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Gramene


NAR Molecular Biology Database Collection entry number 607
Monaco MK, Stein J, Naithani S, Wei S, Dharmawardhana P, Kumari S, Amarasinghe V, Youens-Clark K, Thomason J, Preece J, Pasternak S, Olson A, Jiao Y, Lu Z, Bolser D, Kerhornou A, Staines D, Walts B, Wu G, D'Eustachio P, Haw R, Croft D, Kersey PJ, Stein L, Jaiswal P, Ware D.
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK, Informatics and Bio-computing Program, Ontario Institute of Cancer Research, Toronto M5G 1L7, Canada, Department of Biochemistry & Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA and NAA Plant, Soil & Nutrition Laboratory Research Unit, USDA-ARS, Ithaca, NY 14853, USA.

Database Description

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses. Both automatic and manual curation are performed to combine and interrelate information on genomic and EST sequences, genetic, physical, and sequence-based maps, proteins, molecular markers, mutant phenotypes and QTL, and publications. There are currently nine main search modules within Gramene: Genome Browser, BLAST, CMap, Marker, Protein, Ontology, Mutant, QTL, and Literature. The Genome Browser (http://www.gramene.org/japonica/mapview?chr=1) allows users to view the sequenced rice genome with sequenced features from multiple grass species aligned to it. BLAST (http://www.gramene.org/db/searches/blast) is a local alignment tool that allows users to find the best match to a sequence of interest. CMap (http://www.gramene.org/cmap/), a comparative mapping tool, allows users to view maps from different grass species and to construct comparisons between them. The Marker database (http://www.gramene.org/markers/) allows users to search for markers used for mapping in multiple grass species. The Protein database (http://www.gramene.org/protein/) allows users to find known rice proteins, learn about their functions, and find orthologs from other grasses. The Ontology database (http://www.gramene.org/plant_ontology/) allows users to search the standardized (controlled) vocabularies to find associated genes, proteins and phenotypes. The Mutant database (http://www.gramene.org/rice_mutant/) allows users to find rice genes with known phenotypes. The QTL database (http://www.gramene.org/qtl/) allows users to find quantitative trait loci for multiple grass species such as rice, maize, oat, barley, pearl and foxtail millets and wild rice. The Literature database (http://www.gramene.org/literature/) allows users to search Gramene's collection of curated citations.

Future Plans:Future plans for Gramene include completing the migration to MySQL, the addition of a Diversity module, the addition of new maps and markers for millet in CMap, integration of the Plant Structure (anatomy) ontology from the Plant Ontology Consortium, the addition of phenotypes (QTL and mutants) and proteins from other grass species, updating of the existing data types, the addition of advanced search interfaces, off-site curation tools, and the furthering of outreach activities which will include the development of species specific educational pages and the organization of Research Coordination Network workshops.

The Gramene project is a collaborative effort between Cold Spring Harbor Laboratory (http://www.cshl.edu/), the Department of Plant Breeding and Genetics at Cornell University (http://plbrgen.cals.cornell.edu/), and various national and international projects dedicated to cereal genomics and genetics research (see http://www.gramene.org/collaborators/). The database and the datasets are freely available for local use and installation. Quarterly releases provide researchers with current information and tools. For information about the most recent release, view the release notes at http://www.gramene.org/documentation/release_notes/ , and the database statistics at ftp://ftp.gramene.org/pub/gramene/CURRENT_RELEASE/data/statistics/.

Gramene hosts the sequenced genome assembly of rice (Rice-japonica) and Arabidopsis provided by TIGR, in addition to the clone-based map of maize provided by AGI (http://www.genome.arizona.edu/fpc/maize/). Users may browse and search genes, markers, ESTs, cDNAs, clones, etc. on these genomes, as well as sequenced features from, sorghum, Triticeae (wheat, oat and barley), other grasses mapped on rice and maize genomes. See http://www.gramene.org/genome_browser/. The CMap Viewer can be used to search over 160 map sets (each with multiple maps of linkage groups or chromosomes) from 22 species, see http://www.gramene.org/cmap/. Over 4.5 million markers from more than 180 species can be searched to find a marker and get its detailed information on species, source and mapped locations, see http://www.gramene.org/markers/. The database contains over 68,000 protein entries detailing their biochemical characteristics and expression in association with the Gene (GO) and Plant (PO) Ontologies, sequence and cited literature, see http://www.gramene.org/protein/. The database contains about 1,400 genes from rice which have been characterized by phenotype. Among them, 425 genes have been fully annotated with phenotypic descriptions, associations to trait (TO), plant (PO) and gene ontologies (GO), map positions, alleles, phenotypic studies, germplasms, sequences, gene products, and related public references, see http://www.gramene.org/rice_mutant/. Over 9,800 QTL (http://www.gramene.org/qtl/) have been identified for numerous agronomic traits in rice, maize, barley, oat, wheat, pearl millet, foxtail millet and wild rice. The Ontologies link (http://www.gramene.org/plant_ontology/) can be used to find keywords for plant structure, growth stages, traits, function, process, cellular component, environment and taxonomy. The Literature link (http://www.gramene.org/literature/) allows searching for articles about genes, proteins, QTL, markers, or ontologies. Sequence similarity matches can be done using the BLAST link (http://www.gramene.org/Multi/blastview). GrameneMart (http://www.gramene.org/Multi/martview) is a search tool that allows complex searches to filter out large amounts of superfluous data.

Recent Developments

Frequent workshops (http://www.gramene.org/outreach/outreach.html), as well as on-line tutorials, FAQ's, help documents (http://www.gramene.org/workshop_tutorial.html) and an active list-serve (http://www.gramene.org/mailarch/) help users with the database and tools. The website also offers information and links of interest, including resources on genetic research (http://www.gramene.org/resources/), bioinformatics, and cereal species (http://www.gramene.org/species/).

Acknowledgements

This work is funded by the National Science Foundation (NSF) and the USDA-Agricultural Research Service, and was previously funded by the USDA Initiative for Future Agriculture and Food Systems (IFAFS). We are thankful to numerous collaborators and contributors for help in curation and for sharing their datasets and tools.

References

1. D. Ware, P. Jaiswal, J. Ni, X. Pan, K. Chang, K. Clark, L. Teytelman, S. Schmidt, W. Zhao, S. Cartinhour, S. McCouch and L. Stein. (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Res. 30: 103-105.
2. D. Ware, P. Jaiswal, J. Ni, I. Yap, X. Pan, K. Youens-Clark, L. Teytelman, S. Schmidt, W. Zhao, K. Chang, S. Cartinhour, L. Stein, and S. McCouch. (2002) Gramene, a tool for grass genomics. Plant Physiol. 130: 1606-1613.
3. Jaiswal P., Ware D., Ni J., Chang K., Zhao W., Schmidt S., Pan X., Clark K., Teytelman L., Cartinhour S., Stein L., McCouch S. (2002) Gramene: development and integration of trait and gene ontologies for rice. Comp. Funct. Genomics 3: 132-136.
4. Gramene. A Bird's Eye View of Grass Genomes (http://dev.gramene.org/tutorials/gr_brochure.pdf). NY: Gramene; 2005.

Category: Plant databases

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