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Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
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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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“In a previous study, the genomes of 343 yeast/fungi species combined with comprehensive genome annotations were publicly available 63 .”
From Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (2022) · cites this paper as [63]
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Metadata
- 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
- Shen, Xing-Xing
- Opulente, Dana A.
- Kominek, Jacek
- Zhou, Xiaofan
- Steenwyk, Jacob L.
- Haase, Max A.B.
- Wisecaver, Jennifer H.
- Wang, Mingshuang
- Doering, Drew T.
- Langdon, Quinn K.
- Ohkuma, Moriya
- 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
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-11
- Volume
- 175
- Issue
- 6
- Pages
- 1533-1545.e20
- ISSN
- 0092-8674 (ISSN-L)
- 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
- bronze
- doi.org
- 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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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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