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Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

Author

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  • Manolis Kellis

    (Massachusetts Institute of Technology and Harvard University
    MIT Computer Science and Artificial Intelligence Laboratory)

  • Bruce W. Birren

    (Massachusetts Institute of Technology and Harvard University)

  • Eric S. Lander

    (Massachusetts Institute of Technology and Harvard University
    Whitehead Institute for Biomedical Research)

Abstract

Whole-genome duplication followed by massive gene loss and specialization has long been postulated as a powerful mechanism of evolutionary innovation. Recently, it has become possible to test this notion by searching complete genome sequence for signs of ancient duplication. Here, we show that the yeast Saccharomyces cerevisiae arose from ancient whole-genome duplication, by sequencing and analysing Kluyveromyces waltii, a related yeast species that diverged before the duplication. The two genomes are related by a 1:2 mapping, with each region of K. waltii corresponding to two regions of S. cerevisiae, as expected for whole-genome duplication. This resolves the long-standing controversy on the ancestry of the yeast genome, and makes it possible to study the fate of duplicated genes directly. Strikingly, 95% of cases of accelerated evolution involve only one member of a gene pair, providing strong support for a specific model of evolution, and allowing us to distinguish ancestral and derived functions.

Suggested Citation

  • Manolis Kellis & Bruce W. Birren & Eric S. Lander, 2004. "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae," Nature, Nature, vol. 428(6983), pages 617-624, April.
    • Handle: RePEc:nat:nature:v:428:y:2004:i:6983:d:10.1038_nature02424
    DOI: 10.1038/nature02424
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    Cited by:

    1. Alex N Nguyen Ba & Bob Strome & Jun Jie Hua & Jonathan Desmond & Isabelle Gagnon-Arsenault & Eric L Weiss & Christian R Landry & Alan M Moses, 2014. "Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-15, December.
    2. S Konini & E J Janse van Rensburg, 2017. "Mean field analysis of algorithms for scale-free networks in molecular biology," PLOS ONE, Public Library of Science, vol. 12(12), pages 1-34, December.
    3. Lit-Hsin Loo & Danai Laksameethanasan & Yi-Ling Tung, 2014. "Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins," PLOS Computational Biology, Public Library of Science, vol. 10(3), pages 1-17, March.
    4. Anupama Yadav & Aparna Radhakrishnan & Anshuman Panda & Amartya Singh & Himanshu Sinha & Gyan Bhanot, 2016. "The Modular Adaptive Ribosome," PLOS ONE, Public Library of Science, vol. 11(11), pages 1-23, November.

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