Fractionation, Rearrangement, Consolidation, Reconstruction

The reconstruction of ancestral gene orders based on models of chromosomal rearrangement mechanisms is complicated when some of the input genomes have undergone whole genome duplications followed by fractionation, the massive loss of some or most of the duplicate genes. We describe a reconstruction protocol that uses maximum weight matching in two phases to overcome the fragmented nature of results based on gene adjacency only. We review consolidation methods for recovering synteny patterns from fractionated genomes, and show how to integrate these into the reconstruction protocol. The procedure is applied to reconstruct the common ancestral gene order of grape and poplar. Simulation of the evolution of comparable genomes reveals the narrow ranges within which the rearrangement and fractionation parameters must be set in order to emulate statistical attributes of the extant genomes.