ON EXONS, INTRONS AND SPACERS:COMPLEXITY OF COMPARING SEQUENCES OF Arabidopsis thaliana AND Brassica oleracea HOMOLOGS

¹ Department of Vegetable Crops University of California Davis, CA 95616

² UMR CNRS 5545, Universite de Perpignan, 66860 Perpignan Cedex, France

³ Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland

We sequenced the region corresponding to the ABI1-Rps2-CK1 segment on chromosome 4 of the A. thaliana in B. oleracea, using the Rps2 gene as a probe to isolate cosmid clones. As in A. thaliana, the B. oleracea homolog to this gene, BoRps2, is present in single copy. Sequencing of BoRps2 and its flanking genes revealed the following structural features: 1) Spacers: A synteny break between Rps2 and CK1 due to the presence of a N-myristoyl transferase gene (N-myr) was found in B. oleracea. Homologs to the N-myr gene in Arabidopsis are on chromosomes 2 and 5. Although larger spacers were found between the Brassica than between the A. thaliana homologs, the changes in gene content makes it difficult to generalize about spacer size differences at this juncture. 2) Promoters: These were partially conserved for ABI1 homologs but poorly conserved for Rps2 homologs of both species. 3) Exons: High homology was observed for the coding sequences of all genes examined. For example, exon size and sequence in three A. thaliana and two B. oleracea CK1 homologs was conserved. 4) Introns: These were variable in size in the CK1 homologs, and served to distinguish each of them. Microsynteny studies based on sequencing accurately reveals gene content and structure and will therefore permit a survey of genome structure in other crucifers. The complexity of the genomic regions observed in the present study demonstrates that broad based hypotheses of genomic origin and structure based on conventional genetic mapping must be taken with caution.