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Gramene: A Resource for Comparative Grass Genomics

Extensive research over the past two decades has shown there is a remarkably consistent conservation of gene order within large segments of linkage groups in agriculturally important grasses such as rice, maize, sorghum, barley, oats, wheat, and rye. Grass genomes are substantially colinear at both large and short scales with each other, opening the possibility of using syntenic relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum.

As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the grass genomes and take advantage of genomic sequence known in one species for identifying and understanding corresponding genes, pathways and phenotypes in other grass species. This is achieved by building automated and curated relationships between cereals for both sequence and biology. The automated and curated relationships are queried and displayed using controlled vocabularies and web-based displays. The controlled vocabularies (Ontologies), currently being used include Gene ontology, Plant ontology, Trait ontology, Environment ontology and Gramene Taxonomy ontology. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database.


Funding

This work was initially supported (2001-2004) by the USDA Initiative for Future Agriculture and Food Systems (IFAFS) (grant no. 00-52100-9622) and a Cooperative State Research and Education Service (CSREES) agreement through the USDA Agricultural Research Service (1907-21000-030 "Identification of Functional Sequence in Plant Genomes Through Bioinformatic, Genomic, and Genetic Approaches").

The National Science Foundation (NSF) supported this work through NSF Plant Genome Initiative grant award #0321685 during the years 2004-2007, NSF award #0851652 (REU Bioinformatics and Computational Biology Summer Undergraduate Program) in 2009-2012, and since 2007, through NSF Plant Genome Research Resource grant award #0703908. Current work is being supported by NSF Improving Plant Genome Annotation grant award #1127112 (Gramene - Exploring Function through Comparative Genomics and Network Analysis).


Name

The name Gramene is a play on Gramineae, a synonym for "Poaceae," the grass family as well as on the name of the Grameen Bank which specializes in small loans to the poor (mostly women) in emerging economies. In 2006, Muhammad Yunus, founder of the Grameen Bank, won a Nobel Prize for "efforts to create economic and social development from below."


Contact Information

Doreen Ware (PI)
USDA-ARS at Cold Spring Harbor Laboratory
ware--at--cshl.edu

Pankaj Jaiswal (Co-PI)
Oregon State University
jaiswalp--at--science.oregonstate.edu

Paul Kersey (Senior Personnel)
EMBL - European Bioinformatics Institute
pkersey--at--ebi.ac.uk

Helen Parkinson (Senior Personnel)
EMBL - European Bioinformatics Institute
parkinson--at--ebi.ac.uk

Lincoln Stein (Senior Personnel)
Ontario Cancer Research Institute
lincoln.stein--at--gmail.com

Crispin Taylor (Senior Personnel)
American Society of Plant Biology
ctaylor--at--aspb.org

Other Personnel

Gramene Copyright Statement

Copyright © 2000-2008 Cold Spring Harbor Laboratory and Cornell University, USA.

Copyrights:

The purpose of Gramene is to work in collaboration with others on database software and planning, and to integrate contributions from researchers with publicly available genomic data to make a comprehensive cereal genomic and comparative resource available to the scientific community. The information and software used in the development and building of the Gramene database and web site is available from various sources within the public domain. Permission for reproduction has been given or implied by the researchers/institutes who contributed or published the original materials. However, there may be patents, copyrights or intellectual property rights associated with the original data, and users of the Gramene database contents are solely responsible for compliance with original restrictions and acknowledgement requirements when using original data.

Citing Gramene

Citing Gramene Data

The Gramene database is freely available for download and use as long as Gramene is cited as the source. This includes the tools available at Gramene including but not limited to RiceCyc, CMap Viewer, Gramene Mart and the Genome Browser. When using Gramene or the information derived from Gramene kindly acknowledge the Gramene project by citing the web address http://www.gramene.org/ and identifying the version of Gramene being used (identified on the Home page) and the date accessed.

For information on linking directly to particular data items, see this document.

Publications: Citing the Gramene Project:

    When citing the Gramene project for other purposes, please refer to any one of the following papers:

  • Youens-Clark K, Buckler E, Casstevens T, Chen C, Declerck G, Derwent P, Dharmawardhana P, Jaiswal P, Kersey P, Karthikeyan AS, Lu J, McCouch SR, Ren L, Spooner W, Stein JC, Thomason J, Wei S, Ware D. Gramene database in 2010: updates and extensions. Nucleic Acids Res. 2010 Nov 13 (Gramene Reference ID 54914)

  • Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L. Gramene: a growing plant comparative genomics resource. Nucleic Acids Res. 2008 Jan;36(Database issue):D947-53. Epub 2007 Nov 4. PMID: 17984077 (Gramene Reference ID 11653)

  • Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006)Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research, 34: D717-723. (Gramene Reference ID 11021)

  • Ware D, Jaiswal P, Ni J, Pan X, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L (2002) Gramene: a resource for comparative grass genomics. Nucleic Acids Research, 30, 103-105. (Gramene Reference ID 6446)

  • Ware DH, Jaiswal P, Ni J, Yap IV, Pan X, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002) Gramene, a tool for grass genomics. Plant Physiol 130: 1606-1613. (Gramene Reference ID 7071)

Citing Ontologies at Gramene:

  • 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. Comparative and Functional Genomics 3: 132-136. (Gramene Reference ID 6902)

  • Yamazaki Y, Jaiswal P (2005) Biological ontologies in rice databases. An introduction to the activities in Gramene and Oryzabase. Plant Cell Physiol 46: 63-68. Epub 2005 Jan 2019. (Gramene Reference ID 9505)

Other Publications

*End Note users - Download Gramene Citations

Reporting Errors

Apart from our in-house and/or community wide quality measures that are in place, we request that users who notice inaccurate or missing data to please offer Feedback and inform us so that it can be corrected in a future version.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.