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Genomic and ecological factors shaping specialism and generalism across an entire subphylum.
Opulente, Dana A; Leavitt LaBella, Abigail; Harrison, Marie-Claire; Wolters, John F; Liu, Chao; Li, Yonglin; Kominek, Jacek; Steenwyk, Jacob L; Stoneman, Hayley R; VanDenAvond, Jenna; Miller, Caroline R; Langdon, Quinn K; Silva, Margarida; Gonçalves, Carla; Ubbelohde, Emily J; Li, Yuanning; Buh, Kelly V; Jarzyna, Martin; Haase, Max A B; Rosa, Carlos A; Cadez, Neza; Libkind, Diego; DeVirgilio, Jeremy H; Beth Hulfachor, Amanda; Kurtzman, Cletus P; Sampaio, José Paulo; Gonçalves, Paula; Zhou, Xiaofan; Shen, Xing-Xing; Groenewald, Marizeth; Rokas, Antonis; Hittinger, Chris Todd.
Affiliation
  • Opulente DA; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Biology Department Villanova University, Villanova, PA 19085
  • Leavitt LaBella A; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232 USA; Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte NC 28223.
  • Harrison MC; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
  • Wolters JF; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Liu C; College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China.
  • Li Y; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
  • Kominek J; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; LifeMine Therapeutics, Inc., Cambridge, MA 02140, USA.
  • Steenwyk JL; Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, U
  • Stoneman HR; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • VanDenAvond J; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Miller CR; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Langdon QK; Laboratory of Genetics, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Silva M; UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
  • Gonçalves C; UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Department of Biological Sciences, Vanderbilt University, Na
  • Ubbelohde EJ; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Li Y; Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China.
  • Buh KV; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Jarzyna M; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Graduate Program in Neuroscience and Department of Biology,
  • Haase MAB; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA; Vilcek Institute of Graduate Biomedical Sciences and Institu
  • Rosa CA; Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
  • Cadez N; Food Science and Technology Department, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
  • Libkind D; Centro 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.
  • DeVirgilio JH; Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA.
  • Beth Hulfachor A; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
  • Kurtzman CP; Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, Peoria, IL 61604, USA.
  • Sampaio JP; UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
  • Gonçalves P; UCIBIO, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal; Associate Laboratory i4HB, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
  • Zhou X; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China.
  • Shen XX; Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; College of Agriculture and Biotechnology and Centre for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou 310058, China.
  • Groenewald M; Westerdijk Fungal Biodiversity Institute, 3584 Utrecht, The Netherlands.
  • Rokas A; Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA.
  • Hittinger CT; Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Center for Genomic Science Innovation, J. F. Crow Institute for the Study of Evolution, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA.
bioRxiv ; 2023 Sep 08.
Article in En | MEDLINE | ID: mdl-37425695
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,049 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2023 Document type: Article Country of publication: United States
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Full text: 1 Collection: 01-internacional Database: MEDLINE Language: En Journal: BioRxiv Year: 2023 Document type: Article Country of publication: United States