Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

Mapping Brassica Genes And Genomes Onto Arabidopsis Using Ensembl

Christopher G. Love^1,2 , Timothy A. Erwin^1,2 , Erica G. Logan^1,2 , Geraldine A.C. Lim^1,2 , Nick James³ , Sean May³ , German C. Spangenberg^1,2,4 , DAVID EDWARDS^1,2

¹  Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia

²  Victorian Bioinformatics Consortium, Plant Biotechnology Centre, La Trobe University, Bundoora, Victoria 3086, Australia

³  Nottingham Arabidopsis Stock Centre, Plant Science Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

⁴  Molecular Plant Breeding CRC, Plant Biotechnology Centre, Primary Industries Research Victoria, Department of Primary Industries, La Trobe University, Bundoora, Victoria 3086, Australia

The growing availability of Brassica expressed sequence and genomic sequence data presents the opportunity of conducting detailed comparison between the Brassica genomes and the complete genome sequence of the model plant Arabidopsis thaliana. Through the Multinational Brassica Genome Sequencing Project, there are a growing number of Brassica rapa (A genome) BAC (Bacterial Artificial Chromosome) end sequences being produced. We have developed a computational tool for the comparative mapping of these Brassica BACs onto the Arabidopsis genome by comparing the sequence flanking each BAC with the Arabidopsis genome sequence and selecting matches in an inverse orientation within a specified genomic distance (<500,000bp). Furthermore, we have compared the publicly available Brassica oleracea (C genome) shotgun sequences with the Arabidopsis genome sequence. To date, homologous Brassica sequences have been identified covering over half the Arabidopsis genome, predominantly around conserved genic regions. This Brassica genomic data, along with over 60 000 Brassica expressed gene sequences have been placed on a public Arabidopsis Ensembl database. Expressed sequences are linked directly to a public Brassica ASTRA database which maintains GenBank, SwissProt and Gene Ontology annotation. An analysis of the resulting data provides the opportunity to identify conserved regions between the three genomes, regions of gene duplication as well as regions of conserved synteny between B. oleracea, B. rapa and Arabidopsis. The results provide an insight into the comparative structure of the three genomes and assists in the efficient selection of candidate B. rapa BACs to be sequenced as part of the Multinational Brassica Genome Sequencing Project.