title: Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution.
abstract: In our prior work by Hose et al., we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of S. cerevisiae. We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10-30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose et al., we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres et al. refutes our prior work. Here, we provide a response to Torres et al., along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of S. cerevisiae that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures.
authors.affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.|Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States.
authors.forename: Audrey P
authors.identifier: http://orcid.org/0000-0002-8182-257X
authors.initials: AP
authors.lastname: Gasch
authors.affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.
authors.forename: James
authors.initials: J
authors.lastname: Hose
authors.affiliation: Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States.|Department of Statistics, University of Wisconsin-Madison, Madison, United States.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Newton
authors.affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.
authors.forename: Maria
authors.initials: M
authors.lastname: Sardi
authors.affiliation: Laboratory of Genetics, University of Wisconsin-Madison, Madison, United States.
authors.forename: Mun
authors.initials: M
authors.lastname: Yong
authors.affiliation: Department of Statistics, University of Wisconsin-Madison, Madison, United States.
authors.forename: Zhishi
authors.initials: Z
authors.lastname: Wang
mesh_terms: D000782:Aneuploidy; D018628:Gene Dosage; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D012333:RNA, Messenger / Q000032:analysis; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000502:physiology*
chemical_list: D012333:RNA, Messenger
keywords: <i>s. cerevisiae</i>; aneuploidy; computational biology; copy number variation; dosage compensation; evolution; evolutionary biology; genomics; systems biology