Plant Physiology 138:38-46 (2005)
© 2005 American Society of Plant Biologists
BIOINFORMATICS-PLANT DATABASES
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome1
Steven B. Cannon,
John A. Crow,
Michael L. Heuer,
Xiaohong Wang,
Ethalinda K.S. Cannon,
Christopher Dwan2,
Anne-Francoise Lamblin3,
Jayprakash Vasdewani,
Joann Mudge,
Andrew Cook,
John Gish,
Foo Cheung,
Steve Kenton,
Timothy M. Kunau,
Douglas Brown,
Gregory D. May,
Dongjin Kim,
Douglas R. Cook,
Bruce A. Roe,
Chris D. Town,
Nevin D. Young and
Ernest F. Retzel*
Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108 (S.B.C., X.W., E.K.S.C., J.V., J.M., N.D.Y.); Center for Computational Genomics and Bioinformatics, University of Minnesota, Minneapolis, Minnesota 55455 (J.A.C., M.L.H., C.D., A.F.L., T.M.K., E.F.R.); Department of Plant Pathology, University of California, Davis, California 95616 (A.C., J.G., D.J.K., D.R.C.); The Institute for Genomic Research, Rockville, Maryland 20850 (F.C., C.D.T.); Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019 (B.A.R., S.K.); Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401 (G.D.M.); and North Carolina State University, Fungal Genomics Laboratory, Department of Plant Pathology, Raleigh, North Carolina 27695 (D.B.)
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker-anchored bacterial artificial chromosome (BAC) sequencing strategy. Existing physical and genetic maps and deep BAC-end sequencing help to guide the sequencing effort, while EST databases provide essential resources for genome annotation as well as transcriptome characterization and microarray design. Finished BAC sequences are joined into overlapping sequence assemblies and undergo an automated annotation process that integrates ab initio predictions with EST, protein, and other recognizable features. Because of the sequencing project's international and collaborative nature, data production, storage, and visualization tools are broadly distributed. This paper describes databases and Web resources for the project, which provide support for physical and genetic maps, genome sequence assembly, gene prediction, and integration of EST data. A central project Web site at medicago.org/genome provides access to genome viewers and other resources project-wide, including an Ensembl implementation at medicago.org, physical map and marker resources at mtgenome.ucdavis.edu, and genome viewers at the University of Oklahoma (www.genome.ou.edu), the Institute for Genomic Research (www.tigr.org), and Munich Information for Protein Sequences Center (mips.gsf.de).
1 This work was supported by the National Science Foundation (awards DBI–0321460, DBI–0196197, DBI–0110206, DBI–9975806, and DBI–9872565), by the U.S. Department of Agriculture Cooperative State Research, Education, and Extension Service/National Research Initiative Program, and by the Samuel Noble Roberts Foundation.
2 Present address: BioTeam Inc., Cambridge, MA.
3 Present address: University of Minnesota Cancer Center, MMC 806, 420 Delaware St. SE, Minneapolis, MN 55455.
www.plantphysiol.org/cgi/doi/10.1104/pp.104.059204.
* Corresponding author; e-mail ernest{at}ccgb.umn.edu; fax 612–626–6069.
Received December 31, 2004;
returned for revision March 4, 2005;
accepted March 21, 2005.
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