ArticleScience (New York, N.Y.)2024
Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.
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Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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94citing papers in PubMed
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94 citing papers in PubMed, 115 citations in OpenAlex.
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- The carbohydrate utilization regulator Cbr1 coordinates nutrient-specific gene activation with selective carbon catabolite repression in a basidiomycete yeast.PLoS biology · 2026Article
- Genetic Tools in the Nakaseomyces clade for Evolutionary Comparisons of Signal Transduction Pathways.Yeast (Chichester, England) · 2026Article
- Evolutionary diversification of invertase paralogs couples carbon metabolism and sexual reproduction in fission yeasts.Molecular biology and evolution · 2026Article
- Evolutionary relationship between yeast telomeric protein Cdc13 and Pot1.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2026Article
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- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 2026Article
- Genotypic and Phenotypic Diversity of Maudiozyma humilis: The Multiple Evolutionary Trajectories of a Domesticated Yeast.Genome biology and evolution · 2026Article
- Taxonomic revision of the genusPersoonia · 2026Article
- Diversity and extracellular enzymatic activity of culturable yeasts isolated from soil in a Brazilian Amazonian rainforest biome.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.Cell research · 2026Article
- Regions of low gene expression promote maintenance and adaptation of horizontally acquired genes in yeasts.Communications biology · 2026Article
- Convergent evolution of aerobic fermentation through divergent mechanisms acting on key shared glycolytic genes.The EMBO journal · 2026Article
- Nitrogen management in the optimization of microbial plastic waste upcycling.Bioresources and bioprocessing · 2026Article
- Genome sequence of the yeastMicrobiology resource announcements · 2026Article
34 more citing papers are in PubMed but not listed here.
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Authors and funding
32 authors at 14 institutions in 8 countries.
Dana A Opulente *Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0003-3224-7510
Abigail Leavitt LaBella *Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0003-0068-6703
Marie-Claire Harrison *Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0002-3013-9906
John F Wolters *Laboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0002-5477-4250
Chao LiuCollege of Agriculture and Biotechnology and Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou 310058, China.ORCID 0000-0002-4252-4019
Yonglin LiGuangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.ORCID 0009-0008-2774-9106
Jacek KominekLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0002-1916-0122
Jacob L SteenwykDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0002-8436-595X
Hayley R StonemanLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Jenna VanDenAvondLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0009-0007-1229-1617
Caroline R MillerLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0009-0000-7177-4618
Quinn K LangdonLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0002-2141-3571
Margarida SilvaUCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Carla GonçalvesLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Emily J UbbelohdeLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0003-3672-429X
Yuanning LiDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0002-2206-5804
Kelly V BuhLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.
Martin JarzynaLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0002-2485-6589
Max A B HaaseLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0002-8962-0446
Carlos A RosaDepartamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.ORCID 0000-0002-0056-9075
Neža ČCadežFood Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.ORCID 0000-0002-4987-0539
Diego LibkindCentro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Universidad Nacional del Comahue, CONICET, CRUB, Quintral 1250, San Carlos de Bariloche, 8400, Río Negro, Argentina.ORCID 0000-0001-9687-6186
Jeremy H DeVirgilioMycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.ORCID 0009-0004-8147-364X
Amanda Beth HulfachorLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0009-0009-7387-3287
Cletus P KurtzmanMycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.
José Paulo SampaioUCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Paula GonçalvesUCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
Xiaofan ZhouDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0002-2879-6317
Xing-Xing ShenDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0001-5765-1419
Marizeth GroenewaldWesterdijk Fungal Biodiversity Institute, 3584 CT Utrecht, Netherlands.ORCID 0000-0003-0835-5925
Antonis RokasDepartment of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.ORCID 0000-0002-7248-6551
Chris Todd HittingerLaboratory of Genetics, Wisconsin Energy Institute, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA.ORCID 0000-0001-5088-7461
Great Lakes Bioenergy Research Center · USVanderbilt University · USSouth China Agricultural University · CNUniversidade Nova de Lisboa · PTAgricultural Research Service · USEnergy Center of Wisconsin · USConsejo Nacional de Investigaciones Científicas y Técnicas · ARHoward Hughes Medical Institute · USUniversidade Federal de Minas Gerais · BRUniversity of Ljubljana · SIUniversity of North Carolina at Charlotte · USWashington University in St. Louis · USWesterdijk Fungal Biodiversity Institute · NLZhejiang University · CN
Funding
Institutional Training in the Genomic SciencesT32HG002760 · NHGRI · UNIVERSITY OF WISCONSIN-MADISON · PI Qiongshi Lu · 2003 to 2026
$17.7MPREDOCTORAL TRAINING PROGRAM IN GENETICST32GM007133 · NIGMS · UNIVERSITY OF WISCONSIN-MADISON · PI PERNA, NICOLE T · 1985 to 2023
$16.5MDeciphering the phenotypic and genomic traits that underlie the evolution of pathogenicity differences among Aspergillus fumigatus and its close relativesR01AI153356 · NIAID · VANDERBILT UNIVERSITY · PI Antonis Rokas · 2022 to 2026
$3.5MDeciphering the phenotypic and genomic traits that underlie the evolution of pathogenicity differences among Aspergillus fumigatus and its close relativesR56AI146096 · NIAID · VANDERBILT UNIVERSITY · PI ROKAS, ANTONIS · 2020 to 2020
$592kNHGRI NIH HHS T32 HG002760NIAID NIH HHS R01 AI153356NIAID NIH HHS R56 AI146096NIGMS NIH HHS T32 GM007133
Abstract
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Two general paradigms have been proposed to explain this variation: (i) trade-offs between performance efficiency and breadth and (ii) the joint influence of extrinsic (environmental) and intrinsic (genomic) factors. We assembled genomic, metabolic, and ecological data from nearly all known species of the ancient fungal subphylum Saccharomycotina (1154 yeast strains from 1051 species), grown in 24 different environmental conditions, to examine niche breadth evolution. We found that large differences in the breadth of carbon utilization traits between yeasts stem from intrinsic differences in genes encoding specific metabolic pathways, but we found limited evidence for trade-offs. These comprehensive data argue that intrinsic factors shape niche breadth variation in microbes.
Indexed as
AscomycotaCarbonGene-Environment InteractionNitrogenGenome, FungalMetabolic Networks and PathwaysPhylogenyCarbonNitrogen
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