A Physical Map for the Amborella Genome Sheds Light on the Evolution of Angiosperm Genome Structure

Analysis of BAC ends sequenced from FPC contigs suggests that the density of LTR retrotransposons is negatively correlated with the density of protein coding genes in Amborella. Further characterization of gene density and the repetitive DNA fraction of the Amborella genome was done using whole genome shotgun sequences. Syntenic, presumably ancestral gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis, Populus, Vitis and Oryza genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change (e.g. rearrangements) has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The g paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other angiosperms from the lineage leading to Amborella.