from the introduction pages.
- Gramene Data Summary for select species: The species pages now have a summary overview of all the genomic data for that specie in Gramene. For an example see the Rice Data
Gramene Database:
- Genomes: Much new and updated data. Also, tree-based visualisation of orthologs/paralogs for rice/maize/arabidopsis. (See More info)
- Maps: (See More info)
- Markers: (See More info)
- Proteins: (See More info)
- Ontologies: We are making progress on integrating ontologies with other databases, as shown in their associations. (See More info)
- Genes: We're making progress in ontology associations to TO, PO or GO; new microRNA genes, and map position links. (See More info)
- QTL: New - when available you will find multiple links to QTL mapping positions and the inferred positions on the Gramene Annotated Nipponbare Sequence. (See More info)
- Pathways: (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- The browser tracks for EST/mRNA/GSS were updated with latest NCBI Genbank records
- New contigview tracks added to Rice genome browser
- MaizeCornchip0_ArrayConsensus_Affy8K: Maize Corchip0 array consensus sequences downloaded from Plexdb (mapping document)
- Sugarcane_ArrayConsensus_Affy8K: Sugarcane array consensus sequences downloaded from Affymetrix (mapping document)
- Imported 171 Oryza sativa miRNA genes from miRBase (for example: osa-MIR159b )
- Import of the Oryza rufipogon FPC map produced by the OMAP project (OP__B from Jan 2006). Check here.
- Mapping of the clones from the O. rufipogon FPC map to the rice genome based on the mappings of O.rufipogon BAC end sequences. Check here .
- Mapping of the FPContigs from the O. rufipogon FPC map to the rice genome based on the mappings of O.rufipogon clones. Check here .
- Tree-based visualisation of orthologs/paralogs between rice, Arabidopsis and maize gene models. (for example: Rice gene LOC_Os06g16370 ). The method used to generate the data is described in detail here .
Maps Release Notes
The Maps Module has been updated to the latest CMap 0.16 release. There have been numerous changes to both the code base and user interface, which should improve query response times as well as provide a more intuitive user interface.
With this release, all data (map sets, maps, features, and correspondences) in the Maps Module are built from the Markers Module. Users are encouraged to consult the Markers Module for primary information about markers and their mappings. The Maps Module should be considered to be primarily a visualization tool.
The Gramene Annotated Nipponbare Sequence no longer includes all features on the Ensembl Rice Genome Assembly, but only features that have correspondences to other maps. This was done to reduce visual clutter as well as improve server response time. All mappings are still present in the Markers Module and can be visualized in the Rice Genome Browser. The map set still includes all rice gene models. In addition, we have for the first added QTL to the map set.
To faciliate comparison with the OMAP physical maps, we have produced a new map set: OMAP Gramene Annotated Nipponbare Sequence. This map set includes features not exported to the regular Gramene Annotated Nipponbare Sequence map set. Furthermore, the OMAP FPC maps are also available as ordered maps. These ordered maps offer faster rendering and a more compact arrangement, where contigs are displayed as a single map rather than as individual entities. The order of contigs on these ordered maps is based on correspondences to a reference map, namely the rice TIGR genome assembly. The user may view contig and clone mappings based on BAC end sequence alignments across a given chromosome.
New and Updated Sequence Maps
- Rice-Gramene Annotated Nipponbare Sequence 2006
- Rice-OMAP Gramene Annotated Nipponbare Sequence 2006
New and Updated Physical Maps
- African rice-Non-anchored FPC OG_BB 2006
- African rice-Anchored FPC OG_BB 2006
- Oryza alta-Non-anchored FPC OA_BB 2006
- Oryza australiensis-Non-anchored FPC OA_AB 2006
- Oryza brachyantha-Non-anchored FPC OB__B 2006
- Oryza granulata-Non-anchored FPC OG_AB 2006
- Oryza minuta-Non-anchored FPC OM__B 2006
- Oryza nivara-Non-anchored FPC OR_BB 2006
- Oryza nivara-Anchored FPC OR_BB 2006
- Oryza officinalis-Non-anchored FPC OO__B 2006
- Oryza punctata-Non-anchored FPC OP__B 2006
- Oryza ridleyi-Non-anchored FPC OR_AB 2006
- Oryza rufipogon-Anchored FPC OR_CB 2006
- Oryza rufipogon-Non-anchored FPC OR_CB 2006
- Porteresia coarctata-Non-anchored FPC OC__B 2006
New Ordered Physical Maps
- African rice-Anchored Ordered FPC OG_BB
- Oryza alta-Non-anchored Ordered FPC OA_BB
- Oryza australiensis-Non-anchored Ordered FPC OA_AB
- Oryza brachyantha-Non-anchored Ordered FPC OB__B
- Oryza granulata-Non-anchored Ordered FPC OG_AB
- Oryza minuta-Non-anchored Ordered FPC OM__B
- Oryza nivara-Anchored Ordered FPC OR_BB
- Oryza officinalis-Non-anchored Ordered FPC OO__B
- Oryza punctata-Non-anchored Ordered FPC OP__B
- Oryza ridleyi-Non-anchored Ordered FPC OR_AB
- Oryza rufipogon-Anchored Ordered FPC OR_CB
- Porteresia coarctata-Non-anchored Ordered FPC OC__B
New QTL Maps
- Barley-Tadmor/Er Apm RI RFLP/AFLP/SSR QTL 1998
- Barley-Apex/H. spontaneum BC SSR QTL 2003
- Barley-Galleon/Haruna nijo RFLP/AFLP/SSR QTL 2003
- Barley-Steptoe/Morex DH RFLP QTL 2006
- Wheat-Geneva/Augusta RI RFLP QTL 2000
- Wheat-Wheat composite QTL 2004
- Wheat-Synthetic/Opata RI RFLP/SSR QTL 1995
- Wheat-WL711/HD29 KBunt SSR QTL 2003
- Wheat-Cheyenne/Wichita RI RFLP QTL 1999
A detailed Map Module statistics report can be found here.
Markers Release Notes
This release of Gramene marks the first time that the Markers Module contains all map sets, maps, and mappings. All visualizations in the Maps Module are now generated from the Markers Module. The latter should be considered to be the primary source for information about maps and markers. For more information, see the release notes for the Maps Module.
The Marker Module now contains a total of 12,827,182 markers from 232 species.
Marker breakdown by type
Marker Type Markers AFLP 8039 Breakpoint interval 303 Centromere 49 Clone 2312107 EST 4417532 EST Cluster 1325127 FPC 19339 Gene 9321 Gene Model 57753 Gene Primer 19 GSS 4412241 Maize Bin 100 mRNA 99536 OVERGO 16496 Primer 4206 QTL 10962 RAPD 174 RFLP 17718 SSR 14748 SSR Primer Pair 16884 STS 2234 Undefined 68872 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 681,567 Maize (Zea spp.) 4,590,526 Oat (Avena spp.) 8,836 Rice (Oryza spp.) 4,339,744 Rye (Secale spp.) 13,412 Sorghum (Sorghum spp.) 1,293,104 Sugarcane (Saccharum spp.) 340,022 Wheat (Triticum spp. + Aegilops spp.) 1,315,656 Other 244,315 A more detailed Marker Module statistics report can be found here.
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.
- Total number of proteins: 93712
- Proteins from SWISS-PROT: 2508
- Proteins from TrEMBL: 91204
- Proteins with Pfam annotations: 50755
- Proteins with Prosite annotations: 28509
- Proteins with Signal peptide predicted by TargetP: 48379
- Proteins with Transmembrane domains predicted by TMHMM: 17790
- Proteins with Gene Ontology (GO): 63842
- Proteins with Plant Ontology (PO): 113
Ontologies Release Notes
Various ontologies and their associations to genes, gene models, proteins, QTL, markers and maps were updated. Below is a summary of the ontologies data.
Ontology Total terms Total Terms w/Associations Total Associations Gene Ontology (GO) 22568 1710 258754 Plant Ontology (PO) 787 85 2063 Growth stage Ontology (GRO) 236 42 1945 Trait Ontology (TO) 778 423 12358 Taxonomy Ontology (GR_tax) 2478 1186 113876 Environment Ontology (EO) 491 44 413
Genes and Alleles Release Notes
Content: Number of genes
- Total -- 8783
- Rice -- 2104 (241 new genes include 186 microRNA genes)
- Maize -- 6676 (no changes)
- Sorghum -- 3 (no change)
Improvements include:
- Most of the rice genes with the first character of the gene symbol from "A" to "G" in our database now have ontology associations to TO, PO or GO.
- 186 Rice microRNA genes were added for the first time.
- Whenever available we have added the map position on the Gramene Annotated Nipponbare Sequence 2006 map in addition to the original "experimental" gene positions on various genetic maps. These genome positions are displayed on both Gramene Maps and Genome Browser and will greatly enhance users' ability to do comparative mapping research. The users can visit the gramene map from the Map position section and to the the genome browser via the Rice Ensembl Gene link provided in the Nucleotide (DNA) section of the gene detail page.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database now contains a total of 10,961 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
As part of a continuing collaboration and integration, 170 newly imported wheat and barley QTLs from GrainGenes have been integrated into the Gramene QTL database. The integration also includes 9 new QTL map sets that have been imported into Gramene's Markers and Maps data modules.
An improvement in this release is the provision of multiple links to QTL mapping positions when available. For rice QTL with genome positions, we currently also provide the inferred positions on the Gramene Annotated Nipponbare Sequence map in addition to the original "experimental" QTL positions. These genome positions are displayed on both Gramene Maps and Genome Browser and will greatly enhance users' ability to do comparative mapping research.
A more detailed QTL database statistics report can be found here.
Pathways Release Notes
The Pathway tool is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants, rice (Oryza sativa) and Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.
These pathways (also called RiceCyc) are curated by Gramene.
RiceCyc version 1.2 has following contents.
- Pathways: 325
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- Transporters: 62
- Compounds: 1265
This tool also allows you to upload your own gene expression data on the pathways to visualise an overview of the cellular level expression profile. For more info please visit http://www.gramene.org/pathway/.
Diversity Release Notes
The Gramene Genetic Diversity database contains SSR allelic data for rice, SNP data for Wheat, and phenotypic, SSR and SNP data for maize. Allelic variation on loci of multiple germplasms of a species and genome-wide allelic variation of germplasms can be viewed by searching for locus/marker name, germplasm name or accession number.
On this release,
- Rice: 626 germaplasm accessions (587 unique); 524 SSR markers (247 unique).
- Wheat: 48 germplasm accessions; 3802 SNP markers.
- Maize: 302 germplasm accessions with SNP data; 1543 germplasm accessions with SSR data. 897 SNP and 520 SSR markers.
Click here for database summary.