Fractionation, Rearrangement, Consolidation, Reconstruction

Part of the Computational Biology book series (COBO, volume 19)

Abstract

The reconstruction of ancestral gene orders based on models of chromosomal rearrangement mechanisms is complicated when some of the input genomes have undergone whole genome duplications followed by fractionation, the massive loss of some or most of the duplicate genes. We describe a reconstruction protocol that uses maximum weight matching in two phases to overcome the fragmented nature of results based on gene adjacency only. We review consolidation methods for recovering synteny patterns from fractionated genomes, and show how to integrate these into the reconstruction protocol. The procedure is applied to reconstruct the common ancestral gene order of grape and poplar. Simulation of the evolution of comparable genomes reveals the narrow ranges within which the rearrangement and fractionation parameters must be set in order to emulate statistical attributes of the extant genomes.

Keywords

Fractionation Saccharomyces Poplar CoGe 

Notes

Acknowledgements

We thank Katharina Jahn for many valuable comments and suggestions during the work reported here, and Vic Albert and Eric Lyons for guidance to current trends in angiosperm genomics. Research supported in part by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC). DS holds the Canada Research Chair in Mathematical Genomics.

References

  1. 1.
    Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4, 11 (2008) MathSciNetCrossRefGoogle Scholar
  2. 2.
    Alekseyev, M.A., Pevzner, P.A.: Breakpoint graphs and ancestral genome reconstructions. Genome Res. 19, 943–957 (2009) CrossRefGoogle Scholar
  3. 3.
    Gagnon, Y., Blanchette, M., El-Mabrouk, M.: A flexible ancestral genome reconstruction method based on gapped adjacencies. BMC Bioinform. 13(S19), S4 (2012) Google Scholar
  4. 4.
    Zheng, C., Chen, E., Albert, V.A., Lyons, E., Sankoff, D.: Ancient eudicot hexaploidy meets ancestral eurosid gene order. BMC Genomics 14 (2013, in press) Google Scholar
  5. 5.
    Langham, R.J., Walsh, J., Dunn, M., Ko, C., Goff, S.A., Freeling, M.: Genomic duplication, fractionation and the origin of regulatory novelty. Genetics 166, 935–945 (2004) CrossRefGoogle Scholar
  6. 6.
    Soltis, D.E., Albert, V.A., Leebens-Mack, J., Bell, C.D., Paterson, A.H., Zheng, C., Sankoff, D., dePamphilis, CW, Wall, P.K., Soltis, P.S.: Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009) CrossRefGoogle Scholar
  7. 7.
    El-Mabrouk, N.: Genome rearrangement by reversals and insertions/deletions of contiguous segments. In: Giancarlo, R., Sankoff, D. (eds.) Combinatorial Pattern Matching (CPM 2000), Proceedings of the 11th Annual Symposium. Lecture Notes in Computer Science, vol. 1848, pp. 222–234 (2000) CrossRefGoogle Scholar
  8. 8.
    Sankoff, D., Zheng, C.: Fractionation, rearrangement and subgenome dominance. Bioinformatics 28, 402–408 (2012) CrossRefGoogle Scholar
  9. 9.
    Jahn, K., Zheng, C., Kováč, J., Sankoff, D.: A consolidation algorithm for genomes fractionated after higher order polyploidization. BMC Bioinform. 13(S19), S8 (2012) Google Scholar
  10. 10.
    Lyons, E., Freeling, M.: How to usefully compare homologous plant genes and chromosomes as DNA sequences. Plant J. 53, 661–673 (2008). http://genomevolution.org/CoGe/ CrossRefGoogle Scholar
  11. 11.
    Lyons, E., Pedersen, B., Kane, J., Alam, M., Ming, R., Tang, H., Wang, X., Bowers, J., Paterson, A., Lisch, D., Freeling, M.: Finding and comparing syntenic regions among Arabidopsis and the outgroups papaya, poplar and grape: CoGe with rosids. Plant Physiol. 148, 1772–1781 (2008) CrossRefGoogle Scholar
  12. 12.
    Zheng, C., Swenson, K., Lyons, E., Sankoff, D.: OMG! Orthologs in multiple genomes—competing graph-theoretical formulations. In: Przytycka, T.M., Sagot, M.-F. (eds.) Algorithms in Bioinformatics, Proceedings of the 11th International Workshop. Lecture Notes in Computer Science, vol. 6833, pp. 364–375 (2011) CrossRefGoogle Scholar
  13. 13.
    Galil, Z.: Efficient algorithms for finding maximum matching in graphs. ACM Comput. Surv. 18, 23–38 (1986) MathSciNetCrossRefMATHGoogle Scholar
  14. 14.
    Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinform. 10, 120 (2009) CrossRefGoogle Scholar
  15. 15.
    Warren, R., Sankoff, D.: Genome aliquoting revisited. J. Comput. Biol. 18, 1065–1075 (2011) MathSciNetCrossRefGoogle Scholar
  16. 16.
    Manuch, J., Patterson, M., Wittler, R., Chauve, C., Tannier, E.: Linearization of ancestral multichromosomal genomes. BMC Bioinform. 13(S19), S11 (2012) Google Scholar
  17. 17.
    Wolfe, K.H., Shields, D.C.: Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708–713 (1997) CrossRefGoogle Scholar
  18. 18.
    Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pöhlmann, R., Luedi, P., Choi, S., Wing, R.A., Flavier, A., Gaffney, T.D., Philippsen, P.: The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304, 304–307 (2004) CrossRefGoogle Scholar
  19. 19.
    Kellis, M., Birren, B.W., Lander, E.S.: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 428, 617–624 (2004) CrossRefGoogle Scholar
  20. 20.
    Gordon, J.L., Byrne, K.P., Wolfe, K.H.: Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet. 5, e1000485 (2009) CrossRefGoogle Scholar
  21. 21.
    Ouangraoua, A., Tannier, E., Chauve, C.: Reconstructing the architecture of the ancestral amniote genome. Bioinformatics 27, 2664–2671 (2011) CrossRefGoogle Scholar
  22. 22.
    Byrnes, J.K., Morris, G.P., Li, W.-H.: Reorganization of adjacent gene relationships in yeast genomes by whole-genome duplication and gene deletion. Mol. Biol. Evol. 23, 1136–1143 (2006) CrossRefGoogle Scholar
  23. 23.
    van Hoek, M.J., Hogeweg, P.: The role of mutational dynamics in genome shrinkage. Mol. Biol. Evol. 24, 2485–2494 (2007) CrossRefGoogle Scholar
  24. 24.
    Sankoff, D., Zheng, C., Zhu, Q.: The collapse of gene complement following whole genome duplication. BMC Genomics 11, 313 (2010) CrossRefGoogle Scholar
  25. 25.
    Wang, B., Zheng, C., Sankoff, D.: Fractionation statistics. BMC Bioinform. 12(S9), S5 (2011) Google Scholar
  26. 26.
    Sankoff, D., Zheng, C., Wang, B.: A model for biased fractionation after whole genome duplication. BMC Genomics 13(S1), S8 (2012) CrossRefGoogle Scholar
  27. 27.
    Schnable, J., Springer, N., Freeling, M.: Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc. Natl. Acad. Sci. USA 108, 4069–4074 (2011) CrossRefGoogle Scholar
  28. 28.
    Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A. et al.: The genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray). Science 313, 1596–1604 (2006) CrossRefGoogle Scholar
  29. 29.
    Jaillon, O., Aury, J.M., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg, S., Vitulo, N., Jubin, C., et al.: The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449, 463–467 (2007) CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London 2013

Authors and Affiliations

  1. 1.University of OttawaOttawaCanada

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