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Natural history and evolutionary principles of gene duplication in fungi
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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“Evolution of genetic signaling and regulatory systems usually proceeds through gene duplication and loss with concomitant processes of neofunctionalization and subfunctionalization leading to functional changes”
From Mitochondrial retrograde control of transcription evolves with respiratory stress, metabolic adaptation, and virulence in budding yeasts (2026) · cites this paper as Wapinski et al. 2007
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Metadata
- 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
- Venue
- Nature
- Published
- 2007-09
- Volume
- 449
- Issue
- 7158
- Pages
- 54-61
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- 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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