Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Towards Brachypodium Genomics: Analysis Of 60,000 BAC End Sequences And Sequence Comparison With Cereal Crops

Yong Qiang Gu¹ , Naxin Huo¹ , Gerard R Lazo¹ , John Vogel¹ , Ming-Cheng Luo² , Yajin Ma² , Jan Dvorak² , Teresa Hill¹ , Devin Coleman-Derr¹ , Daniel Hayden¹ , Frank You¹ , Olin D Anderson¹

¹  USDA-ARS, Western Regional Research Center Genomics and Gene Discovery Research Unit 800 Buchanan Street, Albany, CA 94710, USA

²  Department of Plant Sciences University of California, Davis Davis, CA 95616, USA

Brachypodium distachyon, with a genome size of ~355 Mb, is an emerging model system for temperature grasses (including wheat and barley) and energy crops such as switchgrass. In an effort to develop Brachypodium resources for genomics studies, we developed three deep-coverage BAC libraries, which are being employed to construct physical maps for the Brachypodium distachyon genome. In this study, we generated over 60,000 BAC end sequences (BES) from large-insert BAC clones. This provided us with the first view of its genome composition, structure, and organization. Using a cutoff expectation value of E less than 10-10, only ~ 10% of the BES show similarity to known repetitive DNA sequences in existing databases, whereas ~ 40% have matches to sequences in the EST database, which suggests that a considerable portion of the Brachypodium genome is transcribed. The large number of gene-related sequences identified for the Brachypodium genome allows us to align in silico the BES to the sequenced rice genome. Both conserved and divergent regions were identified based on gene colinearity between Brachypodium and rice. BES with significant matches to wheat ESTs that have been mapped to individual chromosome bin positions were identified. These BACs represent colinear regions to mapped ESTs and will be useful in identifying additional markers for specific wheat chromosome regions.