Gene Order Divergence and Fractionated Gene Loss in Ancient Plant Tetraploids

• Activity Number: 521
• Type: Topic Contributed
• Date/Time: Wednesday, August 7, 2013 : 10:30 AM to 12:20 PM
• Sponsor: Biometrics Section
• Author(s): David Sankoff*+
• Keywords: whole genome duplication ; gene order ; angiosperms ; phylogeny ; reconstruction

Abstract

With the fixation of a whole genome duplication (WGD) in a species, two very different types of mechanism may operate simultaneously to scramble gene order on the chromosomes. One consists of rearrangement events, notably inversion, reciprocal translocation, and chromosome fusions and fissions. The other is duplicate gene loss on a massive scale, affecting both members of each pair of homeologous chromosomes or regions, a process called fractionation. It is misleading to analyze the results of fractionation in terms of parsimonious combinations of rearrangement, insertion and deletion events, because these yield systematically biased results. We analyze fractionated genomes in three steps: 1. consolidation, finding common (but incomplete) intervals in all the descendant genomes which descend from identical intervals in the original polyploid. The entire genomes are partitioned into such intervals. 2. ancestor reconstruction where the genes are replaced by consolidated intervals. 3. sorting each interval internally. We apply our methods to reconstruct the gene order of a number of ancestral flowering plants, specifically the cereals, and the core eudicots.