Plant & Animal Genomes XVII Conference

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

Annotation And Data Mining For The Brassica rapa Genome Sequencing Project

Martin Trick¹ , Nizar Drou¹ , Ian Bancroft² , Foo Cheung³ , Christopher D. Town³

¹  Computational & Systems Biology Department John Innes Centre Norwich Research Park Norwich NR4 7UH UK

²  Crop Genetics Department John Innes Centre Norwich Research Park Norwich NR4 7UH UK

³  The J. Craig Venter Institute 9704 Medical Center Drive Rockville MD 20850 USA

We have developed an automated annotation pipeline for finished BAC sequences as they emerge from the Brassica rapa Genome Sequencing Project (BrGSP). We have annotated the 523 sequenced seed BACs and 162 BAC sequences, generated by the UK-China collaboration, from linkage groups A1 and A8, using a prototype version of the pipeline. These data are made available through a GBrowse genome viewer at http://brassica.bbsrc.ac.uk. We will shortly be re-annotating the sequences with weighted gene predictions that exploit EST evidence and deploy this improved pipeline for all sequences from the BrGSP. The features and facilities of the system, including those which we use in our quality control and clone extension strategies, will be demonstrated during the presentation. Coherent, paired in silico alignments of end sequences from the B. rapa BACs to the Arabidopsis genome have been used at the outset for seed BAC selection. We have mined the complete set of alignments in order to discover BACs that, conversely, may span breakpoints in microsynteny with Arabidopsis. These techniques and the results of the analysis, which are of practical value in new seed selection, will also be discussed.