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Research: Independent evolution of transcript abundance and gene regulatory dynamics
- Gat Krieger,
- Offir Lupo,
- Avraham A. Levy,
- and Naama Barkai
Genome Res. July 2020 30: 1000-1011; Published in Advance July 22, 2020, doi:10.1101/gr.261537.120
..., but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels...
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Research: Global deceleration of gene evolution following recent genome hybridizations in fungi
- Sira Sriswasdi,
- Masako Takashima,
- Ri-ichiroh Manabe,
- Moriya Ohkuma,
- Takashi Sugita,
- and Wataru Iwasaki
Genome Res. August 2016 26: 1081-1090; Published in Advance July 20, 2016, doi:10.1101/gr.205948.116
.... glabrata, and L. waltii were downloaded from the National Center for Biotechnology Information (NCBI), the Saccharomyces Genome Database, the Candida Genome Database, and the Yeast Gene Order Browser database (http://ygob.ucd.ie/), respectively. Synteny structure reconstruction Synteny relationships...
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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
...of singletons. Analyses of yeast gene expression conditions showed a larger variation in the duplicates’ expression than that of singletons under a range of stress conditions, sparking the idea that regulatory robustness allowed a wider range of phenotypic responses to environmental stresses, hence faster...
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Methods: SyMAP: A system for discovering and viewing syntenic regions of FPC maps
- Carol Soderlund,
- William Nelson,
- Austin Shoemaker,
- and Andrew Paterson
Genome Res. September 2006 16: 1159-1168; doi:10.1101/gr.5396706
....P. , Wolfe K.H. ( 2005 ) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species . Genome Res. 15 : 1456 – 1461 . ↵ Calabrese P.P. , Chakravarty S. , Vision T.J. ( 2003 ) Fast identification and statistical evaluation of segmental homologies...
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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
...A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Devin R. Scannell 1 , 2 and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland Abstract...
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12 Drosophila Genomes/Methods: Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
- Matthew D. Rasmussen and
- Manolis Kellis
Genome Res. December 2007 17: 1932-1942; Published in Advance November 7, 2007, doi:10.1101/gr.7105007
...whole- duplication data set, we used S. cerevisiae , S. castellii , and C. glabrata ohnologs from the Yeast Gene Order Browser (YGOB) ( Byrne and Wolfe 2005 ). Ohnologs were clustered by best reciprocal BLAST hits. Clusters were filtered such that exactly one ohnolog pair from each species is present...
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LETTER: Relaxation of yeast mitochondrial functions after whole-genome duplication
- Huifeng Jiang,
- Wenjun Guan,
- David Pinney,
- Wen Wang,
- and Zhenglong Gu
Genome Res. September 2008 18: 1466-1471; Published in Advance July 30, 2008, doi:10.1101/gr.074674.107
...of fourteen hemiascomycetous yeasts . FEMS Yeast Res. 5 : 545 – 558 . ↵ Byrne, K.P. , Wolfe, K.H. ( 2005 ) The Yeast Gene Order Browser: Combining curated homology and syntenic context reveals gene fate in polyploid species . Genome Res. 15 : 1456 – 1461 . ↵ Castillo-Davis, C.I. , Hartl, D.L. ( 2003 ) Gene...
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LETTER: Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans
- Quinn M. Mitrovich,
- Brian B. Tuch,
- Christine Guthrie,
- and Alexander D. Johnson
Genome Res. April 2007 17: 492-502; Published in Advance March 9, 2007, doi:10.1101/gr.6111907
.... The hemiascomycetous yeasts, which include C. albicans and the well-studied model organism Saccharomyces cerevisiae , in contrast, have experienced exceptionally high rates of intron loss ( Dujon 2006 ). As a result, only 5% of genes in S. cerevisiae contain introns, and most of these genes contain only one ( Davis et...
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Resource: Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae
- Zhaolian Lu and
- Zhenguo Lin
Genome Res. July 2019 29: 1198-1210; Published in Advance May 10, 2019, doi:10.1101/gr.245456.118
...in their orthologous sequences obtained from the Yeast Gene Order Browser (YGOB) (Supplemental Methods; Supplemental Data S2; Byrne and Wolfe 2005). We also determined whether peptides have been detected in the potentially misannotated regions based on a large collection of proteomic data compiled by the Global...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
.... S1, S2; see Methods). Irx complexes are linked to Sowah genes in nearly all bilaterian lineages, with the exception of tetrapods, tunicates, and the leech Helobdella robusta. Alignment of intron/exon structures of metazoan Sowah genes revealed that several intron positions (ancestral introns 5...

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