Plant & Animal Genomes XVII Conference

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

Report Of The Brachypodium Repeat Annotation Consortium (BRAC)

Thomas Wicker¹ , Michael Bevan² , Jan Buchmann¹ , Yong Q Gu³ , Heidrun Gundlach⁴ , Ning Jiang⁵ , Jinsheng Lai⁶ , Janxin Ma⁷ , Klaus Mayer⁴ , Ellen Pritham⁸ , Jaakko Tanskanen⁹ , Alan Schulman⁹

¹  University Zurich, Zollikerstrasse 107, Zurich, 8008, Switzerland

²  Head, Cell and Developmental Biology Dept, John Innes Centre, Norwich NR4 7UJ, UK

³  Western Regional Research Center, U. S. Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA

⁴  MIPS/IBIS, German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, Neuherberg, 85764, Germany

⁵  Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA

⁶  China Agricultural University, No.2 YuanMingYuan West Road, Beijing, 100094, China

⁷  Agricultural Genomics, Purdue University, 915 W. State Street, West Lafayette, Indiana 47907-2054, USA

⁸  University of Texas, Arlington, Texas 76019, USA

⁹  MTT/BI, Plant Genomics Lab, Helsinki, FIN-00014, Finland

Transposable elements (TEs) and other repetitive sequences are often poorly annotated or entirely missed in whole-genome sequence annotations. The Brachypodium repeat annotation consortium (BRAC) focuses exclusively on repeat annotation and aims at providing a quality that is similar to the annotation quality of genes in the complete genome sequence of Brachypodium. BRAC is an international collaboration which includes TE experts from (in alphabetical order) China, England, Finland, Germany, USA and Switzerland. With our effort, we intend to establish high quality standards for repeat annotation for future genome sequencing projects. Different TE superfamilies (e.g. Copia, Gypsy, etc) were assigned to individual research teams so that each team could focus on detailed analysis of only one or two Superfamilies of their particular interest. The experts annotated simultaneously their specific types of repeats and results are compiled subsequently. To guarantee consistent quality, annotators follow specific common guidelines and, for the first time in a plant genome, TEs are classified based on a broad scientific consensus. The Brachypodium genome is slightly smaller than the rice genome but still contains considerable amounts of repetitive sequences. This report provides an update on the activities and results of the individual BRAC members and will summarise the biological and evolutionary insights we have gained from the analysis of repeat populations in the Brachypodium genome. Additionally, methods and technical and bioinformatics challenges of repeat identification and annotation will be discussed.