C. Liang1, W. Spooner1, K. Youens-Clark1, S. Wei1, K. Kumar1, P. Canaran1, P. Jaiswal2, S. Schmidt1, W. Zhao1, I. Yap2, J. Ni2, S. Pasternak1, D. Ware,1,3 and L. Stein1
1Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724;
2Department of Plant Breeding, Cornell University, Ithaca, NY 14853;
3USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit
Gramene (www.gramene.org) is a database for rice genome and genetics, and a resource for comparative grass analysis. The grass family, Gramineae, contains a large and diverse set of agronomically important crops. It is the main source of dietary calories for both humans and animals around the world. Gramene uses the rice genome assembly (~390Mb) as a framework to associate many of currently unsequenced grass genomes represented by genomic sequences, ESTs, or genetic/physical maps. These sequences/markers are ordered and oriented based upon their synteny in rice, which can aid researchers discover candidate genes in the other crops and develop genetic/physical marker resources.
Gramene currently provides a view of the complete rice and Arabidopsis genomes and the partial maize genome. Over 5 million sequences from more than 60 sequence datasets (e.g., ESTs, BACs, etc.) have been mapped to the rice genome. Orthologous gene sets and syntenic regions between the genomes are also provided, where the gene models from Arabidopsis thaliana (a non-grass model plant for functional analysis) are used to derive putative orthologs with rice genes, thus facilitating the identification of gene function in grasses. Protein sequences are annotated through comparison with databases of known functional domains, e.g., Interpro. In addition to the sequenced genomes, Gramene also hosts more than 160 genetic/physical maps from more than 20 cereal species through a comparative map viewer, CMap.
The project is supported by National Science Foundation grant No. 0321685 and USDA ARS.
Created on ... November 02, 2005