@article{1845,
  keywords = {Gene Expression Profiling, Molecular Sequence Annotation, Fungal Proteins, Genome, Fungal, Oxidative Stress, Saccharomyces},
  author = {Amy Caudy and Yuanfang Guan and Yue Jia and Christina Hansen and Chris DeSevo and Alicia Hayes and Joy Agee and Juan Alvarez-Dominguez and Hugo Arellano and Daniel Barrett and Cynthia Bauerle and Namita Bisaria and Patrick Bradley and Scott Breunig and Erin Bush and David Cappel and Emily Capra and Walter Chen and John Clore and Peter Combs and Christopher Doucette and Olukunle Demuren and Peter Fellowes and Sam Freeman and Evgeni Frenkel and Daniel Gadala-Maria and Richa Gawande and David Glass and Samuel Grossberg and Anita Gupta and Latanya Hammonds-Odie and Aaron Hoisos and Jenny Hsi and Yu-Han Hsu and Sachi Inukai and Konrad Karczewski and Xiaobo Ke and Mina Kojima and Samuel Leachman and Danny Lieber and Anna Liebowitz and Julia Liu and Yufei Liu and Trevor Martin and Jose Mena and Rosa Mendoza and Cameron Myhrvold and Christian Millian and Sarah Pfau and Sandeep Raj and Matt Rich and Joe Rokicki and William Rounds and Michael Salazar and Matthew Salesi and Rajani Sharma and Sanford Silverman and Cara Singer and Sandhya Sinha and Max Staller and Philip Stern and Hanlin Tang and Sharon Weeks and Maxwell Weidmann and Ashley Wolf and Carmen Young and Jie Yuan and Christopher Crutchfield and Megan McClean and Coleen Murphy and Manuel Llin{\'a}s and David Botstein and Olga Troyanskaya and Maitreya Dunham},
  title = {A new system for comparative functional genomics of Saccharomyces yeasts.},
  abstract = {<p>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.</p>},
  year = {2013},
  journal = {Genetics},
  volume = {195},
  pages = {275-87},
  month = {09/2013},
  language = {eng},
}