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Comparative Methods for Reconstructing Ancient Genome Organization

  • Yoann Anselmetti
  • Nina Luhmann
  • Sèverine Bérard
  • Eric Tannier
  • Cedric Chauve
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1704)

Abstract

Comparative genomics considers the detection of similarities and differences between extant genomes, and, based on more or less formalized hypotheses regarding the involved evolutionary processes, inferring ancestral states explaining the similarities and an evolutionary history explaining the differences. In this chapter, we focus on the reconstruction of the organization of ancient genomes into chromosomes. We review different methodological approaches and software, applied to a wide range of datasets from different kingdoms of life and at different evolutionary depths. We discuss relations with genome assembly, and potential approaches to validate computational predictions on ancient genomes that are almost always only accessible through these predictions.

Key words

Comparative genomics Paleogenomics Ancient genomes Ancestral genomes 

Notes

Acknowledgment

C.C. is funded by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant 249834. E.T., S.B., and Y.A. are funded by the French Agence Nationale pour la Recherche (ANR) through PIA Grant ANR-10-BINF-01-01 “Ancestrome”. N.L. is funded by the International DFG Research Training Group GRK 1906/1.

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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Yoann Anselmetti
    • 1
  • Nina Luhmann
    • 2
    • 3
    • 4
  • Sèverine Bérard
    • 1
  • Eric Tannier
    • 5
  • Cedric Chauve
    • 6
  1. 1.Institut des Sciences de l’ÉvolutionUniversité Montpellier 2MontpellierFrance
  2. 2.Faculty of TechnologyBielefeld UniversityBielefeldGermany
  3. 3.Center for Biotechnology (CeBiTec)Bielefeld UniversityBielefeldGermany
  4. 4.International Research Training Group1906Bielefeld UniversityBielefeldGermany
  5. 5.UMR CNRS 5558 - LBBE “Biométrie et Biologie Évolutive”Inria Grenoble Rhône-Alpes and University of LyonLyonFrance
  6. 6.Department of MathematicsSimon Fraser UniversityBurnabyCanada

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