Cited by 614Fungal and yeast genetics researchChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

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Natural history and evolutionary principles of gene duplication in fungi

Wapinski, Ilan, Pfeffer, Avi, Friedman, Nir, Regev, Aviv·2007·Nature

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Abstract

Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.

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The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,959
MUSCLE: multiple sequence alignment with high accuracy and high throughput
Edgar, R. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh340 · Cited by 44,662
Gene Ontology: tool for the unification of biology
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Improved tools for biological sequence comparison.
Pearson, W. R., & Lipman, D. J. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.8.2444 · Cited by 11,227
Evolution by Gene Duplication
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
The COG database: an updated version includes eukaryotes
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S., Nikolskaya, A. N., et al. (2003) · BMC Bioinformatics · doi:10.1186/1471-2105-4-41 · Cited by 4,410
Proteome survey reveals modularity of the yeast cell machinery
Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,570
Functional Discovery via a Compendium of Expression Profiles
Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R. B., Armour, C. D., Bennett, H. A., Coffey, E. M., Dai, H. A., He, Y. D., et al. (2000) · Cell · doi:10.1016/s0092-8674(00)00015-5 · Cited by 2,534

Show all 59 references

Research works printed but not linked: 1

Arnaud, M. B. C. M. et al. Candida Genome Database 〈 http://www.candidagenome.org 〉 (2006)

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Authors: Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A.
Affiliations: Broad Institute (US)
Harvard University (US)
Hebrew University of Jerusalem (IL)
Corresponding author: Regev, Aviv
ORCID: Pfeffer, Avi
Friedman, Nir
Regev, Aviv
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2007-09
Volume: 449
Issue: 7158
Pages: 54-61
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature06107
OpenAlex: W1992140809
Cited by: 614
References: 59
Citations by year: 2026: 7 · 2025: 10 · 2024: 6 · 2023: 14 · 2022: 11 · 2021: 17 · 2020: 22 · 2019: 20 · 2018: 37 · 2017: 44 · 2016: 33 · 2015: 34 · 2014: 34 · 2013: 44 · 2012: 59
FWCI: 23.70
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: gene duplication, gene loss, fungi, Ascomycota, whole-genome duplication, orthology, paralogy, gene tree inference, functional innovation, stress-related genes, growth-related genes, Saccharomyces cerevisiae, Schizosaccharomyces pombe
MeSH terms: Algorithms, Ascomycota, Genes, Fungal, Phylogeny, Genome, Fungal, Gene Deletion, Gene Dosage, Evolution, Molecular, Genes, Duplicate, Gene Duplication

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Natural history and evolutionary principles of gene duplication in fungi

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