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Whole Genome Duplication in Plants: Implications for Evolutionary Analysis

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Comparative Genomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1704))

Abstract

The recurrent cycle of whole genome duplication (WGD) followed by massive duplicate gene loss (fractionation) differentiates plant evolutionary history from that of most other phylogenetic domains, where WGD has occurred relatively rarely, even on an evolutionary time scale. We discuss the mechanism of WGD and its biological consequences. We survey the prevalence of WGD in the flowering plants. We outline some of the major kinds of combinatorial optimization problems arising in computational biology for analyzing WGD. Fractionation and its consequences are the subject of mathematical modeling questions and further combinatorial algorithms. A strong connection is made between WGD in phylogenetic context and the theory of gene trees and species trees. We illustrate the analysis of WGD with studies involving a large number of sequenced plant genomes, including grape, the crucifers and other rosids, the asterid tomato, the eudicot Nelumbo nucifera and pineapple, a monocot.

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Acknowledgements

Research supported in part by grants from the Natural Sciences and Engineering Research Council of Canada (NSERC) and by National Science Foundation IOS –1339156. DS holds the Canada Research Chair in Mathematical Genomics.

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The authors declare that they have no competing interests.

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Authors and Affiliations

  1. Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, ON, K1N 6N5, Canada

    David Sankoff & Chunfang Zheng

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  1. David Sankoff
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  2. Chunfang Zheng
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Correspondence to David Sankoff .

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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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Sankoff, D., Zheng, C. (2018). Whole Genome Duplication in Plants: Implications for Evolutionary Analysis. 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_10

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  • DOI: https://doi.org/10.1007/978-1-4939-7463-4_10

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