Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

Annotation Of The Brachypodium distachyon Transcriptome

Samuel E Fox¹ , Henry D Priest¹ , Sergei A Filichkin¹ , Scott A Givan¹ , Mei Wang² , Erika Lindquist² , John Vogel³ , Jennifer Bragg³ , Todd P Michael⁴ , Samuel Hazen⁵ , Michael Bevan⁶ , David F Garvin⁷ , Jeff Chang¹ , Debbie Laudencia³ , Yiqun Weng⁸ , Todd C Mockler¹

¹  Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, 97331, USA

²  DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA

³  Western Regional Research Center, U.S. Department of Agriculture, Albany, CA, 94710, USA

⁴  Waksman Institute of Microbiology, Rutgers, Piscataway, NJ, 08854-8020, USA

⁵  Biology Department, University of Massachusetts Amherst, Amherst, MA, 01003, USA

⁶  Cell and Developmental Biology Dept, John Innes Centre, Norwich, NR4 7UJ, UK

⁷  USDA-ARS, University of Minnesota, St. Paul, MN, 55108-6026, USA

⁸  USDA-ARS, University of Wisconsin, Madison, WI, 53705, USA

Brachypodium distachyon is a model for temperate grasses and bioenergy crops. To facilitate genomic studies in Brachypodium we used Illumina (Solexa), 454/Roche, and Sanger EST sequencing to sample a collection of cDNA libraries representing a diverse array of tissues, treatments and developmental stages. The resulting EST data were aligned to the Brachypodium genome and used to assemble transcriptional units, including splice variants. The use of different types of sequence data allowed us to overcome the drawbacks of individual sequencing platforms. The high depth of sequencing available from the Illumina platform increases the chance of identifying low abundance transcripts. The relatively longer 454 and Sanger reads allow the confirmation of multiple splice junctions in the same cDNA molecule and enable resolution of short repeated sequences. The directionally cloned Sanger reads enable identification of transcription unit boundaries, including alternative terminal exons. Our analysis provides a comprehensive view of the Brachypodium transcriptome structure, composition, and organization, and will increase the accuracy and coverage of annotation efforts.