Internal Validation of Ancestral Gene Order Reconstruction in Angiosperm Phylogeny

Authors:
David Sankoff;Chunfang Zheng;P. Kerr Wall;Claude Depamphilis;Jim Leebens-Mack;Victor A. Albert
Affiliations:
Dept. of Mathematics & Statistics and Dept. of Biology, University of Ottawa, Ottawa, Canada K1N 6N5;Dept. of Mathematics & Statistics and Dept. of Biology, University of Ottawa, Ottawa, Canada K1N 6N5;Biology Department, Penn State University, USA PA 16802;Biology Department, Penn State University, USA PA 16802;Department of Plant Biology, University of Georgia, Athens, USA GA 30602;Department of Biological Sciences, SUNY Buffalo, Buffalo, USA NY 14260
Venue:
RECOMB-CG '08 Proceedings of the international workshop on Comparative Genomics
Year:
2008

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Abstract

Whole genome doubling (WGD), a frequent occurrence during the evolution of the angiopsperms, complicates ancestral gene order reconstruction due to the multiplicity of solutions to the genome halving process. Using the genome of a related species (the outgroup) to guide the halving of a WGD descendant attenuates this problem. We investigate a battery of techniques for further improvement, including an unbiased version of the guided genome halving algorithm, reference to two related genomes instead of only one to guide the reconstruction, use of draft genome sequences in contig form only, incorporation of incomplete sets of homology correspondences among the genomes and addition of large numbers of "singleton" correspondences. We make use of genomic distance, breakpoint reuse rate, dispersion of sets of alternate solutions and other means to evaluate these techniques, while reconstructing the pre-WGD ancestor of Populus trichocarpaas well as an early rosid ancestor.