Polyploidy has been a major force in the evolution of plants, but our ability to detect ancient polyploidy events has limited. Extensive DNA sequence, such as we now have for a number of model plants, allows us to detect common ancestry between protien coding genes that diverged hundreds of millions of years ago. Provided that gene order rearrangements are not too extensive, one can use this to detect common ancestry between chromosomal regions. Applying this principle to the recently completed Arabidopsis thaliana genome sequence, we have identified extensive regions of putative common ancestry among all chromosomes. The extent of sequence divergence suggests that there have been at least four major duplication events, possibly genome-wide in scale, and that they occurred roughly 100-200 million years ago. Thus, these duplications are likely to have shaped the ancestral genome(s) of many plant taxa.

Key words: Arabidopsis thaliana, genome evolution, polyploidy