The Effect of Massive Gene Loss Following Whole Genome Duplication on the Algorithmic Reconstruction of the Ancestral Populus Diploid

We improve on guided genome halving algorithms so that several thousand gene sets, each containing two paralogs in the descendant T of the doubling event and their single ortholog from an undoubled reference genome R, can be analyzed to reconstruct the ancestor A of T at the time of doubling. At the same time, large numbers of defective gene sets, either missing one paralog from T or missing their ortholog in R, may be incorporated into the analysis in a consistent way. We apply this genomic rearrangement distance-based approach to the recently sequenced poplar (Populus trichocarpa) and grapevine (Vitis vinifera) genomes, as T and R respectively.