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Prediction of Contiguous Regions in the Amniote Ancestral Genome

  • Aïda Ouangraoua
  • Frédéric Boyer
  • Andrew McPherson
  • Éric Tannier
  • Cedric Chauve
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5542)

Abstract

We investigate the problem of inferring contiguous ancestral regions (CARs) of the genome of the last common ancestor of all extant amniotes, based on the currently sequenced and assembled amniote genomes as ingroups and three teleost fish genomes as outgroups. We combine a methodological framework using conserved syntenies computed from whole genome alignments of amniote species together with double conserved syntenies (DCS) using gene families from amniote and fish genomes, to take into account the whole genome duplication that occurred in the teleost lineage. From these comparisons, ancestral genome segments are computed using techniques inspired by physical mapping. Due to the difficulty caused by the whole genome duplication and the large evolutionary distance to the closest assembled outgroup, very few methods have been published with a reconstruction of the amniote ancestral genome. This one is the first which is founded on a simple and formal methodological framework, whose good stability is shown and whose CARs cover large regions of the human and chicken genomes.

Keywords

Mammalian Genome Genome Duplication Whole Genome Duplication Chicken Genome Ancestral 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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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Aïda Ouangraoua
    • 1
  • Frédéric Boyer
    • 2
  • Andrew McPherson
    • 1
  • Éric Tannier
    • 3
  • Cedric Chauve
    • 1
  1. 1.Department of MathematicsSimon Fraser UniversityBurnaby (BC)Canada
  2. 2.Institut de Recherches en Technologies et Sciences pour le Vivant; Laboratoire Biologie, Informatique et MathématiquesCEA GrenobleGrenobleFrance
  3. 3.Laboratoire de Biométrie et Biologie ÉvolutiveINRIA Rhône-Alpes; Université de Lyon; Université Lyon 1; CNRS, UMR5558VilleurbanneFrance

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