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
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5267)


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.


Genomic Distance Angiosperm Phylogeny Black Edge Breakpoint Graph Duplicate Genome 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Bafna, V., Pevzner, P.: Genome rearrangements and sorting by reversals. SIAM Journal of Computing 25, 272–289 (1996)zbMATHCrossRefMathSciNetGoogle Scholar
  2. 2.
    Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163–173. Springer, Heidelberg (2006)CrossRefGoogle Scholar
  3. 3.
    Cui, L., Wall, P.K., Leebens-Mack, J.H., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S., Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V.A., Ma, H., de Pamphilis, C.W.: Widespread genome duplications throughout the history of flowering plants. Genome Research 16, 738–749 (2006)CrossRefGoogle Scholar
  4. 4.
    El-Mabrouk, N., Sankoff, D.: The reconstruction of doubled genomes. SIAM Journal on Computing 32, 754–792 (2003)zbMATHCrossRefMathSciNetGoogle Scholar
  5. 5.
    Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., et al.: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007), CrossRefGoogle Scholar
  6. 6.
    Pevzner, P.A., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proceedings of the National Academy of Sciences USA 100, 7672–7677 (2003)CrossRefGoogle Scholar
  7. 7.
    Li, L., Stoeckert Jr., C.J., Roos, D.S.: OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Research 13, 2178–2189 (2003)CrossRefGoogle Scholar
  8. 8.
    Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., et al.: The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452, 991–996 (2008), CrossRefGoogle Scholar
  9. 9.
    Sankoff, D.: The signal in the genomes. PLoS Computational Biology 2, e35 (2006)CrossRefGoogle Scholar
  10. 10.
    Sankoff, D., Zheng, C., Zhu, Q.: Polyploids, genome halving and phylogeny. Bioinformatics 23, i433–i439 (2007)CrossRefGoogle Scholar
  11. 11.
    Soltis, D., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A., Zheng, C., Sankoff, D., dePamphilis, C.W., Wall, P.K., Soltis, P.S.: Polyploidy and angiosperm diversification. American Journal of Botany (in press, 2008)Google Scholar
  12. 12.
    Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. In: Workshop on Algorithms in Bioinformatics WABI 2008 (in press, 2008)Google Scholar
  13. 13.
    Tesler, G.: Efficient algorithms for multichromosomal genome rearrangements. Journal of Computer and System Sciences 65, 587–609 (2002)zbMATHCrossRefMathSciNetGoogle Scholar
  14. 14.
    Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., et al.: The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006)CrossRefGoogle Scholar
  15. 15.
    Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D.A., Cestaro, A., et al.: A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2, e13–e26 (2007)CrossRefGoogle Scholar
  16. 16.
    Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21, 3340–3346 (2005)CrossRefGoogle Scholar
  17. 17.
    Zheng, C., Zhu, Q., Adam, Z., Sankoff, D.: Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. Bioinformatics 24, i96–i104 (2008)CrossRefGoogle Scholar
  18. 18.
    Zheng, C., Zhu, Q., Sankoff, D.: Genome halving with an outgroup. Evolutionary Bioinformatics 2, 319–326 (2006)Google Scholar
  19. 19.
    Zheng, C., Zhu, Q., Sankoff, D.: Descendants of whole genome duplication within gene order phylogeny. Journal of Computational Biology 15 (in press, 2008)Google Scholar
  20. 20.
    Zheng, C., Wall, P.K., Leebens-Mack, J., Albert, V.A., dePamphilis, C.W., Sankoff, D.: The effect of massive gene loss following whole genome duplication on the algorithmic reconstruction of the ancestral Populus diploid. In: Proceedings of the International Conference on Computational Systems Bioinformatics CSB 2008 (in press, 2008)Google Scholar

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© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • David Sankoff
    • 1
  • Chunfang Zheng
    • 1
  • P. Kerr Wall
    • 2
  • Claude dePamphilis
    • 2
  • Jim Leebens-Mack
    • 3
  • Victor A. Albert
    • 4
  1. 1.Dept. of Mathematics & Statistics and Dept. of BiologyUniversity of OttawaOttawaCanada
  2. 2.Biology DepartmentPenn State UniversityUSA
  3. 3.Department of Plant BiologyUniversity of GeorgiaAthensUSA
  4. 4.Department of Biological SciencesSUNY BuffaloBuffaloUSA

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