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Using the extensive segmental duplications of the Arabidopsis thaliana genome, a comparative study of homoeologous segments occurring in chromosomes 1, 2, 4 and 5 was performed. The gene-by-gene BLASTP approach was applied to identify duplicated genes in homoeologues. The levels of synonymous substitutions between duplicated coding sequences suggest that these regions were formed by at least two rounds of duplications. Moreover, remnants of even more ancient duplication events were recognised by a whole-genome study. We describe a subchromosomal organisation of genes, including the tandemly repeated genes, and the distribution of transposable elements (TEs). In certain cases, evidence of the possible mechanisms of structural rearrangements within the segments could be found. We provide a probable scenario of the rearrangements that took place during the evolution of the homoeologous regions. Furthermore, on the basis of the comparative analysis of the chromosomal segments in the Columbia and Landsberg erecta accessions, an additional structural variation in the A.thaliana genome is described. Analysis of the segments, spanning 7 Mb or 5.6% of the genome, permitted us to propose a model of evolution at the subchromosomal level.

Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome