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LETTER: Metabolic functions of duplicate genes in Saccharomyces cerevisiae
- Lars Kuepfer,
- Uwe Sauer,
- and Lars M. Blank
Genome Res. October 2005 15: 1421-1430; doi:10.1101/gr.3992505
..., is currently lacking. In a systems biology approach, we classify here back-up, regulatory, and gene dosage functions for the 105 duplicate gene families of Saccharomyces cerevisiae metabolism. The key tool was the reconciled -scale metabolic model iLL672, which was based on the older iFF708. Computational...
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LETTER: The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast
- Gabriel Musso,
- Michael Costanzo,
- ManQin Huangfu,
- Andrew M. Smith,
- Jadine Paw,
- Bryan-Joseph San Luis,
- Charles Boone,
- Guri Giaever,
- Corey Nislow,
- Andrew Emili,
- and Zhaolei Zhang
Genome Res. July 2008 18: 1092-1099; Published in Advance May 7, 2008, doi:10.1101/gr.076174.108
.... , Scharfe, C. , Davis, R.W. , Li, W.H. ( 2003 ) Role of duplicate genes in genetic robustness against mutations . Nature 421 : 63 – 66 . ↵ Guan, Y. , Dunham, M.J. , Troyanskaya, O.G. ( 2007 ) Functional analysis of gene duplications in Saccharomyces cerevisiae . Genetics 175 : 933 – 943 . ↵ Hakes, L...
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Research: Genomic evidence for adaptation by gene duplication
- Wenfeng Qian and
- Jianzhi Zhang
Genome Res. August 2014 24: 1356-1362; Published in Advance June 5, 2014, doi:10.1101/gr.172098.114
...to the conclusion that duplication rarely results in adaptation. Here we contend that the above comparison is unfair because of a known duplication bias among genes with different fitness contributions. To rectify this problem, we compare homologous genes from the budding yeast Saccharomyces cerevisiae...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...(TEs) and other repetitive sequences are known to be one of the major causes of structural variations within individuals and species, promoting expansion, gene duplication, gene loss, genomic rearrangements, and reshaping of the overall genomic regulatory network (Bourque et al. 2018). Among fungi...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...values (Ks = 3 to 4) in the gymnolaemate bryozoans, which could indicate ancient WGD in this lineage, but the signal is very weak (Supplemental Fig. S7).Given this uncertainty, we then used MCScanX (Wang et al. 2012) to identify and align collinear blocks of genes within each . The presence of duplicated...
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PERSPECTIVE: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
- Michael Freeling and
- Brian C. Thomas
Genome Res. July 2006 16: 805-814; doi:10.1101/gr.3681406
...dosage effects has engendered a robust “gene balance hypothesis,” with a theoretical base that makes specific predictions as to gene content changes following different types of gene duplication. Genomic data from both chordate and angiosperm s fit these predictions: Each type of duplication provides...
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LETTER: Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels
- Francesca Chiaromonte,
- Webb Miller,
- and Eric E. Bouhassira,
Genome Res. December 2003 13: 2602-2608; Published in Advance January 1, 2003, doi:10.1101/gr.1169203
...expression of neighboring genes, and conversely, gene silencing associated with aging ( Issa 2000 ) could activate neighboring genes. Transcriptional interference might also partially explain the recent finding that in Saccharomyces cerevisiae , adjacent pairs of genes tend to be coregulated ( Cohen et al...
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LETTER: A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast
- Devin R. Scannell and
- Kenneth H. Wolfe
Genome Res. January 2008 18: 137-147; Published in Advance November 19, 2007, doi:10.1101/gr.6341207
...asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. We discuss the contribution of neofunctionalization to duplicate gene preservation and propose that a form of subfunctionalization mediated by coding region...
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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
...evolution using only branch length information. This offers two key advantages: (1) it allows us to leverage precompiled libraries of gene trees such as PANTHER, eliminating the need to construct a custom data set; and (2) it enables the analysis of ancient gene duplication events, where nucleotide...
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Research: Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters
- Danny Zeevi,
- Shai Lubliner,
- Maya Lotan-Pompan,
- Eran Hodis,
- Rita Vesterman,
- Adina Weinberger,
- and Eran Segal
Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114
...by expressing in S. cerevisiae 668 ribosomal protein (RP) gene promoters taken from nine yeast species and by further examining several pairs of orthologous promoters through a library of 91 chimeric promoters. Our results shed new light on how yeast promoters can evolve in sequencewhile preserving...

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