CHUNFANG ZHENG
Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
P. KERR WALL
Biology Department, Penn State University, University Park, PA 16802, USA
JAMES LEEBENS-MACK
Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
CLAUDE DE PAMPHILIS
Biology Department, Penn State University, University Park, PA 16802, USA
VICTOR A. ALBERT
Department of Biological Sciences, SUNY Buffalo, Buffalo, NY 14260, USA
DAVID SANKOFF
Corresponding author.
Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada

Received 18 July 2008
Revised 6 November 2008
Accepted 11 November 2008

We develop criteria to detect neighborhood selection effects on gene loss following whole genome duplication, and apply them to the recently sequenced poplar (Populus trichocarpa) genome. 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 poplar and grapevine (Vitis vinifera) genomes, as T and R respectively. We conclude that, after chromosome doubling, the "choice" of which paralogous gene pairs will lose copies is random, but that the retention of strings of single-copy genes on one chromosome versus the other is decidedly non-random.

Whole genome duplication; genome rearrangement; genome halving; Populus trichocarpa; Vitis vinifera