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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
...the introgression of Saccharomyces cerevisiae, such as those involved in the maltose metabolism. Finally, the patterns of recombination and LOH suggest an allotetraploid origin of S. bayanus. The gene acquisition and rapid LOH in the hybrid probably facilitated its adaptation to maltose brewing environments...
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Research: Extensive sampling of Saccharomyces cerevisiae in Taiwan reveals ecology and evolution of predomesticated lineages
- Tracy Jiaye Lee,
- Yu-Ching Liu,
- Wei-An Liu,
- Yu-Fei Lin,
- Hsin-Han Lee,
- Huei-Mien Ke,
- Jen-Pan Huang,
- Mei-Yeh Jade Lu,
- Chia-Lun Hsieh,
- Kuo-Fang Chung,
- Gianni Liti,
- and Isheng Jason Tsai
Genome Res. May 2022 32: 864-877; Published in Advance March 31, 2022, doi:10.1101/gr.276286.121
...yeast Saccharomyces cerevisiae before human domestication remain poorly understood. Taiwan is regarded as part of this yeast's geographic birthplace, where the most divergent natural lineage was discovered. Here, we extensively sampled the broadleaf forests across this continental island to probe...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...RNA–DNA sequence differences in Saccharomyces cerevisiae Isabel X. Wang 1 , Christopher Grunseich 2 , Youree G. Chung 3 , Hojoong Kwak 1 , 4 , Girish Ramrattan 1 , 4 , Zhengwei Zhu 1 and Vivian G. Cheung 1 , 4 , 5...
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Research: Fitness benefits of loss of heterozygosity in Saccharomyces hybrids
- Samuel M. Lancaster,
- Celia Payen,
- Caiti Smukowski Heil,
- and Maitreya J. Dunham
Genome Res. October 2019 29: 1685-1692; Published in Advance September 23, 2019, doi:10.1101/gr.245605.118
...that are beneficial when lost in order to determine how prevalent this mode of adaptation may be and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create...
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Research: Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
- Orla M. Keane,
- Christina Toft,
- Lorenzo Carretero-Paulet,
- Gary W. Jones,
- and Mario A. Fares
Genome Res. November 2014 24: 1830-1841; Published in Advance August 22, 2014, doi:10.1101/gr.176792.114
...Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae Orla M. Keane 1 , 2 , 8 , Christina Toft 3 , 4 , 8 , Lorenzo Carretero-Paulet 5 , Gary W. Jones 6 and Mario A...
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Research: Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes
- Monica R. Sanchez,
- Celia Payen,
- Frances Cheong,
- Blake T. Hovde,
- Sarah Bissonnette,
- Adam P. Arkin,
- Jeffrey M. Skerker,
- Rachel B. Brem,
- Amy A. Caudy,
- and Maitreya J. Dunham
Genome Res. March 2019 29: 396-406; Published in Advance January 11, 2019, doi:10.1101/gr.232330.117
...-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent...
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Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
- Casey L. McGrath,
- Jean-Francois Gout,
- Parul Johri,
- Thomas G. Doak,
- and Michael Lynch
Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
...in the Paramecium aurelia complex. [Supplemental material is available for this article.] Whole- duplications (WGDs) are widespread among eukaryotic lineages and have been identified in the ancestry of many model systems, including Saccharomyces cerevisiae (Wolfe and Shields 1997), Xenopus laevis (Morin et al. 2006...
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Method: Unveiling the functional fate of duplicated genes through expression profiling and structural analysis
- Alex Warwick Vesztrocy,
- Natasha Glover,
- Paul D. Thomas,
- Christophe Dessimoz,
- and Irene Julca
Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124
...4NE, United Kingdom; 4Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA Corresponding author: irene.julca@unil.chAbstractGene duplication is a major evolutionary source of functional innovation...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture -wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae, thereby assaying nearly 1 million mutant...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
...Analysis of the Saccharomyces cerevisiae pan- reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments Barbara Dunn1, Chandra Richter2, Daniel J. Kvitek1, Tom Pugh2 and Gavin Sherlock1,3 1Department of Genetics, Stanford University, Stanford...

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