Analysis of the Brassica 'A' and 'C' genomes and comparison with the genome of Arabidopsis thaliana

The growing availability of Brassica genomic sequence data presents the opportunity of conducting a detailed analysis into the relationships between the Brassica A and C genomes as well as a comparison between these two Brassica genomes and the complete genome sequence of the model plant Arabidopsis thaliana. Through the Multinational Brassica Genome Project, there are a growing number of Brassica rapa (A genome) BAC end sequences being produced, with the aim of delivering the end sequences of 110,000 BACs by 2005. We have developed a computational tool for the comparative mapping of these Brassica BACs onto the Arabidopsis genome. The tool electronically maps BACs onto Arabidopsis by aligning the end sequences for each BAC with regions of the Arabidopsis genome sequence, followed by filtering for BAC ends aligning in an inverse orientation within a specified genomic distance (<500,000 bp). Furthermore, we have compared the publicly available B. oleracea (C genome) shotgun sequences both with the Arabidopsis genome and the B. rapa BAC end sequences. An analysis of the resulting data provides the opportunity to identify regions of conservation between the three genomes, regions of gene duplication, as well as regions of conserved synteny between B. rapa and Arabidopsis. The results provide an insight into the comparative structure of the three genomes and assist in the efficient selection of candidate B. rapa BACs to be sequenced as part of the Multinational Brassica Genome Project.