Ancient angiosperm hexaploidy meets ancestral eudicot gene order

We propose a protocol for reconstructing and analyzing the post-polyploidization ancestor of a set of genomes. Our method, applied to the post-hexaploid ancestor of six core eudicot flowering plants, reconstructs ancestral gene order, based on orthologs obtained for each pair of data genomes, harmonized into disjoint ortholog sets for multiple genomes. We take two independent approaches to infering the gene order at the root of the rosid phylogeny: the Pathgroups method for the small phylogeny problem based on a chromosomal rearrangements (inversions, translocations, transpositions) model of evolution; the maximum weight matching uses only gene adjacencies in the data genomes. We confirm the triplication documented in the original grapevine and cacao genome sequence publications, and detect, in our reconstructed ancestor preceding the radiation of the core eudicots, the three regions corresponding to each of the seven original chromosomes hypothesized in these papers.