The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
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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“0 Vanderwaltozyma polyspora VAPO DSM 70294 (Scannell et al., 2007b) Wickerhamomyces ciferrii WICI NRRL Y-1031 F-60-10 (Schneider et al., 2012) Yarrowia lipolytica YALI CLIB122 (Dujon et al., 2004) Zygosaccharomyces bailii ZYBA CLIB 213 (Galeote et al., 2013) Zygosaccharomyces rouxii ZYRO CBS732…”
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All detectable ancient whole-genome duplications involve hybridizationPreprint
Gaynor, M. L., Feng, K., Soltis, D. E., Soltis, P. S., & Smith, S. A. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.25.747000
“In other cases, for example yeasts, low sequence divergence was attributed to an autopolyploid origin (41), with subsequent analyses supporting an allopolyploid origin (42).”
Graph-based methods for large-scale protein classification and orthology inference
Kuzniar, A. (2009) · doi:10.18174/12707
“An analysis of fungal genomes has indicated that, by incorporating the information of CGNs into orthology detection, approximately half of the predicted one-to-one orthologs are, in fact, out-paralogs owing to reciprocal gene losses (Scannell et al., 2007).”
Background
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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