SEQUENCE-LEVEL ANALYSIS OF HOMOEOLOGOUS REGIONS OF THE GENOMES OF ARABIDOPSIS AND RICE

Department of Brassica and Oilseeds Research, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH U.K.

In order to investigate the degree of genome conservation detectable between the model dicot plant Arabidopsis thaliana (Arabidopsis) and the model monocot plant rice, we have identified a 0.5Mb region of the rice genome that is homoeologous to a sequenced portion of the Arabidopsis genome. In order to be able to do this, we first had to develop a suitable strategy. Using the sequences of rice cDNA clones that had been used as RFLP markers to identify homologs in the sequenced portions of the Arabidopsis genome proved unreliable. This was because of the extreme bias in the Arabidopsis data (<15% of the genome complete at that time and only one sequence contig available in the megabase size range). Starting from a fully sequenced region of the Arabidopsis genome as the query sequence to find homologous rice ESTs, that could then be used to identify a homoeologous region, proved more successful. Our data show there to be too little conservation of genome structure to expect to find multiple homologous EST clones hybridizing to individual BACs, but we were able to identify a 530kb YAC that hybridized to two adjacent RFLP markers from rice chromosome 2, and 3 further cDNAs, all of which had highly homologous genes in a 200kb region of the FCA sequenced region of Arabidopsis chromosome 4. We have assembled a complete BAC contig of this 0.5 Mb region of rice chromosome 2, and 7 clones have been distributed for sequencing. We hope to be able to present a preliminary analysis of these sequence data.