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Methods Mol Biol. 2018;1704:343-362. doi: 10.1007/978-1-4939-7463-4_13.

Comparative Methods for Reconstructing Ancient Genome Organization.

Author information

1
Institut des Sciences de l'Évolution, Université Montpellier 2, Montpellier, France.
2
Faculty of Technology, Bielefeld University, Bielefeld, Germany.
3
Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
4
International Research Training Group1906, Bielefeld University, Bielefeld, Germany.
5
UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive", Inria Grenoble Rhône-Alpes and University of Lyon, Lyon, France.
6
Department of Mathematics, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6. cedric.chauve@sfu.ca.

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.

KEYWORDS:

Ancestral genomes; Ancient genomes; Comparative genomics; Paleogenomics

PMID:
29277873
DOI:
10.1007/978-1-4939-7463-4_13
[Indexed for MEDLINE]

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