Internal validation of ancestral gene order reconstruction in angiosperm phylogeny

David Sankoff, Chunfang Zheng, P. Kerr Wall, Claude DePamphilis, Jim Leebens-Mack, Victor A. Albert

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

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 trichocarpa as well as an early rosid ancestor.

Original languageEnglish (US)
Title of host publicationComparative Genomics, International Workshop, RECOMB-CG 2008, Proceedings
Pages252-264
Number of pages13
DOIs
StatePublished - 2008
EventRECOMB Workshop on Comparative Genomics, RECOMB-CG 2008 - Paris, France
Duration: Oct 13 2008Oct 15 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5267 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

OtherRECOMB Workshop on Comparative Genomics, RECOMB-CG 2008
CountryFrance
CityParis
Period10/13/0810/15/08

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

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