Databases and Information Integration for the Medicago truncatula Genome and Transcriptome

• Published in: Plant physiology (Bethesda) Vol. 138; no. 1; pp. 38 - 46
• Main Authors: Cannon, Steven B, Crow, John A, Heuer, Michael L, Wang, Xiaohong, Cannon, Ethalinda K.S, Dwan, Christopher, Lamblin, Anne-Francoise, Vasdewani, Jayprakash, Mudge, Joann, Cook, Andrew, Gish, John, Cheung, Foo, Kenton, Steve, Kunau, Timothy M, Brown, Douglas, May, Gregory D, Kim, Dongjin, Cook, Douglas R, Roe, Bruce A, Town, Chris D, Young, Nevin D, Retzel, Ernest F
• Format: Journal Article
• Language: English
• Published: United States American Society of Plant Biologists 01-05-2005
• Subjects: Base Sequence; Bioinformatics; Chromosomes, Artificial, Bacterial; Databases, Genetic; forage legumes; gene banks; Genes; Genetic mapping; genome; genome annotation; Genome, Plant; Genomes; Genomics; Internet; Internet resource; Legumes; literature reviews; Medicago truncatula; Medicago truncatula - genetics; Medical genetics; Pipelines; plant genetics; Sequencing; Transcription, Genetic; transcriptome; world wide web
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.104.059204

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).