Plant genomes are complex entities, comprised of much more than the minimal set of genes necessary to produce a plant. Moreover, they are evolutionarily dynamic, with little long-term conservation in non-genic sequences and rapid changes in features such as gene content and order. While the recent flood of comparative genomic data has revealed many intriguing evolutionary patterns, we are just beginning to understand the underlying evolutionary processes, and what, if any, organismal consequences there are to genome-scale modifications. Here, I illustrate these points with the phenomenon of gene and genome duplication. It has long been appreciated that gene duplication can lead to functional diversification within gene families. There is now accumulating evidence that gene duplication, and subsequent gene loss, is a major force in the evolution of genome structure. Much of our current knowledge of genome evolution has been obtained from comparisons between the genomes of long-diverged lineages. Future advances will require integrating these approaches with the study of microevolutionary variation.

Key words: Arabidopsis thaliana, diploidization, gene duplication, genomics, polyploidy, synteny