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Comparative Methods for Reconstructing Ancient Genome Organization

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Book cover Comparative Genomics

Part of the book series: Methods in Molecular Biology ((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.

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Notes

  1. 1.

    see the GOLD database for example https://gold.jgi.doe.gov/statistics .

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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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Authors and Affiliations

  1. Institut des Sciences de l’Évolution, Université Montpellier 2, Montpellier, France

    Yoann Anselmetti & Sèverine Bérard

  2. Faculty of Technology, Bielefeld University, Bielefeld, Germany

    Nina Luhmann

  3. Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Nina Luhmann

  4. International Research Training Group1906, Bielefeld University, Bielefeld, Germany

    Nina Luhmann

  5. UMR CNRS 5558 - LBBE “Biométrie et Biologie Évolutive”, Inria Grenoble Rhône-Alpes and University of Lyon, Lyon, France

    Eric Tannier

  6. Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6

    Cedric Chauve

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  1. Yoann Anselmetti
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  2. Nina Luhmann
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  3. Sèverine Bérard
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  4. Eric Tannier
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  5. Cedric Chauve
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Correspondence to Cedric Chauve .

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Editors and Affiliations

  1. Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, São Paulo, Brazil

    João C. Setubal

  2. Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany

    Jens Stoye

  3. Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany

    Peter F. Stadler

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Anselmetti, Y., Luhmann, N., Bérard, S., Tannier, E., Chauve, C. (2018). Comparative Methods for Reconstructing Ancient Genome Organization. In: Setubal, J., Stoye, J., Stadler, P. (eds) Comparative Genomics. Methods in Molecular Biology, vol 1704. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7463-4_13

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_13

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