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Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication.
Open accessAbstract
Among yeasts that underwent whole-genome duplication (WGD), Kluyveromyces polysporus represents the lineage most distant from Saccharomyces cerevisiae. By sequencing the K. polysporus genome and comparing it with the S. cerevisiae genome using a likelihood model of gene loss, we show that these species diverged very soon after the WGD, when their common ancestor contained >9,000 genes. The two genomes subsequently converged onto similar current sizes (5,600 protein-coding genes each) and independently retained sets of duplicated genes that are strikingly similar. Almost half of their surviving single-copy genes are not orthologs but paralogs formed by WGD, as would be expected if most gene pairs were resolved independently. In addition, by comparing the pattern of gene loss among K. polysporus, S. cerevisiae, and three other yeasts that diverged after the WGD, we show that the patterns of gene loss changed over time. Initially, both members of a duplicate pair were equally likely to be lost, but loss of the same gene copy in independent lineages was increasingly favored at later time points. This trend parallels an increasing restriction of reciprocal gene loss to more slowly evolving gene pairs over time and suggests that, as duplicate genes diverged, one gene copy became favored over the other. The apparent low initial sequence divergence of the gene pairs leads us to propose that the yeast WGD was probably an autopolyploidization.
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“These Ty-like retrotransposons genes (named here Tkp5-1 to -9) were most similar to the Tkp5 protein from V. polyspora, a yeast representing the postwhole-genome duplication lineage most divergent from S. cerevisiae (Scannell et al. 2007).”
From Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates (2017) · cites this paper as Scannell et al. 2007
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A Recent Whole-Genome Duplication Divides Populations of a Globally Distributed Microsporidian
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InfluentialGenome Duplications as the Basis of Vertebrates’ Evolutionary Success
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BackgroundArchitectural groups of a subtelomeric gene family evolve along distinct paths in Candida albicans
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BackgroundParallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event
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Ancient Gene Duplication Provided a Key Molecular Step for Anaerobic Growth of Baker's Yeast
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Discovery of additional ancient genome duplications in yeasts
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InfluentialGenome doubling enabled the expansion of yeast vesicle traffic pathways
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“Gene gain and loss and even chromosomal rearrangements are common (De Smet et al. 2013; Ma et al. 2013; Ma et al. 2014a; Ma et al. 2015; Scannell et al. 2007; Schnable et al. 2012; Zhang 2003).”
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11 Phylogenomics Enabling Genome-Based Mycology
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Improvisation in evolution of genes and genomes: whose structure is it anyway?
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“al to use likelihood models to better understand the dynamics of gene loss[16].”
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“Whole genome duplications produce syntenic paralogs that can be reciprocally lost [7, 8], sub or neofunctionalized [9], or even retained in the same functional roles as a result of relative or absolute dosage constraints [10].”
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“The protein, coding and genomic sequences for recently sequenced K. polysporus are from Scannell et al 2007 [29].”
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Epigenetics of Eukaryotic Microbes
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Effects of therapeutic passive exercise of hip and knee joints on the soleus H-reflex.
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A Class of Allopolyploidy Showing High Duplicate Retention and Continued Homoeologous Exchanges
Coppage, A., Bhatnagar, E., Joshi, M., Siddiqui, M., McRae, L., & Conant, G. C. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf054 · Cited by 3
“Many of these losses are likely to have oc-curred quite quickly relative to the timescale of speciation events, given the large number of shared ohnolog losses typically observed in the different genomes descending from the same polyploidy (Scannell et al. 2007; Hao et al. 2022).”
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“The gene loss in polyploidy plants is realized quite early (Leitch and Bennett 2004), and duplicate gene loss after WGD is common (Sankoff and Zheng 2018; Scannell et al. 2007).”
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Fungal horizons: The Asilomar Fungal Genetics Conference 2007
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POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics
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Evolutionary Genomics of Yeasts
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Fitness Benefits of Loss of Heterozygosity in Saccharomyces HybridsPreprint
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Copy Number Variation: A Substrate for Plant Adaptation and Stress Response in ArabidopsisPreprint
Karunarathne, P., Schäfer, Y., Glushkevich, A., Scott, A. D., Abraham, L., de Meaux, J., Novikova, P. Y., Wiehe, T., & Rose, L. E. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.15.670553 · Cited by 2
“This dynamic balance between preservation and loss shapes long-term gene family evolution (Scannell et al., 2007; Smet et al., 2013).”
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Copy number variation: a substrate for plant adaptation and stress response in Arabidopsis
Karunarathne, P., Schäfer, Y., Glushkevich, A., Scott, A. D., Abraham, L., de Meaux, J., Novikova, P. Y., Wiehe, T., & Rose, L. E. (2026) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkag183 · Cited by 3
Horizontal gene transfer in Saccharomyces cerevisiae and other Saccharomycotina yeasts: a review
Grassi, A., Rogo, U., Fambrini, M., Pugliesi, C., & Agnolucci, M. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-05118-2 · Cited by 1
“This event occurred shortly before the divergence of Vanderwaltozyma polyspora , giving rise to a clade of post-WGD species (Scannell et al. 2007).”
Moix, S., Glover, N., & Majidian, S. (2023) · F1000Research · doi:10.12688/f1000research.128656.1 · Cited by 1
Co-option of pre-existing pathways during Rhizobium-legume symbiosis evolution
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Metadata
- Authors
- Scannell, D. R., Frank, A. C., Conant, G. C., Byrne, K. P., Woolfit, M., & Wolfe, K. H.
- Affiliations
- Trinity College Dublin (IE)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2007-05-15
- Volume
- 104
- Issue
- 20
- Pages
- 8397-8402
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC1895961
- OpenAlex
- W2064322162
- Cited by
- 235
- References
- 30
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 3 · 2023: 6 · 2022: 8 · 2021: 9 · 2020: 9 · 2019: 6 · 2018: 11 · 2017: 15 · 2016: 10 · 2015: 14 · 2014: 10 · 2013: 12 · 2012: 17
- FWCI
- 28.69
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- whole-genome duplication, gene loss, paralogs, orthologs, Saccharomyces cerevisiae, yeast evolution, autopolyploidization, gene family evolution, genome size reduction
- MeSH terms
- Base Sequence, Kluyveromyces, Models, Genetic, Molecular Sequence Data, Saccharomyces cerevisiae, Sequence Homology, Nucleic Acid, Time Factors, Likelihood Functions, Genome, Fungal, Conserved Sequence, Evolution, Molecular, Genes, Duplicate, Gene Duplication, Gene Order
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