title: The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral populus diploid.
abstract: 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.
authors.affiliation: Department of Biology, University of Ottawa, Ottawa, Ontario KIN 6N5, Canada. czh033@uottawa.ca
authors.forename: Chunfang
authors.initials: C
authors.lastname: Zheng
authors.forename: P Kerr
authors.initials: PK
authors.lastname: Wall
authors.forename: Jim
authors.initials: J
authors.lastname: Leebens-Mack
authors.forename: Victor A
authors.initials: VA
authors.lastname: Albert
authors.forename: Claude
authors.initials: C
authors.lastname: dePamphilis
authors.forename: David
authors.initials: D
authors.lastname: Sankoff
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D004171:Diploidy; D020440:Gene Duplication; D014644:Genetic Variation / Q000235:genetics*; D008957:Models, Genetic