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Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex

Geiser DM 1 , Al-Hatmi AMS 2 , Aoki T 3 , Arie T 4 , Balmas V 5 , Barnes I 6 Show all authors , Bergstrom GC 7 , Bhattacharyya MK 8 , Blomquist CL 9 , Bowden RL 10 , Brankovics B 11 , Brown DW 12 , Burgess LW 13 , Bushley K 14 , Busman M 12 , Cano-Lira JF 15 , Carrillo JD 16 , Chang HX 17 , Chen CY 18 , Chen W 19 , Chilvers M 20 , Chulze S 21 , Coleman JJ 22 , Cuomo CA 23 , de Beer ZW 6 , de Hoog GS 24 , Del Castillo-Múnera J 25 , Del Ponte EM 26 , Diéguez-Uribeondo J 27 , Di Pietro A 28 , Edel-Hermann V 29 , Elmer WH 30 , Epstein L 25 , Eskalen A 25 , Esposto MC 31 , Everts KL 32 , Fernández-Pavía SP 33 , da Silva GF 34 , Foroud NA 35 , Fourie G 6 , Frandsen RJN 36 , Freeman S 37 , Freitag M 38 , Frenkel O 37 , Fuller KK 39 , Gagkaeva T 40 , Gardiner DM 41 , Glenn AE 42 , Gold SE 42 , Gordon TR 25 , Gregory NF 43 , Gryzenhout M 44 , Guarro J 45 , Gugino BK 1 , Gutierrez S 46 , Hammond-Kosack KE 47 , Harris LJ 48 , Homa M 49 , Hong CF 18 , Hornok L 50 , Huang JW 18 , Ilkit M 51 , Jacobs A 52 , Jacobs K 53 , Jiang C 54 , Jiménez-Gasco MDM 1 , Kang S 1 , Kasson MT 55 , Kazan K 41 , Kennell JC 56 , Kim HS 12 , Kistler HC 57 , Kuldau GA 1 , Kulik T 58 , Kurzai O 59 , Laraba I 12 , Laurence MH 60 , Lee T 61 , Lee YW 62 , Lee YH 62 , Leslie JF 63 , Liew ECY 60 , Lofton LW 42 , Logrieco AF 64 , López-Berges MS 28 , Luque AG 65 , Lysøe E 66 , Ma LJ 67 , Marra RE 30 , Martin FN 68 , May SR 1 , McCormick SP 12 , McGee C 1 , Meis JF 24 , Migheli Q 69 , Mohamed Nor NMI 70 , Monod M 71 , Moretti A 64 , Mostert D 72 , Mulè G 64 , Munaut F 73 , Munkvold GP 74 , Nicholson P 75 , Nucci M 76 , O'Donnell K 12 , Pasquali M 77 , Pfenning LH 78 , Prigitano A 31 , Proctor RH 12 , Ranque S 79 , Rehner SA 80 , Rep M 81 , Rodríguez-Alvarado G 33 , Rose LJ 72 , Roth MG 82 , Ruiz-Roldán C 28 , Saleh AA 83 , Salleh B 70 , Sang H 84 , Scandiani MM 65 , Scauflaire J 85 , Schmale DG 86 , Short DPG 87 , Šišić A 88 , Smith JA 89 , Smyth CW 90 , Son H 62 , Spahr E 55 , Stajich JE 91 , Steenkamp E 6 , Steinberg C 92 , Subramaniam R 48 , Suga H 93 , Summerell BA 60 , Susca A 64 , Swett CL 25 , Toomajian C 63 , Torres-Cruz TJ 1 , Tortorano AM 31 , Urban M 47 , Vaillancourt LJ 94 , Vallad GE 16 , van der Lee TAJ 11 , Vanderpool D 95 , van Diepeningen AD 11 , Vaughan MM 12 , Venter E 96 , Vermeulen M 97 , Verweij PE 24 , Viljoen A 72 , Waalwijk C 11 , Wallace EC 1 , Walther G 59 , Wang J 98 , Ward TJ 12 , Wickes BL 99 , Wiederhold NP 100 , Wingfield MJ 6 , Wood AKM 47 , Xu JR 100 , Yang XB 75 , Yli-Mattila T 101 , Yun SH 102 , Zakaria L 70 , Zhang H 19 , Zhang N 103 , Zhang SX 104 , Zhang X 54

Affiliations 

  • 1 Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
  • 2 Directorate General of Health Services, Ministry of Health, Ibri, Oman
  • 3 Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan
  • 4 Tokyo University of Agriculture and Technology, Fuchu, Japan
  • 5 Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
  • 6 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
  • 7 Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
  • 8 Department of Agronomy, Iowa State University, Ames, IA 50011, U.S.A
  • 9 Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832, U.S.A
  • 10 Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Manhattan, KS 66506, U.S.A
  • 11 Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
  • 12 Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
  • 13 Sydney Institute of Agriculture, Faculty of Science, University of Sydney, Sydney, Australia
  • 14 Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, U.S.A
  • 15 Mycology Unit and IISPV, Universitat Rovira i Virgili Medical School, Reus, Spain
  • 16 Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
  • 17 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
  • 18 Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
  • 19 State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
  • 20 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
  • 21 Research Institute on Mycology and Mycotoxicology, National Scientific and Technical Research Council, National University of Rio Cuarto, Rio Cuarto, Córdoba, Argentina
  • 22 Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
  • 23 Broad Institute of Harvard and MIT, Cambridge, MA 02142, U.S.A
  • 24 Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
  • 25 Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
  • 26 Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
  • 27 Department of Mycology, Real Jardín Botánico CSIC, Madrid, Spain
  • 28 Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
  • 29 French National Institute for Agriculture, Food, and Environment (INRAE), Dijon, France
  • 30 Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
  • 31 Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
  • 32 Wye Research and Education Center, University of Maryland, Queenstown, MD 21658, U.S.A
  • 33 Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
  • 34 Embrapa Amazônia Ocidental, Manaus, Brazil
  • 35 Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
  • 36 Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
  • 37 Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
  • 38 Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, U.S.A
  • 39 Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
  • 40 Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection, St. Petersburg-Pushkin, Russia
  • 41 CSIRO Agriculture and Food, St. Lucia, Australia
  • 42 Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
  • 43 Department of Plant and Soil Sciences, University of Delaware, DE 19716, U.S.A
  • 44 Department of Genetics, University of the Free State, Bloemfontein, South Africa
  • 45 Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Universitat Rovira i Virgili, Reus, Spain
  • 46 Department of Molecular Biology, Universidad de Leon, Leon, Spain
  • 47 Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
  • 48 Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
  • 49 MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences, University of Szeged, Szeged, Hungary
  • 50 Institute of Plant Protection, Szent István University, Gödöllő, Hungary
  • 51 Division of Mycology, Faculty of Medicine, University of Çukurova, Sarıçam, Adana, Turkey
  • 52 Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
  • 53 Department of Microbiology, Stellenbosch University, Matieland, South Africa
  • 54 College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
  • 55 Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
  • 56 Biology Department, St. Louis University, St. Louis, MO 63101, U.S.A
  • 57 USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
  • 58 Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
  • 59 German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
  • 60 Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
  • 61 Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
  • 62 Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
  • 63 Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
  • 64 Institute of Sciences of Food Production, Research National Council, Bari, Italy
  • 65 Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
  • 66 Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Høgskoleveien, Ås, Norway
  • 67 Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
  • 68 Crop Improvement and Protection Research Unit, ARS-USDA, Salinas, CA 93905, U.S.A
  • 69 Dipartimento di Agraria and Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Sassari, Italy
  • 70 School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
  • 71 Laboratoire de Mycologie, Service de Dermatologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
  • 72 Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
  • 73 Brussels, Belgium
  • 74 Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
  • 75 Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
  • 76 Hospital Universitário, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
  • 77 Department of Food, Environmental and Nutritional Sciences, University of Milano, Milan, Italy
  • 78 Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais State, Brazil
  • 79 Institut Hospitalier Universitaire Méditerranée Infection, Aix Marseille University, Marseille, France
  • 80 Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
  • 81 Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands
  • 82 Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, U.S.A
  • 83 Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
  • 84 Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
  • 85 Centre de Recherche et de Formation Agronomie, Haute Ecole Louvain en Hainaut, Montignies-sur-Sambre, Belgium
  • 86 School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, U.S.A
  • 87 Amycel/Spawn Mate, San Juan Bautista, CA 95045, U.S.A
  • 88 Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
  • 89 School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, U.S.A
  • 90 Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902, U.S.A
  • 91 Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
  • 92 Agroécologie, AgroSup Dijon, INRAE, University of Bourgogne Franche-Comté, Dijon, France
  • 93 Life Science Research Center, Gifu University, Gifu, Japan
  • 94 Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
  • 95 Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
  • 96 Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, South Africa
  • 97 Department of Microbial Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
  • 98 DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94702
  • 99 Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
  • 100 Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
  • 101 Department of Biochemistry, University of Turku, Turku, Finland
  • 102 Department of Medical Biotechnology, Soonchunhyang University, Asan, Republic of Korea
  • 103 Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, U.S.A
  • 104 Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, U.S.A
Phytopathology, 2021 Jul;111(7):1064-1079.
PMID: 33200960 DOI: 10.1094/PHYTO-08-20-0330-LE

Abstract

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

* Title and MeSH Headings from MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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