Gramene Release 25 June 2007This release includes:.
Gramene website features:
- Quick Search - The search box at the top of every Gramene page has been upgraded to a new search so that results are now faster. You may select a single module to search, or search the entire site. For consistency, this search has been put in the same location on the home page, and the Database Version number has been moved to the upper left column below the navigation bar. For more information, read the help document. For more in-depth module searches, you should still use the module specific searches on their pages (such as maps, markers, genes, etc.)
- New FAQ format - the New FAQ format is quicker to navigate and is much less cluttered. There is now a quick search for searching only the FAQ.
- Did you ever want to better understand where the data in Gramene comes from? The Gramene Collaborators page has been updated with more descriptive explanations of each project's contributions to Gramene. Links to sources and references are supplied as they have been provided are available on the more in-depth page.
- Genomes: (See More info)
- Maps: (See More info)
- Markers: (See More info)
- Proteins: (See More info)
- Ontologies: (See More info)
- Genes: (See More info)
- QTL: (See More info)
- Pathways: (See More info)
- Diversity: (See More info)
Genomes Release Notes
New Genomes Data
- Rice Gene Annotation updated to TIGR Rice(Oryza sativa ssp. japonica) Genome Annotation - Release 5. In this release, Gene model structure has been improved for 33,882 gene models (28,706 genes) with ~ 1.2 million of EST and/or full length cDNA evidence using the TIGR PASA program. A portion of models has been manually curated using the expression evidence and comparative genomics studies.
TIGR5 Genes: 57923 TIGR5 Transcripts: 68388
- 230 curated miRNA genes
- Rice QTLs have been updated with 6293 Rice QTLs mapped to rice pseudomolecules
- Mapping of new poaceae EST/mRNA/GSS dna sequences downloaded from NCBI genbank to Oryza sativa TIGR v5 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: 272 Maize_mRNA: 148 Other-poaceae_mRNA: 592 Rice_est: 424 Maize_est: 40 Sorghum_est: 15 Barley_est: 25 Wheat_est: 364772 Other-poaceae_est: 887 RiceJaponica_BACend_OMAP: 638 RiceRufipogon_BACend_OMAP: 54938
- The whole genome alignment comparative analyses were done for Oryza sativa ssp. japonica and Arabidopsis thaliana using both Translated Blat and Blastz-chain-net. User can view the alignments from both ContigView and MultiContigView by selecting the Compara Menu on the Detailed View panel
- Gene tree orthologs/paralogs were computed for four plant species (O.sativa (ssp japonica), O.sativa (ssp indica), Arabidopsis, and poplar) and four model metazoan species (human, Drosophila melanogaster, Caenorhabditis elegans and Saccharomyces cerevisiae. For example, from 41908 genes on O.sativa (ssp japonica), we identified that;
29901 have orthologs in O.sativa (ssp indica) 18520 have orthologs in Arabidopsis 19684 have orthologs in poplar 5324 have orthologs in Saccharomyces cerevisiae 7175 have orthologs in Caenorhabditis elegans 7449 have orthologs in Drosophila melanogaster 8313 have orthologs in human
Maps Release Notes
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 is the new cytogenetic map of maize from the Cytogenetic Map of Maize project. The gene predictions in the rice genome have been updated to reflect the latest annotations from TIGR release 5.
- Maize - CMM Cytogenetic FISH 2007
- Rice - USMSU O sativa CL16/O.nivara IRGC 80470 SSR QTL 2006
- Maize - UWM B73/Mo17 RFLP SSR QTL 1996
- Rice - CNNAU IR50/Tatsumimochi/Miyukimochi SSR QTL 2006
Updated gene prediction positions
Updated with new curated QTL
- Rice - UGA BTx623/IS3620C RL SSR RFLP QTL 2006
- Rice - IRRI IR74/Jalmagna RI AFLP/RFLP QTL 2001
- Rice - JUT Akihikari/IRAT109 BC1F4 SSR QTL 2004
See also the detailed Map Module statistics report.
Markers Release Notes
For release 25, the markers database contains a total of 13,952,872 markers. For the sake of clarity, we have changed the name of the marker type "Gene Model" to "Gene Prediction"; these are genes predicted by TIGR on the rice genome. With the addition of the cytogenetic map of maize, a new marker type "FISH probe" has been added.
Marker breakdown by type
Marker Type Markers AFLP 8150 Breakpoint interval 303 Centromere 22 Clone 2605818 deletion 895 EST 4661596 EST Cluster 1325127 FISH probe 31 FPC 22651 Gene 9806 Gene Prediction 96234 Gene Primer 19 GSS 4868955 insertion 686 Maize Bin 114 mRNA 142278 OVERGO 25006 Primer 21482 QTL 11437 RAPD 174 RFLP 17744 SSR 14826 SSR Primer Pair 16883 STS 2234 Unclassified DNA 31524 Undefined 68877
Marker breakdown by species
Species Markers Barley (Hordeum spp.) 682451 Maize (Zea spp.) 4653569 Oat (Avena spp.) 8839 Rice (Oryza spp.) 5124238 Rye (Secale spp.) 13513 Sorghum (Sorghum spp.) 1341868 Sugarcane (Saccharum spp.) 340044 Wheat (Triticum spp. + Aegilops spp.) 1554422 Other 233928
See also the more detailed Marker Module statistics report.
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: 159664
- Proteins from SWISS-PROT: 2631
- Proteins from TrEMBL: 157033
- Proteins with Pfam annotations: 57768
- Proteins with Prosite annotations: 32344
- Proteins with Signal peptide predicted by TargetP: 79933
- Proteins with Transmembrane domains predicted by TMHMM: 32039
- Proteins with Gene Ontology (GO): 101312
- Proteins with Plant Ontology (PO): 179
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) 24324 3591 454548 Plant Ontology (PO) 828 151 15924 Growth stage Ontology (GRO) 236 90 16081 Trait Ontology (TO) 829 484 13741 Taxonomy Ontology (GR_tax) 2619 1328 180848 Environment Ontology (EO) 497 50 566
Genes and Alleles Release Notes
Content: Number of genes
- Total -- 9307
- Rice -- 2624 (80 new genes)
- Maize -- 6680
- Sorghum -- 3
- Most of the rice genes with the first character of the gene symbol from "A" to "S" 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 11,437 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
One important improvement in this release is the provision of QTL associated molecular marker info. We currently provide two types of associated markers for a particular QTL: Co-localized markers are the markers co-localized or overlapped with a QTL region on the original QTL map, and neighboring markers are those not overlapped but closely adjacent to a QTL region. The associated marker info is crucial for QTL fine mapping, map-based positional cloning, and marker-assisted selection (MAS) for plant breeding.
Another improvement in this release is the provision of the inferred rice genome positions for recently curated rice QTL. Together with previous QTL genome positions, currently we provide the inferred positions for more than 6,000 rice QTL. These genome positions are displayed on both Gramene Maps and the Genome Browser, and will greatly enhance users' ability to perform comparative mapping research and candidate gene discovery.
Another recent improvement 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. These 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.A more detailed QTL database statistics report can be found here.
Pathways Release Notes (version 1.3)
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in plants: rice (Oryza sativa), Arabidopsis thaliana and bacteria E. coli. This tool also allows you to draw comparisons among the data sets from the above three species.
Sixteen pathways have been deleted and fifteen pathways added during this round of curation. All the pathways changes are recorded here
- Pathways: 278
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- 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 phenotype, SSR and RFLP 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: 954 germplasm accessions and 672 BC2F1/F2 lines; 782 SSRs and 241 RFLPs; Phenotype data on 21 traits from multi-environment experiments.
- 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.
- Interface improvement: Now, by clicking the experiment title you can have an overview of all the data, including all the markers and germplasm accessions used, QTLs identified, and phenotype data, available from a study.
Click here for database summary.