Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Gramene Comparative Genome Views: How Can Gramene Leverage Rice For The Other Grasses?

Ken Youens-Clark ¹ , Kiran Kumar¹ , Immanuel Yap² , Pankaj Jaiswal² , JunJian Ni² , Steven Schmidt¹ , William Spooner¹ , Wei zhao¹ , Liya Ren¹ , Susan McCouch² , Edward Buckler^{3, 4} , Lincoln Stein¹ , Doreen Ware^1,3

¹  Cold Spring Harbor Labs, Cold Spring Harbor, NY 11724

²  Department of Plant Breeding, Cornell University, Ithaca, NY 14853

³  USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit US Plant, Soil & Nutrition Laboratory, Tower Road, Ithaca, NY 14853-2901

⁴  Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853

Due to the large size and complexity of many of the cereals genomes, finished genomic assemblies are unlikely to be available in the next few years. Many of these genomes will be represented by genomic sequences, ESTs, genetic and finger print contig physical maps. While these resources themselves are useful, it is often not possible to anchor many of the sequences to a physical location in their respective genomes. By leveraging the rice genome assembly, it is possible to order and orient many unanchored cereal sequenced based upon synteny in rice. These alignments will accelerate identification of genes using traditional mapped based cloning and the development of genetic and physical marker resources.
Gramene (http://www.gramene.org/), with support of funds from NSF and USDA, contributes to the development and implementation of bioinformatic resources for the plant community. One such resource, CMap, is a web-based comparative genetic and physical map tool that allows a user to dynamically generate comparative map views between the cereal genomes. Gramene implements the EnsEMBL genome browser, to display the rice assembly with anchored cereal annotations and a BLAST view. Both resources provide the users with interactive displays to link within the Gramene database and to act as a web-based portal to other genome resources. Over the next year we will be improving the CMap tool (available at http://www.gmod.org/) and supporting additional plant genome views in the EnsEMBL framework.