Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

Conservation of gene order in vertebrates is evident after hundreds of millions of years of divergence1,2, but comparisons of the Arabidopsis thaliana sequence3 to partial gene orders of other angiosperms (flowering plants) sharing common ancestry ∼170–235 million years ago4 yield conflicting results5,6,7,8,9,10,11. This difference may be largely due to the propensity of angiosperms to undergo chromosomal duplication (‘polyploidization’) and subsequent gene loss12 (‘diploidization’); these evolutionary mechanisms have profound consequences for comparative biology. Here we integrate a phylogenetic approach (relating chromosomal duplications to the tree of life) with a genomic approach (mitigating information lost to diploidization) to show that a genome-wide duplication3,13,14,15,16,17 post-dates the divergence of Arabidopsis from most dicots. We also show that an inferred ancestral gene order for Arabidopsis reveals more synteny with other dicots (exemplified by cotton), and that additional, more ancient duplication events affect more distant taxonomic comparisons. By using partial sequence data for many diverse taxa to better relate the evolutionary history of completely sequenced genomes to the tree of life, we foster comparative approaches to the study of genome organization, consequences of polyploidy, and the molecular basis of quantitative traits.