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Cited by 628Yeasts and Rust Fungi StudiesFungal and yeast genetics researchGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 112 of the 112 references it cites were found in a registry or an index.

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

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Shen, Xing-Xing, Opulente, Dana A., Kominek, Jacek, Zhou, Xiaofan, Steenwyk, Jacob L., Buh, Kelly V., Haase, Max A.B., Wisecaver, Jennifer H., Wang, Mingshuang, Doering, Drew T., Boudouris, James T., Schneider, Rachel M., Langdon, Quinn K., Ohkuma, Moriya, Endoh, Rikiya, Takashima, Masako, Manabe, Ri-ichiroh, Čadež, Neža, Libkind, Diego, Rosa, Carlos A., DeVirgilio, Jeremy, Hulfachor, Amanda Beth, Groenewald, Marizeth, Kurtzman, Cletus P., Hittinger, Chris Todd, Rokas, Antonis·2018·Cell
DOI 10.1016/j.cell.2018.10.023PMC PMC6291210
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Abstract

Budding yeasts (subphylum Saccharomycotina) are found in every biome and are as genetically diverse as plants or animals. To understand budding yeast evolution, we analyzed the genomes of 332 yeast species, including 220 newly sequenced ones, which represent nearly one-third of all known budding yeast diversity. Here, we establish a robust genus-level phylogeny comprising 12 major clades, infer the timescale of diversification from the Devonian period to the present, quantify horizontal gene transfer (HGT), and reconstruct the evolution of 45 metabolic traits and the metabolic toolkit of the budding yeast common ancestor (BYCA). We infer that BYCA was metabolically complex and chronicle the tempo and mode of genomic and phenotypic evolution across the subphylum, which is characterized by very low HGT levels and widespread losses of traits and the genes that control them. More generally, our results argue that reductive evolution is a major mode of evolutionary diversification.

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Authors
Shen, X.-X., Opulente, D. A., Kominek, J., Zhou, X., Steenwyk, J. L., Buh, K. V., Haase, M. A. B., Wisecaver, J. H., Wang, M., Doering, D. T., Boudouris, J. T., Schneider, R. M., Langdon, Q. K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R.-I., Čadež, N., Libkind, D., Rosa, C. A., DeVirgilio, J., Hulfachor, A. B., Groenewald, M., Kurtzman, C. P., Hittinger, C. T., & Rokas, A.
Affiliations
  • Vanderbilt University (US)
  • University of Wisconsin–Madison (US)
  • South China Agricultural University (CN)
  • RIKEN BioResource Research Center (JP)
  • RIKEN Center for Integrative Medical Sciences (JP)
  • University of Ljubljana (SI)
  • Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
  • Universidade Federal de Minas Gerais (BR)
  • Agricultural Research Service (US)
  • Westerdijk Fungal Biodiversity Institute (NL)
Corresponding author
  • Hittinger, Chris Todd
  • Rokas, Antonis
ORCID
Venue
Cell
Publisher
Elsevier BV
Published
2018-11
Volume
175
Issue
6
Pages
1533-1545.e20
ISSN
0092-8674 (ISSN-L)
DOI
10.1016/j.cell.2018.10.023
PMC
PMC6291210
OpenAlex
W2899763402
Cited by
619
References
112
Citations by year
2026: 56 · 2025: 72 · 2024: 109 · 2023: 83 · 2022: 70 · 2021: 116 · 2020: 68 · 2019: 43 · 2018: 1
FWCI
20.28
Type
journal article
Language
en
Open access
Licence
Locations
  • Cell (publishedVersion)
  • PubMed (publishedVersion)
  • KNAW Research Portal (The Royal Netherlands Academy of Arts and Sciences) (publishedVersion, other-oa)
  • LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
  • PubMed Central (acceptedVersion)
  • Data Archiving and Networked Services (DANS) (submittedVersion)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • CONICET Digital (CONICET) (submittedVersion, cc-by-nc-sa)
Funders
  • National Science Foundation (DEB-1442113, DEB-1442148, IOS-1401682, DGE-1256259)
  • DOE Great Lakes Bioenergy Research Center (DE-FC02-07ER64494, DE-SC0018409)
  • Pew Charitable Trusts
  • Vilas Trust Estate
  • Guggenheim
  • Vanderbilt
  • National Key Project for Basic Research of China (2015CB150600)
  • NHGRI (5T32HG002760)
  • NIH (5T32GM007133)
  • CONICET (PIP 392)
  • FONCyT (PICT 2542)
  • Universidad Nacional del Comahue (B199)
  • Conselho Nacional de Desenvolvimento Científico e Tecnológico
  • Fundação de Amparo a Pesquisa do Estado de Minas Gerais
Topics
  • Life Sciences › Immunology and Microbiology › Microbiology › Yeasts and Rust Fungi Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
Saccharomyces cerevisiae, Saccharomycotina, genome evolution, phylogeny, horizontal gene transfer, metabolic phenotypes, common ancestor, reductive evolution, gene loss
MeSH terms
Saccharomycetales, Phylogeny, Genome, Fungal, Evolution, Molecular, Gene Transfer, Horizontal

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