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Home | Seminars and Symposia | Past seminars/symposia: Monday, December 12, 2005

Annotating the Medicago transcriptome: what to do with unknowns and ORFans


Kevin Silverstein
Kathryn VandenBosch
Plant Biology

Monday, December 12, 2005
2:30 pm

402 Walter Library

Medicago truncatula is a model species for plants in the legume family, which includes many crops important for human and animal nutrition. Medicago was selected for its small genome size, tractable genetics and as a model for interactions with symbiotic and pathogenic bacteria and fungi. Via deep sequencing of expressed sequence tags (ESTs), genome scale sequencing and transcriptional profiling we are gaining insights into the mechanisms by which host and microbes interact. In analyzing the transcriptional data (primarily EST and microarray analysis), we have encountered the problem in which differentially regulated transcripts have little or no functional annotation. To begin to overcome this difficulty, we have grouped similar unknowns and carried out iterative sequence motif searching against other plant genomes and databases of previously characterized proteins. Here we highlight a case study where this approach has led us toward the identification of a large family of putative antimicrobial peptides in plants.