Fractionation, Rearrangement, Consolidation, Reconstruction

  • David Sankoff
  • Chunfang Zheng
Part of the Computational Biology book series (COBO, volume 19)


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.


Whole Genome Duplication Gene Adjacency Ancestral Genome Whole Genome Duplication Event Poplar 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.



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.


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Copyright information

© Springer-Verlag London 2013

Authors and Affiliations

  1. 1.University of OttawaOttawaCanada

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