A new system for comparative functional genomics of Saccharomyces yeasts

Amy A. Caudy, Yuanfang Guan, Yue Jia, Christina Hansen, Chris DeSevo, Alicia P. Hayes, Joy Agee, Juan R. Alvarez-Dominguez, Hugo Arellano, Daniel Barrett, Cynthia Bauerle, Namita Bisaria, Patrick H. Bradley, J. Scott Breunig, Erin Bush, David Cappel, Emily Capra, Walter Chen, John Clore, Peter A. CombsChristopher Doucette, Olukunle Demuren, Peter Fellowes, Sam Freeman, Evgeni Frenkel, Daniel Gadala-Maria, Richa Gawande, David Glass, Samuel Grossberg, Anita Gupta, Latanya Hammonds-Odie, Aaron Hoisos, Jenny Hsi, Yu Han Huang Hsu, Sachi Inukai, Konrad J. Karczewski, Xiaobo Ke, Mina Kojima, Samuel Leachman, Danny Lieber, Anna Liebowitz, Julia Liu, Yufei Liu, Trevor Martin, Jose Mena, Rosa Mendoza, Cameron Myhrvold, Christian Millian, Sarah Pfau, Sandeep Raj, Matt Rich, Joe Rokicki, William Rounds, Michael Salazar, Matthew Salesi, Rajani Sharma, Sanford Silverman, Cara Singer, Sandhya Sinha, Max Staller, Philip Stern, Hanlin Tang, Sharon Weeks, Maxwell Weidmann, Ashley Wolf, Carmen Young, Jie Yuan, Christopher Crutchfield, Megan McClean, Coleen T. Murphy, Manuel Llinás, David Botstein, Olga G. Troyanskaya, Maitreya J. Dunham

Research output: Contribution to journalArticle

17 Scopus citations

Abstract

Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a genome-wide functional characterization of a sequenced but experimentally understudied budding yeast, Saccharomyces bayanus var. uvarum (henceforth referred to as S. bayanus), allowing us to map changes over the 20 million years that separate this organism from S. cerevisiae. We first created a suite of genetic tools to facilitate work in S. bayanus. Next, we measured the gene-expression response of S. bayanus to a diverse set of perturbations optimized using a computational approach to cover a diverse array of functionally relevant biological responses. The resulting data set reveals that gene-expression patterns are largely conserved, but significant changes may exist in regulatory networks such as carbohydrate utilization and meiosis. In addition to regulatory changes, our approach identified gene functions that have diverged. The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy. A surprising number of genes specific to S. bayanus respond to oxidative stress, suggesting the organism may have evolved under different selection pressures than S. cerevisiae. This work expands the scope of genome-scale evolutionary studies from sequence-based analysis to rapid experimental characterization and could be adopted for functional mapping in any lineage of interest. Furthermore, our detailed characterization of S. bayanus provides a valuable resource for comparative functional genomics studies in yeast.

Original languageEnglish (US)
Pages (from-to)275-287
Number of pages13
JournalGenetics
Volume195
Issue number1
DOIs
StatePublished - Sep 17 2013

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All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Caudy, A. A., Guan, Y., Jia, Y., Hansen, C., DeSevo, C., Hayes, A. P., Agee, J., Alvarez-Dominguez, J. R., Arellano, H., Barrett, D., Bauerle, C., Bisaria, N., Bradley, P. H., Scott Breunig, J., Bush, E., Cappel, D., Capra, E., Chen, W., Clore, J., ... Dunham, M. J. (2013). A new system for comparative functional genomics of Saccharomyces yeasts. Genetics, 195(1), 275-287. https://doi.org/10.1534/genetics.113.152918