![[Home Page]](/images/icons/gramene_logo180new.jpg "[Home Page]"){kind=icon}
Gramene Release 24 March 2007
This release includes:.
Gramene website features:
- New species page - Brachypodium
- New newsletter in PDF format, with articles contributed from the research community - Jan/Feb 2007 PDF Newsletter
. Contact the editor to submit articles.Gramene Database:
- Genomes: New repeat tracks. New mapped data added to alignments. (See More info)
- Maps: Built from the Markers module, encorporates changes from markers, as well as several new and updated QTL maps. (See More info)
- Markers: Mostly maintenance was performed. (See More info)
- Proteins: (See More info)
- Ontologies: QTL now associated with ontologies. (See More info)
- Genes: Addition of siRNA genes, and more ontology associations. (See More info)
- QTL: QTL are now annotated by ontologies, and many QTL have links to multiple mapping positions. (See More info)
- Pathways: Many non-rice pathways have been removed. (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- Repeat features in the rice and Arabidopsis genomes were identified using repeatmasker and the REdat repeat library developed by the Munich Information Center for Protein Sequences (MIPS) [more]. These data have been used to create several new Genome Browser tracks under the 'Repeats' menu;
All repeats
LTRs
RNA repeats
Satellite repeats
Type I Transposons
Type II Transposons
Other/Unknown repeats
- Mapping of the 284 siRNAs reported by Sunkar's group [NAR 2005 Aug 2;33(14):4443-54] to Oryza sativa TIGR v4 assembly with vmatch. 268 succesfully mapped can be viewed as dna align features at contigview (for example, P101-G7), 185 uniquely mapped can also be viewed as genes (for example, P99-H3)
- Mapping of new poaceae EST/mRNA/GSS dna sequences downloaded from NCBI genbank to Oryza sativa TIGR v4 assembly with blat, the succesfully mapped sequences can be viewed as dna align features at contigview. The counts of added align features per track are
Rice_mRNA: 136529 Maize_mRNA: 4461 Other-poaceae_mRNA: 950 Rice_est: 15022 Maize_est: 7975 Other-poaceae_est: 2030 RiceAlta_BACend_OMAP: 124 RiceOfficinalis_BACend_OMAP: 250 RiceMinuta_BACend_OMAP: 478 RiceJaponica_BACend_OMAP: 1392 RiceRufipogon_BACend_OMAP: 279 RiceCoarctata_BACend_OMAP: 51 RiceGranulata_BACend_OMAP: 27 RiceNivara_BACend_OMAP: 75
Maps Release Notes
As with the last release, data in the Maps Module is built out of the mappings in the Markers Module. Updates in the latter module are also reflected here. Of note are two new QTL maps as well as four updated QTL maps upon which new QTL have been added. Pending their curation, OVERGOs on the various OMAP physical maps have not been exported in this build.
New QTL Maps
Updated QTL Maps
- Rice-Aberdeen Bala/Azu QTL 2002
- Barley-Steptoe/Morex DH RFLP QTL 2006
- Barley-Tadmor/Er Apm RI RFLP/AFLP/SSR QTL 1998
- Barley-Apex/H. spontaneum BC SSR QTL 2003
A detailed Map Module statistics report can be found here.
Markers Release Notes
This release of the Markers Module is mostly a maintainance build, fixing and updating the current set of data. As the module integrates information from the Genomes, QTL, and Genes Modules, see their release notes for any notable changes. Note that any updates to mappings are also reflected in the Maps Module. The database currently contains a total of 13,561,886 marker records from 253 species.
Marker breakdown by type
Marker Type Markers AFLP 8150 Breakpoint interval 303 Centromere 49 Clone 2561808 deletion 895 EST 4459675 EST Cluster 1325127 FPC 22651 Gene 9764 Gene Model 95297 Gene Primer 19 GSS 4750481 insertion 686 Maize Bin 100 mRNA 142037 other_dna 30601 OVERGO 16964 Primer 5398 QTL 11210 RAPD 174 RFLP 17739 SSR 14762 SSR Primer Pair 16883 STS 2234 Undefined 68879 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 682030 Maize (Zea spp.) 4630429 Oat (Avena spp.) 8840 Rice (Oryza spp.) 5014771 Rye (Secale spp.) 13512 Sorghum (Sorghum spp.) 1293109 Sugarcane (Saccharum spp.) 340032 Wheat (Triticum spp. + Aegilops spp.) 1345414 Other 233749 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: 97042
- Proteins from SWISS-PROT: 2628
- Proteins from TrEMBL: 94414
- Proteins with Pfam annotations: 57747
- Proteins with Prosite annotations: 32300
- Proteins with Signal peptide predicted by TargetP: 49857
- Proteins with Transmembrane domains predicted by TMHMM: 18516
- Proteins with Gene Ontology (GO): 65793
- Proteins with Plant Ontology (PO): 162
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.
For the first time QTLs are associated with the Plant Ontology terms. Click here for an example.
Ontology Total terms Total Terms w/Associations Total Associations Gene Ontology (GO) 23634 2474 347632 Plant Ontology (PO) 797 138 14180 Growth stage Ontology (GRO) 236 94 4699 Trait Ontology (TO) 779 460 13161 Taxonomy Ontology (GR_tax) 2526 1246 117906 Environment Ontology (EO) 497 49 552
Genes and Alleles Release Notes
Content: Number of genes
- Total -- 9227
- Rice -- 2544 (440 new genes include 284 siRNA genes)
- Maize -- 6680
- Sorghum 3--
Improvements include:
- Added 284 siRNA genes reported by Sunker et al., Nucleic acids research , 2005, 33, pp.4443-4454. If a siRNA was mapped to more than one chromosome the chromosome number is not provided.
- Many of the siRNA genes have "Target gene(s)" field added to their annotation. This section provides a list of rice gene models identified in the rice genome (available in Genome section) with which it is predicted to interact. e.g. GR:0100940, small interfering RNA P108-B7. The prediction is based on the in-silico analyses using the Vmatch sequence analysis software.
- Most of the rice genes with the first character of the gene symbol from "A" to "M" in our database now have ontology associations to TO, GO and PO.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database now contains a total of 11,209 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
An improvement in this release is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO) terms used in previous releases, Plant Ontology (PO) terms have been added to describe Plant Structure and Plant Growth and Development Stage associated with a particular QTL. Those terms have been annotated according to the information from QTL experiments in the cited literature, or by creating a default mapping based on the expertly identified TO and PO associations.
Another recent improvement is the addition of multiple QTL mapping positions when available. For rice QTL with genome positions, we currently 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 (version 1.2)
RiceCyc 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.
Forty six pathways have been deleted during this round of curation. A list of the deleted pathways can be found here
A summary of the key components of RiceCyc is given below.
- Pathways: 279
- 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 information please visit RiceCyc start page.
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: 695 germplasm accessions (651 unique); 572 SSR markers (254 unique).
- Wheat: 48 germplasm accessions; 3802 SNP markers.
- Maize: 449 germplasm accessions with SNP data; 1544 germplasm accessions with SSR data. 1435 SNP and 520 SSR markers.
Click here for database summary.
