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Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic Framework

  • Nina Luhmann
  • Cedric Chauve
  • Jens Stoye
  • Roland Wittler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8826)

Abstract

Ancestral genome reconstruction is an important step in analyzing the evolution of genomes. Recent progress in sequencing ancient DNA led to the publication of so-called paleogenomes and allows the integration of this sequencing data in genome evolution analysis. However, the assembly of ancient genomes is fragmented because of DNA degradation over time. Integrated phylogenetic assembly addresses the issue of genome fragmentation in the ancient DNA assembly while improving the reconstruction of all ancient genomes in the phylogeny. The fragmented assembly of the ancient genome can be represented as an assembly graph, indicating contradicting ordering information of contigs.

In this setting, our approach is to compare the ancient data with extant finished genomes. We generalize a reconstruction approach minimizing the Single-Cut-or-Join rearrangement distance towards multifurcating trees and include edge lengths to avoid a sparse reconstruction in practice. When also including the additional conflicting ancient DNA data, we can still ensure consistent reconstructed genomes.

Keywords

Edge Length Internal Node Yersinia Pestis Ancestral Genome Assembly Graph 
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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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Nina Luhmann
    • 1
  • Cedric Chauve
    • 2
  • Jens Stoye
    • 1
  • Roland Wittler
    • 1
  1. 1.International Research Training Group “Computational Methods for the Analysis of the Diversity and Dynamics of Genomes” and Genome Informatics, Faculty of Technology and Center for BiotechnologyBielefeld UniversityGermany
  2. 2.Department of MathematicsSimon Fraser UniversityBurnabyCanada

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