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Release Notes
Release Notes
Version 29 - February 2009
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 maize IBM2 2005 Neighbors map, which consolidates marker positions from the most significant maize maps.
BAC contigs anchored to genetic maps: Aegilops tauschii BAC contigs are shown aligned to the positions of their anchor markers in the two maps below. Note that only the D-genome maps have this information.
See also the detailed Map Module statistics report.
For release 29, the markers database contains a total of 47,105,576 markers. New markers of note are the TIGR Plant Transcript Assemblies (EST Clusters) from JVCI.
Marker breakdown by type
|
Marker breakdown by species
|
See also the more detailed Marker Module statistics report.
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.
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) | 28051 |
2346 |
509638 |
| Plant Ontology (PO) | 869 |
194 |
17325 |
| Growth stage Ontology (GRO) | 236 |
79 |
14835 |
| Trait Ontology (TO) | 973 |
495 |
14060 |
| Taxonomy Ontology (GR_tax) | 58260 | 45671 |
268602 |
| Environment Ontology (EO) | 501 |
72 |
12107 |
Content: Number of genes
Improvements include addition of about 1800 Maize genes mirrored from MaizeGDB.
A more detailed genes database statistics report can be found here.
Number of QTLs
| Rice | 8,646 |
| Maize | 1,747 |
| Oat | 375 |
| Barley | 299 |
| Pearl millet | 284 |
| Sorghum | 136 |
| Foxtail millet | 65 |
| Wild rice | 41 |
| Wheat | 23 |
| Tetraploid wheat | 8 |
| Total | 11,624 |
Addition of mapped QTL from published reports has halted as we move into the curation of raw genotype and phenotype data in the Diversity module.
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in rice (Oryza sativa).
RiceCyc now allows you to draw comparisons among the data sets from eight species.
There are no major updates to the pathway database. All the pathways changes are recorded here
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.
The Gramene Genetic Diversity database contains phenotype, SSR, RFLP, and AFLP 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.
Note: there are no new additions since release 28.
Click here for database summary.
Version 28 - September 2008
The Mart database will be available shortly after the main release. Estimated delivery is October 1, 2008.
No new maps were added for this release. However, all maps were updated, where necessary, based on updated data from the Markers Module. To decrease display time, the number of features dumped to CMap has been significantly reduced for two rice sequence maps and two maize physical maps. Additionally, CMap has been upgraded to the latest released version (1.01).
See also the detailed Map Module statistics report.
For release 28, the markers database contains a total of 43,727,655 markers. New markers of note are the Microarray Probes, which includes sequence data from rice DNA microarrays, including arrays from Affymetrix, Agilent, and NSF. Sequences (ESTs, GSSs, etc.) have been updated based on data in Genbank as of 2008-07-14. SSRs have a new sequence display that highlights the primer sequence in green and the repeat motif in red (e.g., RM426).
Marker breakdown by type
|
Marker breakdown by species
|
See also the more detailed Marker Module statistics report.
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.
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) | 26546 |
2217 |
414936 |
| Plant Ontology (PO) | 855 |
174 |
17052 |
| Growth stage Ontology (GRO) | 236 |
62 |
14676 |
| Trait Ontology (TO) | 973 |
491 |
14032 |
| Taxonomy Ontology (GR_tax) | 58172 | 3259 |
191465 |
| Environment Ontology (EO) | 496 |
69 |
12105 |
Content: Number of genes
Improvements include:
A more detailed genes database statistics report can be found here.
| Rice | 8,646 |
| Maize | 1,747 |
| Oat | 375 |
| Barley | 299 |
| Pearl millet | 284 |
| Sorghum | 136 |
| Foxtail millet | 65 |
| Wild rice | 41 |
| Wheat | 23 |
| Tetraploid wheat | 8 |
| Total | 11,624 |
One recent change is the improvement of search and display interface.A user can now search QTLs via their associated genes, annotated PO terms (plant structure or plant growth stages, environmental conditions) and markers. In addition, we include the associated markers in QTL search summary page and download. The enhanced query capacity and download function will greatly facilitate gene discovery as well as marker-assisted selection.
A more detailed QTL database statistics report can be found here.
This release includes Updated RiceCyc (v 2.0.2.1), AraCyc mirror (v 4.5), Ecocyc mirror (v 12.0) and MetaCyc (v 12.0). The database is served by the Pathway Tools version 12.0, that is develoed by the SRI International. The pathway databases on SorghumCyc, MedicCyc, LycoCyc, CapCyc, PotatoCyc, CoffeaCyc have not changed in this release.
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in rice (Oryza sativa).
RiceCyc now allows you to draw comparisons among the data sets from eight
species.
2 pathways on Iron uptake were added, All the pathways changes are
recorded here
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.
The Gramene Genetic Diversity database contains phenotype, SSR, RFLP, and AFLP 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: Diversity Release Notes (Build 28, 9/20/2008)
The Gramene Genetic Diversity database contains phenotype, SNP, 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:
Click here for database summary.
Version 27 - April 2008
NULL:not tried to load into ensembl db
Genome breakdown
| track_name | Arabidopsis thaliana TAIR7 | BGI 93-11 Sequence 2005 | Gramene Annotated Nipponbare Sequence 2006 | Oryza glaberrima | Populus trichocarpa JGI 2004 | Sorghum bicolor JGI8X 2007 | vitis vinifera iggp2007 |
| African-rice_EST | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| African-rice_mRNA | 3 | 33 | 36 | 0 | 6 | 28 | 12 |
| American-cotton_EST | NULL | NULL | NULL | NULL | NULL | NULL | 222239 |
| American-cotton_mRNA | NULL | NULL | NULL | NULL | NULL | NULL | 1984 |
| Chinese-cabbage_EST | 473236 | NULL | NULL | NULL | NULL | NULL | NULL |
| Chinese-cabbage_mRNA | 873 | NULL | NULL | NULL | NULL | NULL | NULL |
| Indian-rice_EST | 86554 | 401716 | 241334 | 130342 | 101447 | 347168 | 98719 |
| Indian-rice_mRNA | 4562 | 36118 | 28961 | 8458 | 6085 | 35194 | 6410 |
| Japanese-rice_EST | 244999 | 1736617 | 1533230 | 387429 | 325851 | 1379345 | 307253 |
| Japanese-rice_mRNA | 46724 | 478852 | 366952 | 94908 | 66958 | 462736 | 68026 |
| MEDICAGO-TRUNCATULA_EST | NULL | NULL | NULL | NULL | 297894 | NULL | NULL |
| MEDICAGO-TRUNCATULA_mRNA | NULL | NULL | NULL | NULL | 1751 | NULL | NULL |
| Maize_EST | 340484 | 1938676 | 1257619 | 348984 | 395772 | 2541766 | 378598 |
| Maize_mRNA | 14768 | 77891 | 92894 | 13702 | 17503 | 90395 | 16014 |
| ORYZA-MINUTA_EST | NULL | 11049 | 11007 | NULL | NULL | NULL | NULL |
| ORYZA-MINUTA_mRNA | NULL | 29 | 20 | NULL | NULL | NULL | NULL |
| Porteresia-coarctata_EST | NULL | 211 | 175 | NULL | NULL | NULL | NULL |
| Porteresia-coarctata_mRNA | NULL | 20 | 25 | NULL | NULL | NULL | NULL |
| Rice_EST | NULL | 276377 | 339150 | NULL | NULL | 214671 | NULL |
| Rice_mRNA | NULL | 6214 | 4437 | NULL | NULL | 6778 | NULL |
| Sorghum_EST | 82072 | 469012 | 323895 | 76705 | 99752 | 491145 | 101239 |
| Sorghum_mRNA | 985 | 8467 | 5976 | 82 | 1379 | 10839 | 1328 |
| Wheat_EST | 643579 | 2449623 | 1723307 | 399465 | 693084 | 2249104 | 641461 |
| Wheat_mRNA | 3031 | 15666 | 12710 | 3198 | 3744 | 15136 | 3113 |
| apple_EST | 185614 | NULL | NULL | NULL | 351220 | NULL | 305495 |
| apple_mRNA | 708 | NULL | NULL | NULL | 1544 | NULL | 1310 |
| black-cottonwood_EST | 74086 | 39836 | 39973 | 19386 | 229512 | 36888 | 125251 |
| black-cottonwood_mRNA | 460 | 192 | 205 | 23 | 1350 | 150 | 729 |
| cultivated-barley_EST | 186901 | 773711 | 507915 | 127160 | NULL | 718177 | 207426 |
| cultivated-barley_mRNA | 4876 | 33411 | 3725 | 5150 | NULL | 30717 | 5630 |
| noble-cane_EST | NULL | 589683 | 425508 | 92494 | NULL | 718487 | NULL |
| noble-cane_mRNA | NULL | 1543 | 1209 | 269 | NULL | 1330 | NULL |
| oilseed-rape_EST | 1326584 | NULL | NULL | 118524 | 493856 | NULL | NULL |
| oilseed-rape_mRNA | 3975 | NULL | NULL | 148 | 1442 | NULL | NULL |
| potatoes_EST | NULL | NULL | NULL | NULL | NULL | NULL | 219112 |
| potatoes_mRNA | NULL | NULL | NULL | NULL | NULL | NULL | 3313 |
| soybeans_EST | 233240 | NULL | NULL | NULL | 445881 | NULL | 281747 |
| soybeans_mRNA | 2579 | NULL | NULL | NULL | 5562 | NULL | 3868 |
| thale-cress_EST | 2075040 | 238725 | 224148 | 93984 | 471171 | 234612 | 340373 |
| thale-cress_mRNA | 362705 | 29539 | 29395 | 6166 | 123021 | 28633 | 67919 |
| wine-grape_EST | 285302 | 249934 | 232562 | 101107 | 610750 | 225427 | 823338 |
| wine-grape_mRNA | 748 | 595 | 609 | 118 | 2307 | 620 | 2025 |
See also the detailed Map Module statistics report.
For release 27, the markers database contains a total of 30,216,904 markers. The database includes up-to-date nucleotide sequences of all Viridiplantae contained in the NCBI Genbank Core Nucleotide, dbEST, and dbGSS divisions. We have also new and updated EST Cluster records from NCBI UniGene, PlantGDB PUT, and Plant Gene Indices.
Markers breakdown
Marker breakdown by type
|
Marker breakdown by major species
|
See also the more detailed Marker Module statistics report.
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.
NEW: For the first time we have introduced a Gazetteer (GAZ) in the Gramene project. GAZ is developed by a group of experts and researchers including those from Gramene database. GAZ represents a first step towards an open source gazetteer, constructed on ontological principles (controlled vocabulary), that describes places and place names and the relations between them. In Gramene databse we have used GAZ in the Diversity database to annotate the source site of germplasm colelction.
UPDATED: 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 breakdown
| Ontology | Total terms | Total Terms w/Associations | Total Associations |
| Gene Ontology (GO) | 26143 |
3523 |
441666 |
| Plant Ontology (PO) | 853 |
165 |
16911 |
| Growth stage Ontology (GRO) | 236 |
94 |
17560 |
| Trait Ontology (TO) | 973 |
486 |
13989 |
| Taxonomy Ontology (GR_tax) | 3259 | 3237 |
190486 |
| Environment Ontology (EO) | 496 |
67 |
12074 |
| Gazetteer Ontology (GAZ) | 78214 |
90 |
728 |
Content: Number of genes
A more detailed genes database statistics report can be found here.
Number of QTLs
A more detailed QTL database statistics report can be found here.
Pathways section in the Gramene databases is the home for RiceCyc and SorghumCyc. It also provides mirrors of the MetaCyc based compilation of metabolic pathway databases from seven other species and the reference database MetaCyc listed below. The database provides a curated and predicted catalog of biochemical pathways from 8 species, allows users to find the species specific genes mapped to respective pathways and draw comparisons between the pathways.
Pathways breakdown
| Database | Species | Version | Source |
| RiceCyc # | Oryza sativa japonica cv. Nipponbare | 2.0 | Gramene database |
| SorghumCyc # | Sorghum bicolor cv. BTx623 | 1.0 beta | Gramene database & Sorghum Biomass/Feedstock project |
| AraCyc* | Arabidopsis thaliana strain Columbia | 4.1 | The Arabidopsis Information Resource (TAIR) |
| MedicCyc* | Medicago truncatula, Barrelclover | 1.0.1 | The SR Noble Foundation |
| LycoCyc* | Solanum lycopersicum, Tomato | 1.0.1 | Solanaceae Genomics Network (SGN) |
| CapCyc* | Capsicum annuum, Pepper | 1.0.1 | Solanaceae Genomics Network (SGN) |
| CoffeeCyc* | Coffea canephora, Coffee | 1.0.1 | Solanaceae Genomics Network (SGN) |
| PotatoCyc* | Solanum tuberosum, Potato | 1.0.1 | Solanaceae Genomics Network (SGN) |
| EcoCyc* | Escherichia coli strain K-12 MG1655 | 11 | SRI International |
| MetaCyc* | Reference pathways | 11 | SRI International |
NEW:
SorghumCyc rel 1.0 beta is released for the first time. It is based on Sorghum bicolor cv BTx623 genome assembly v1.4 of the JGI
RiceCyc ver 2.0 is based on the TIGR pseudomolecule assembly release 5 of the IRGSP finished sequence. 83 pathways have been added of which 4 phytoalexin biosynthesis pathways were added manually [e.g. momilactone biosynthesis, oryzalexin A-F biosynthesis, oryzalexin S biosynthesis, phytocassane biosynthesis].
Users are also allowed to upload the gene expression/proteomics/metabolomics data on the pathways to visualise an overview of the cellular level expression profile.
For more information please visit Pathway section.
The Gramene Genetic Diversity database contains phenotype and genotype allelic data for rice, phenotype and genotype data for maize, SNP data for wheat, and Sequencing and SSR data for sorghum. 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.
This is the first time for Gramene to have the sorghum diversity data. The most sorghum data are currently contributed by the Institute for Genomic Diversity (IGD), Cornell University.
For the first time rice germplasms are annotated with Gazetteer ontology (GAZ). For more information, please see Ontology section of release notes.
On this release:
Click here for database summary.
Version 26 - September 2007
The help documentation has also been put into this consistent interface with expandable/collapsible sections. You may view it at http://dev.gramene.org/db/help
| Rice_mRNA: | 6048 |
| Maize_mRNA: | 3 |
| Other-poaceae_mRNA: | 433 |
| Rice_est: | 1 |
| Maize_est: | 156 |
| Wheat_est: | 75 |
| Other-poaceae_est: | 384 |
| RiceAlta_BACend_OMAP: | 162517 |
| RiceOfficinalis_BACend_OMAP: | 164407 |
| RiceBrachyantha_BACend_OMAP: | 74492 |
| RiceMinuta_BACend_OMAP: | 246173 |
| RiceGlaberrima_BACend_OMAP: | 106083 |
| RiceCoarctata_BACend_OMAP: | 152773 |
| RiceRufipogon_BACend_OMAP: | 165183 |
| RiceGranulata_BACend_OMAP: | 133152 |
| RicePunctata_BACend_OMAP: | 114588 |
| RiceNivara_BACend_OMAP: | 257131 |
| RiceAustraliensis_BACend_OMAP: | 185298 |
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 sequence map for indica. As noted in the "Genomes" section above, the OMAP sets have all been updated.
See also the detailed Map Module statistics report.
For release 26, the markers database contains a total of 13,504,402 markers. New markers of note are 2,243 maize eSSRs from the Maize Genome Sequencing Project.
Marker breakdown by type
|
Marker breakdown by species
|
See also the more detailed Marker Module statistics report.
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.
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 | Â Â Â Total Terms w/Associations | Â Â Â Total Associations |
| Gene Ontology (GO)Â Â Â | Â Â 24936 |
3585 |
455272 |
| Plant Ontology (PO)Â Â Â | 834 |
158 |
16057 |
| Growth stage Ontology (GRO)Â Â Â | 236 |
91 |
16118 |
| Trait Ontology (TO)Â Â Â | 834 |
484 |
13846 |
| Taxonomy Ontology (GR_tax)Â Â Â | 2699 | 1419 |
185279 |
| Environment Ontology (EO)Â Â Â | 497 |
56 |
596 |
Content: Number of genes
Improvements include:
A more detailed genes database statistics report can be found here.
Number of QTLs
One recent improvement is that all QTL have been described and annotated by multiple ontologies. In addition to Trait Ontology (TO and Plant Ontology (PO) terms used in previous releases, Environment Ontology (EO) terms have been added this build to describe environmental conditions under which a particular QTL has been identified. These terms have been annotated by creating a default mapping based on the expertly identified TO and EO associations.
Another recent 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.
A more detailed QTL database statistics report can be found here.
RiceCyc is a web based tool for viewing gene annotations mapped to various biochemical pathways in rice (Oryza sativa).
We are pleased to announce the addition of five new species to the Gramene pathway tools (RiceCyc) module. These are Capsicum anuum, Coffea canephora, Medicago truncatula, Solanum lycopersicum and Solanum tuberosum. Taken together with the previously available Arabidopsis thaliana and bacteria E. coli datasets, RiceCyc now allows you to draw comparisons among the data sets from eight species.
Six pathways have been added, two pathways deleted and five pathways modified during this round of curation. All the pathways changes are recorded here
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.
The Gramene Genetic Diversity database contains phenotype, SSR, RFLP, and AFLP 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:
Click here for database summary.
Version 25 - June 2007
Gramene Release 25 June 2007
This 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.
Gramene Database:
- 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.
New maps
- 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
Improvements include:
- 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.
Version 24 - March 2007
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.
Version 23 - November 2006
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.
Version 22 - August 2006
Gramene Release 22 August 2006
This release includes:.
Gramene website features:
- Newsletter : Starting in July, a Gramene Newsletter has been available online. The link to newsletters from the navigation menu (under "Resources") now provides links to many of the cereal industry, database, and genetic newsletters available online.
- Gramene Outreach :
- Workshop Resources : The presentation and exercise materials from the RiceCAP presentation in June have been added to our Workshop Materials resource page.
- Species pages have been completed for rice, maize, wheat, oats, barley, millet, rye, sorghum and wild rice (Zizania). Each organism has a Query summary page listing the information that is available from Gramene.
- Plant Biology Databases: A Needs Assessment - White Paper - Now available from Gramene, this is a summary of a collaborative review the anticipated needs of the plant genome research community for long-lived data collections. The authors offer guidelines for balancing the funding of data production projects with those aimed to manage and integrate the data. In particular, there is a pressing need to develop a trained cadre of skilled knowledge workers who are able to curate complex biological data, and to provide this cadre with a system of stable funding that enables data repositories to be established and maintained over extended periods of time. There is a positive current trend of species-specific databases to expand into comparative genomics-minded clade-oriented databases, but the authors caution that new technologies are needed to facilitate the transparent integration of data among these databases.
Gramene Database:
- Genomes: In an effort to improve navigation through the website, there are significant changes to the page layout at Gramene's Genomes module. (See: More info)
- Maps: Changes to the Maps search view simplify your map search, and additional maps are now available. For a list of all the changes see ... (More info)
- Markers: In addition to an increase in marker information, the new detail information layout uses tabbed navigation to minimize scrolling through long pages of information, putting information right at your fingertips. (More info)
- Proteins: In addition to additional data, the Proteins database now has an advanced search and links to the TIGR rice gene models for a best match. (More info)
- Ontologies: The Ontologies database has grown with additional information, and has a few minor changes in the display. (More info)
- Genes: Several hundred genes have map positions on commonly used genetic maps, as well as the Gramene annotated Nipponbare Sequence 2006. In addition, the detail view for a gene has been enhanced to provide more information.(More info)
- QTL: Additions include information from O. Sativa crosses with wild relatives, as well as Sorghum QTL(More info)
- Pathways: With addition pathways added since the first release, we now present RiceCyc version 1.1. (More info)
- Diversity: (More info)
Genomes Release Notes
New Genomes Data
- Arabidopsis TAIR6 assembly and annotation
- Maize FPC contigs from the AGI 19 Jul 2005 agarose map
- Updated Syntenic regions between the maize FPC map (AGI maize FPC map released on April 5, 2006) and the rice genome (TIGR v4)
- New contigview tracks added to Rice genome browser (TIGR v4)
- Sorghumn_WGS: Sorghumn WGS reads downloade from NCBI trace archive as of June 7, 2006 (mapping document)
- Rice_ArrayOligo_Yale58K: Rice Gene based array Oligs from Timothy Nelson's lab at Yale University (mapping document)
- Rice_MpssTag: The rice oligos from Blake Meyers' lab (mapping document)
- Rice_ArrayOligo_NSF20K: The rice array oligos from NSF Rice Oligonucleotide Array Project (mapping document)
New Genomes Features
The current Gramene Genome Bowsers are developed on top of ensembl-39. Compared with the last build based on ensembl-30, it has had a major redesign, both on the surface and 'under the bonnet'. Most of the dynamic pages (e.g. ContigView, GeneView) have only minor cosmetic changes - in addition to the new template and stylesheets, some links have been moved from the body of the view to the new side-bar.
- New navigation options in ContigView
ContigView navigation has been enhanced with new popup menus and navigation features:
- Click on any blank spot in Overview, Detailed View or Basepair View to get a zoom menu popup
- "Drag'n'zoom" navigation in Overview, Detailed View and Basepair View panels - click anywhere and drag your mouse diagonally to select an area, and then choose an option from the popup menu
- Click on the DNA sequence in Overview to show a popup menu allowing centering of the display and export of clones, contigs, etc.
- In Overview, click on any feature to get a popup of information with a link directly to GeneView
- All popup menus are persistent, so you can open several at once and compare the contents (click on the 'x' in the top right corner to close), and can be "minimised" to show only their title bars (by clicking on the arrow next to the 'x').
- New 'subviews'
- GeneSeqView - displays the sequence section from GeneView
- GeneSpliceView - shows alternative splicing for a gene
- GeneSeqalignView - This new view is based on GeneSeqView, with the added ability to align the given sequence with one or more species.
- Changes to DAS functionality
1. Entrez Gene has been added to the list of DAS mapping types, so it is now possible to display features from DAS sources based on Entrez Gene IDs.
2. Multiple type DAS sources are supported, i.e if a source has a mixture of features, some of which are based on UniProt IDs and some on EnsEMBL Gene IDs, it is now possible to select both mapping types for the same source. This will result in a multiple segment DAS request, e.g features?segment=UNIPROT_ID;segment=ENSEMBL_GENE
3. You can now "link" DAS features, by providing "Previous" and "Next" fields, so that corresponding items are added to the feature's popup menu.
4. Added functionality to add GeneDAS sources through URL. E.g. /geneview?gene=BRCA2;add_das_source=(url=http://myhost:9999/das+dsn=mouse_ko_allele+type=markersymbol+name=MySource+active=1) will attach the MySource DAS source to the Ensembl browser of whomever clicks on the link
5. Data can be displayed on ContigView as a signal map (i.e. as levels above and below a threshold) instead of as a histogram, by selecting this option when configuring the display.
- Karyoview updates
Karyoview has been reorganised to make it easier to create multiple images (e.g. different chromosomes or track colours) from the same set of data. All data is now cached temporarily on our server, allowing you to reconfigure all aspects of the image without re-inputting your data.
Maps Release Notes
The Map 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. Among the user interface improvements are:
- Ability to filter feature types on thhe reference map before the map is drawn.
- Selection of comparative maps now takes place under the "Map Options" menu. Look for the "Add Map Left" and "Add Maps Right" links.
- The "Stack Vertically" option reduces clutter when comparing multiple maps.
- The list of appropriate comparative maps are loaded from the server only after the user has selected "Add Maps Left/Right". This allows for faster page rendering and allows for the user to select display and other options without waiting for a query to return from the server.
Updated Sequence Map
New and Updated Physical Maps
New QTL Maps
- Rice-INDIR IR58025/O. rufipogon BC SSR QTL 2005
- Rice-UGA BTx623/IS3620C RL SSR RFLP QTL 2006
- Rice-UGA BTx623/S. propinquum F2 RFLP SSR QTL 2006
Updated QTL Maps
- Rice-Cornell IR64/Azucena DH QTL
- Rice-KRGRP Milyang23/Gihobyeo AFLP-SSLP-RFLP QTL 1998
- Rice-TAMU Lemont/Teqing RI RFLP QTL 1995
- Rice-JRGP Nipponbare/Kasalath RFLP QTL 2000
Markers Release Notes
The marker database now contains a total of 11,932,099 markers from 217 species.
Marker breakdown by type
Marker Type Markers AFLP 1,230 Centromere 12 Clone 2,390,592 EST 3,675,648 EST Cluster 1,325,059 FPC 1,701 Gene 8,673 Gene Model 5,7501 Gene Primer 19 GSS 4,312,690 Maize Bin 100 mRNA 98,737 OVERGO 15,575 Primer 62 RAPD 133 RFLP 19,643 SSR 16,885 STS 2,213 Undefined 5,621 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 638,042 Maize (Zea spp.) 4,044,148 Oat (Avena spp.) 8,232 Rice (Oryza spp.) 4,412,024 Rye (Secale spp.) 13,346 Sorghum (Sorghum spp.) 1,265,320 Sugarcane (Saccharum spp.) 339,661 Wheat (Triticum spp. + Aegilops spp.) 1,063,010 Other 148,316
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: 77804
- Proteins from SWISS-PROT: 2502
- Proteins from TrEMBL: 75302
- Proteins with Pfam annotations: 49620
- Proteins with Prosite annotations: 24544
- Proteins with Signal peptide predicted by TargetP: 40177
- Proteins with Transmembrane domains predicted by TMHMM: 14678
The improvements in release 22 include:
- Advanced search was added (http://www.gramene.org/db/protein/protein_search) to allow customized query using a name, accession, Protein id (PID) from NCBI/Uniprot/DDBJ, SPTrEMBL ID, GenBank ID, cultivar (germplasm) as well as a selection of the species. In the species list only the major cereal crops are listed. IF your species of interest is not in that list please select "All Poaceae family".
- The rice (Oryza) protein detail pages (e.g. http://www.gramene.org/db/protein/protein_search?acc=P93436) now provide specific link to the TIGR rice gene models for a best match. If you are interested in finding out more number/suitable hits please continue using the BLASTP query link.
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.
- Gene Ontology : 1674 terms with about 2,45,000 associations
- Plant Ontology : 778 terms with 1354 associations
- Gramene Plant Growth Stage Ontology [236 terms with 1893 associations
- Trait Ontology : 769 terms with about 11,700 associations
- Gramene Taxonomy Ontology : 2407 terms with 97,518 associations
- Environment Ontology : 490 terms with 348 associations
Improvements on a term's detail page include:
Anchor links for "Term" and "Annotations". These provide quick browsing to the appropriate section on the same page. Ordering. The list of species in annotations section is now pre-sorted alphabetically from left to right, then top to bottom.
To view these improvements see http://www.gramene.org/db/ontology/search_term?id=GO:0044425 as an example.
Genes and Alleles Release Notes
Continually growing, Gramene release 22 presents a further improvement based on the previously reorganized gene search interface.
Content: Number of genes
- Total -- 8542
- Rice -- 1863 (65 New genes)
- Maize -- 6676
- Sorghum -- 3 (all new)
In order to provide users with the ability to compare gene positions across various genetic and sequence maps, about 800 rice genes now have map positions on most commonly used genetic maps, the "Cornell BS125/2/BS125/WL02 RFLP 2001 Map", the "Cornell IR64/Azucena SSR 2001 Map", the "JRGP Nipponbare/Kasalath RFLP 2000 Map", and the "Hokkaido Morphological 2000 Map". Of these about 250 have mappings to the gene models found on sequence map "Gramene Annotated Nipponbare Sequence 2006". About 45% of the maize genes have been mapped to the "Maize Bins Map".
The Gene details now provide mappings to the "Plant Growth and Development Stages" ontology provided by the Plant Ontology project. This is in addition to the already displayed "Cereal Plant Growth Stages" developed by us. For example go to the gene 'd1'.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database now contains a total of 10,791 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, sorghum, pearl millet, foxtail millet and wild rice.
Around 200 new rice QTLs related to yield and other important traits have been curated from recent publications and added to the database. These new QTLs have been mostly identified from genetic populations derived from inter-specific crosses between cultivated rice (Oryza sativa) and its wild rice relatives such as Oryza rufipogon and Oryza glaberrima. The identification of those QTLs will provide new avenues to increase the yield of rice.
Another improvement in this release is the inclusion of sorghum QTLs, almost 100 of which where detected from sorghum inter-specific and intra-specific populations. Those QTLs are associated with several traits with agronomic importance such as grain weight, leaf senescence and maturity.
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.
This is version 1.1 of the rice pathways. These pathways (also called RiceCyc) are curated by Gramene. The rice genes and their annotation used in this analysis was based on release 4 of the TIGR's assembly of Oryza sativa japonica cv.Nipponbare genome sequenced by IRGSP. Arabidopsis thaliana and E. coli pathways were imported from the AraCyc and EcoCyc project sites. Neither AraCyc nor EcoCyc have been updated in the August release of Gramene.
RiceCyc version 1.1 has following contents.
- Pathways: 323
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- Transporters: 62
- Compounds: 1265
Since the 1.0 release, seven new pathways have been added to RiceCyc; these pathways were added based upon information available from AraCyc. These pathways mainly relate to Gibberellin and include GA12 biosynthesis; ent-kaurene biosynthesis; and gibberellin synthesis I, II and III. The NAD biosynthesis II from tryptophan has also been added; this is based on the fact that in eukaryotes this pathway starts with tryptophan. Additionally the super pathway of pantothenate and coenzyme A biosynthesis has also been added so as to take into account missing components of the pathway.
Based upon information made available from the Nelson lab at Yale University new information related to NADP-dependent malic genes has been added to the dataset. If any groups have knowledge of genes that they feel should be added to the RiceCyc dataset please feel free to contact the Gramene curators. A peptides link to the gene model pages in rice genome. Similarly if the gene model has been mapped to a biochemical pathway it links to particular reaction in pathway database from the genome browser.
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: 419 germaplasms; 280 SSR markers.
- Wheat: 48 germplasms; 3802 SNP markers.
- Maize: 2793 germplasms; 520 SSR and 897 SNP markers.
Click here for database summary.
Version 21 - May 2006
Gramene Release 21 May 2006
This release includes:.
Gramene website features:
- NEW! Introduction of two new modules, Pathways and Diversity
- New species. Some pages are still being worked on for completion, but there is now information for every species listed.
Gramene Database:
- Genomes: This build integrates TIGR 4 into the Rice genome browser. Many datasets were enriched and updated. (See: More info)
- Maps: Gramene has integrated TIGR 4 and several more rice QTL into the maps. For a list of all the new maps see ... (More info)
- Markers: The markers database has almost 12 million markers. The "BAC end sequence" and "Tos17" have been consolidated into "GSS". (More info)
- Proteins: (More info)
- Ontologies: Many associations have been added to Environment Ontologies (EO). (More info)
- Genes: Genes have new search options, as well as the addition of maize genes from MaizeGDB and 260 new rice genes.(More info)
- QTL: The addition of 350 new rice QTLs, and the addition of links to GrainGenes and MaizeGDB are new features.(More info)
- Pathways: NEW! - RiceCyc - for viewing gene annotations mapped to various biochemical pathways of Oryza sativa. (More info)
- Diversity: NEW! - SSR and SNP allelic data and passport descriptions for rice, maize and wheat germplasms, and phenotypic data for maize.(More info)
For more information on the gramene modules, review the release notes (below) and the most recent Gramene Publications
- Gramene: A genomics and genetics resource for rice. Rice Genetics Newsletter, 2006, Vol. 22, No. 1. 9-16.
- Gramene: Sowing the seeds of genomics research. eCALSconnect, March 2006, Vol. 12-3.
Genomes Release Notes
New Genomes Data
- Genome assembly: The rice genome browser has been updated with release 4 of the TIGR Rice Pseudomolecules and Genome Annotation including TIGR gene annotation.
- Chromosomes: Mitochrondrion and chloroplast chromosomes and associated annotations have been added to the browser.
- Browser Tracks: Many datasets were enriched and updated, they are
- 8 EST datasets of various species, updated with NCBI Genbank records
- 13 BACend_OMAP datasets, updated with NCBI Genbank, 3 OMAP species are new in this build (RiceGranulata, RiceOfficinalis, RiceRidleyi)
- 5 ESTcluster_TIGR datasets from TIGR ftp site (TIGR GIs)
- 5 ESTcluster_PlantGDB from PlantGDB website
- Other updated datasets includes:
- Rice_CDS (updated from Genbank)
- RiceJaponica_cDNA_KOME (updated from Genbank)
- Maize_BACend (updated from Genbank)
- Rice_FstTransposon (updated from Genbank)
- Rice_FST-TDNA (updated from Genbank)
- Rice_FSTtos17 (updated from Genbank)
- Rice_BAC (these are Genbank Rice BAC/clones not used by Rice Assembly)
- Due to3rd party data processing delays, the following tracks are omitted, but will be reinstated in the next release;
- Rice_ArrayOligo_NSF20K
- Rice_MPSStag_Meyers
- Rice_SAGEtag_MGOS
- Rice_TE
- SNP Data: Approx. 4M Oryza sativa SNPs from dbSNP version 125 have been mapped to the rice genome assembly. The consequence of each SNP (synonymous, non-synonymous, UTR etc) on affected gene model transcripts have been annotated.
- Xref mapping: The following external database identifiers for Oryza sativa have been mapped directly to the rice gene models via dna/protein homology;
The following identifiers have also been mapped;
- SwissProt/TrEMBL,
- RefSeq,
- TIGR Gene Indices.
- NCBI Genes,
- Gramene GenesDB entries,
- Gramene Pathway entries.
New Genomes Features
- Xref mapping: The GeneView pages now display cross-reference links to external identifiers that have been mapped. These appear in the 'Similarity Matches' section. See, for example, LOC_Os01g56810.
- SNP display: Features in the SNP track of the ContigView display are now color coded according to their consequence w.r.t. overlapping gene models. This color coding extends to the GeneSNPDisplay so that it is easy to find, for example, which SNPs affect the peptide sequence of the gene (i.e. non-synonymous genes).
Maps Release Notes
We have updated our annotated rice sequence to release 4 of the TIGR rice pseudomolecules. As in previous releases, Gramene has added its own annotations to the map, in the form of features such as RFLPs, SSRs, ESTs from rice as well as other species. This map was previously known as the "Gramene TIGR Pseudomolecule Assembly of IRGSP Sequence". To shorten the name, as well as emphasize Gramene's additions to the map, the name of the rice sequence map has been changed to "Rice-Gramene Annotated Nipponbare Sequence".
In addition to the updated sequence map, we have curated additional rice QTL which have been added to four existing QTL maps.
Updated Sequence Map Updated QTL maps Rice-Gramene Annotated Nipponbare Seq 2006
[formerly known as Rice-GR TIGR Pseudomolecule Assembly of IRGSP Sequence 2005]
Markers Release Notes
The marker database now contains a total of 11,832,129 markers. Those markers previously classified into "BAC end sequence" and "Tos17" have been consolidated into "GSS", which contains all Poaceae genomic sequences.
Marker breakdown by type
Marker Type Markers AFLP 950 Centromere 12 Clone 2,033,658 EST 3,675,691 EST Cluster 1,325,059 Gene 8,474 Gene Model 57,503 Gene Primer 19 GSS 4,605,001 mRNA 99,054 Primer 34 RAPD 135 RFLP 7,822 SSR 16,835 STS 65 Undefined 1,817 Marker breakdown by species
Species Markers Barley (Hordeum spp.) 637,879 Maize (Zea spp.) 3,365,983 Oat (Avena spp.) 8,226 Rice (Oryza spp.) 4,395,144 Rye (Secale spp.) 4,91,841 Sorghum (Sorghum spp.) 1,401,556 Sugarcane (Saccharum spp.) 339,661 Wheat (Triticum spp. + Aegilops spp.) 1,062,830 Other 129,009
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: 76745
- Proteins from SWISS-PROT: 2367
- Proteins from TrEMBL: 74378
Almost all the rice proteins encoded by plastid and mitochondrial genomes are annotated.
Ontologies Release Notes
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
Gramene taxonomy ontology now has associations to the species in marker database. e.g. Oryza (GR_tax:013655) has 19 species associated in marker db.
The marker libraries are now associated to Ontology terms from Plant structure (PO), cereal growth (GRO) and Environment ontologies (EO). e.g. plant structure leaf (PO:0009025) has 77 marker libraries, suggesting that individual entries from this library were expressed in the plant structure leaf.
Genes and Alleles Release Notes
Continually growing, Gramene release 21 presents a further improvement based on the previously reorganized gene search interface.
Content:
- Rice -- 1798 (260 New genes)
- Maize -- 6676
- Total -- 8474
1657 of 1798 (92%) rice genes have literature references.
The genes present on rice plastid (157) and mitochondrial (59) genomes were added and curated.
Search improvements:
- Genes can searched by their types, not sequenced, CDS (Protein coding), rRNA (Ribosomal RNA), tRNA (Transfer RNA), Pseudogene (non-functional), and "Not classified".
- For those genes identified by classical genetics method but have no sequenced loci associated with them, please use the gene type 'Not sequenced'.
- Additional filters for 'has phenotype' can be applied to your gene searches. Selecting 'has phenotype' search those genes that have phenotypes.
A more detailed genes database statistics report can be found here.
QTL Release Notes
The Gramene QTL database includes a total of 10,495 QTL identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice.
Almost 350 new rice QTLs related with low nitrogen tolerance, tissue culture performance, and other important traits in rice from recent publications have been curated and added to the database.
Another improvement in this release is the addition of links to the QTL that have been originally integrated from GrainGenes and MaizeGDB which will allow the users to go to the original databases to get more detailed information if necessary.
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.
This is the version 1.0 of the rice pathways. The rice pathways are also called (RiceCyc) and are curated by Gramene. The rice genes and their annotation used in this analyses were based on release 4 of the TIGR's assembly of Oryza sativa japonica cv.Nipponbare genome sequenced by IRGSP.
Arabidopsis thaliana and E. coli pathways were imported from AraCyc (http://www.arabidopsis.org/tools/aracyc/) and EcoCyc (http://www.ecocyc.org/) project sites.
The RiceCyc ver 1.0 has following contents.
- Pathways: 316
- Enzymatic Reactions: 1687
- Transport Reactions: 5
- Polypeptides: 43172
- Protein Complexes: 4
- Enzymes: 10387
- Transporters: 62
- Compounds: 1265
A peptides link to the gene model pages in rice genome. Similarly if the gene model has been mapped to a biochemical pathway it links to particular reaction in pathway database from the genome browser.
This tool also allows you to upload your own gene expression data on the pathways to visualize 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.
Wheat and maize data was obtained from their respective genome projects. For rice, the data was obtained from a paper published by the McCouch rice group.
On this release,
- Rice: 234 germaplasms; 169 SSR markers.
- Wheat: 48 germplasms; 3802 SNP markers.
- Maize: 2793 germplasms; 520 SSR and 897 SNP markers.
For a more detailed summary of the datasets, click here.
Please continue to visit the Gramene Diversity Home Page as we continue to develop our data sources and analysis software tools.
Version 20 - March 2006
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.
Version 19 - October 2005
| New Sequence and Physical Maps | New QTL Map | Updated Maps |
|---|---|---|
|
|
|
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 |
- 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.
Version 18 - May 2005
Version 17 - May 2005
Version 16 - March 2005
Version 15 - Dec 2004
Links from the BlastView display to ContigView have been improved - alignments are now displayed graphically as a new ContigView track.
Rice Gene Nomenclature
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The biological community is moving toward a universal system for the naming of genes. The advantage to scientific communication in recognizing a common genetic language is to facilitate structural, functional and evolutionary comparisons of genes and genetic variation among organisms. With increasing emphasis on the molecular and biochemical nature of genes and gene products, it is important that the gene nomenclature system for rice reflect knowledge about both the phenotypic consequences of a particular allele in a given genetic background and the biochemical features of a specific gene or gene family.
The current rules for gene symbols in rice are based on recommendations from the Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) of the Rice Genetics Cooperative (Kinoshita, 1986). Most of the original gene names and symbols are descriptive of visible phenotypes that provided the earliest evidence for the existence of a gene and these names and symbols are widely used by the rice research community. As new methods for detecting and describing genes are increasingly applied to rice, nomenclature rules are needed that outline the standard procedures for describing genes based on DNA, RNA and protein sequence analysis and assays for biochemical function in addition to those previously outlined for phenotypic variants.
** This document was revised based on the discussions and recommendations from the researchers and database groups. The document was discussed as part of the Rice Annotation Project (RAP1) meeting held at Tsukuba, Japan. The formal finalizing talks will be held at the upcoming IRGS5 meeting in Manila from November 19-22, 2005. Therefore please send your comments and suggestions by writing an e.mail to Susan R. McCouch and the group. |
Web Services
Gramene Gene information for DAS clients
All non-gene DAS services. Information includes by features and entry points information for Arabidopsis thaliana, Oryza sativa indica, and Oryza sativa japonica.
We have made Gramene's cereal QTL resources available as semantic web services using the Simple Semantic Web Services. The use of semantic web services allows Gramene QTLs to be integrated with comparative mapping data, genomic data, germplasm data, and other information that has been made available via the Virtual Plant Information Network (VPIN). More information on semantic web services and the protocol/architecture used is available at the VPIN project website.
Gramene registers its QTL services at the SSWAP discovery service so users/machines can find QTL data and services across the web based on the semantics of the resources offered and the task at hand. To find QTL services, go to the discovery service at above URL and search for "QTL."
The Diversity Advanced Search Tool has these major features:
Standard Operating Procedures
External Use
