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Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the
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Fusarium solani Species Complex
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David M. Geiser1,†, Abdullah M. S. Al-Hatmi2, Takayuki Aoki3, Tsutomu Arie4, Virgilio Balmas5, Irene Barnes6, Gary C. Bergstrom7,
Madan K. Bhattacharyya8, Cheryl L. Blomquist9, Robert L. Bowden10, Balázs Brankovics11, Daren W. Brown12, Lester W.
Burgess13, Kathryn Bushley14, Mark Busman12, José F. Cano-Lira15, Joseph D. Carrillo16, Hao-Xun Chang17, Chi-Yu Chen18,
Wanquan Chen19, Martin Chilvers20, Sofia Chulze21, Jeffrey J. Coleman22, Christina A. Cuomo23, Z. Wilhelm de Beer6, G. Sybren de
Hoog24, Johanna Del Castillo-Múnera25, Emerson M. Del Ponte26, Javier Diéguez-Uribeondo27, Antonio Di Pietro28, Véronique
Edel-Hermann29, Wade H. Elmer30, Lynn Epstein25, Akif Eskalen25, Maria Carmela Esposto31, Kathryne L. Everts32, Sylvia P.
Fernández-Pavía33, Gilvan Ferreira da Silva34, Nora A. Foroud35, Gerda Fourie6, Rasmus J. N. Frandsen36, Stanley Freeman37,
Michael Freitag38, Omer Frenkel37, Kevin K. Fuller39, Tatiana Gagkaeva40, Donald M. Gardiner41, Anthony E. Glenn42, Scott E.
Gold42, Thomas R. Gordon25, Nancy F. Gregory43, Marieka Gryzenhout44, Josep Guarro45, Beth K. Gugino1, Santiago Gutierrez46,
Kim E. Hammond-Kosack47, Linda J. Harris48, Mónika Homa49, Cheng-Fang Hong18, László Hornok50, Jenn-Wen Huang18, Macit
Ilkit51, Adriaana Jacobs52, Karin Jacobs53, Cong Jiang54, María del Mar Jiménez-Gasco1, Seogchan Kang1, Matthew T. Kasson55,
Kemal Kazan41, John C. Kennell56, Hye-Seon Kim12, H. Corby Kistler57, Gretchen A. Kuldau1, Tomasz Kulik58, Oliver Kurzai59, Imane
Laraba12, Matthew H. Laurence60, Theresa Lee61, Yin-Won Lee62, Yong-Hwan Lee62, John F. Leslie63, Edward C.Y. Liew60, Lily W.
Lofton42, Antonio F. Logrieco64, Manuel S. López-Berges28, Alicia G. Luque65 Erik Lysøe66, Li-Jun Ma67, Robert E. Marra30, Frank N.
Martin68, Sara R. May1, Susan P. McCormick12, Chyanna McGee1, Jacques F. Meis24, Quirico Migheli69, N. M. I. Mohamed Nor70,
Michel Monod71, Antonio Moretti64, Diane Mostert72, Giuseppina Mulè64, Françoise Munaut73, Gary P. Munkvold74, Paul
Nicholson75, Marcio Nucci76, Kerry O’Donnell12, Matias Pasquali78, Ludwig H. Pfenning78, Anna Prigitano31, Robert H. Proctor12,
Stéphane Ranque79, Stephen A. Rehner80, Martijn Rep81, Gerardo Rodríguez-Alvarado33, Lindy Joy Rose72, Mitchell G. Roth82,
Carmen Ruiz-Roldán28, Amgad A. Saleh83, Baharuddin Salleh70, Hyunkyu Sang84, María Mercedes Scandiani65, Jonathan
Scauflaire85, David G. Schmale III86 Dylan P. G. Short87, Adnan Šišić88, Jason A. Smith89, Christopher W. Smyth90, Hokyoung Son62,
Ellie Spahr55, Jason E. Stajich91, Emma Steenkamp6, Christian Steinberg92, Rajagopal Subramaniam48, Haruhisa Suga93, Brett A.
Summerell60, Antonella Susca64, Cassandra L. Swett25, Christopher Toomajian63, Terry J. Torres-Cruz1, Anna M. Tortorano31,
Martin Urban47, Lisa J. Vaillancourt94, Gary E. Vallad16, Theo A. J. van der Lee11, Dan Vanderpool95, Anne D. van Diepeningen11,
Martha M. Vaughan12, Eduard Venter96, Marcele Vermeulen97, Paul E. Verweij24, Altus Viljoen72, Cees Waalwijk11, Emma C.
Wallace1, Grit Walther61, Jie Wang20, Todd J. Ward12, Brian L. Wickes98, Nathan P. Wiederhold99, Michael J. Wingfield6, Ana K. M.
Wood47, Jin-Rong Xu100, Xiao-Bing Yang75, Tapani Yli-Mattila101, Sung-Hwan Yun102, Latiffah Zakaria70, Hao Zhang19, Ning
Zhang103, Sean X. Zhang104, Xue Zhang55
Corresponding author: D. Geiser; dgeiser@psu.edu
†
1Department
2Directorate
3National
4Tokyo
of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802
General of Health Services, Ministry of Health, Ibri, Oman
Agriculture and Food Research Organization, Genetic Resources Center, Tsukuba, Japan
University of Agriculture and Technology, Fuchu, Japan
5Dipartimento
di Agraria, Università degli Studi di Sassari, Italy
6Department
of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
7Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853
8Department
9Plant
of Agronomy, Iowa State University, Ames, IA 50011
Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832
10Hard
Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS 66506
11Wageningen
12Mycotoxin
13Sydney
Plant Research, Wageningen University & Research, Wageningen, The Netherlands
Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604
Institute of Agriculture, Faculty of Science, University of Sydney, Sydney, Australia
14Department
of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
15Universitat
Rovira i Virgili Medical School, Mycology Unit and IISPV, Reus, Spain
16Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
17Department
of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
18Department
of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
19State
Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences,
Beijing, P. R. China
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20Department
of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824
21Research
Institute on Mycology and Mycotoxicology (IMICO), National Scientific and Technical Research Council, National University of Rio
Cuarto, Rio Cuarto, Córdoba, Argentina
22Department
23Broad
of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849
Institute of Harvard and MIT, Cambridge, MA 02142
24Department
of Medical Mycology and Infectious Diseass, Center of Expertise in Mycology, Radboud University Medical Center/Canisius
Wilhelmina Hospital, Nijmegen, The Netherlands
25Department
of Plant Pathology, University of California-Davis, Davis, CA 95616
26Departamento
de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
27Department
of Mycology, Real Jardín Botánico CSIC, Madrid, Spain
28Departamento de Genética, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, Córdoba, Spain
29INRAE,
French National Institute for Agriculture, Food, and Environment, Dijon, France
30Department
of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06504
31Department
of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
32Wye
Research and Education Center, University of Maryland, Queenstown, MD 21658
33Laboratorio
34Embrapa
de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
Amazônia Ocidental, Manaus, Brazil
35Lethbridge
Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada T1J 4B1
of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
36Department
37Department
of Plant Pathology and Weed Research, ARO, The Volcani Center, Rishon LeZion, Israel
38Department
of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331
39Department
of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104
40Laboratory
41CSIRO
of Mycology and Phytopathology, All-Russian Institute of Plant Protection, St. Petersburg-Pushkin, Russia
Agriculture and Food, St. Lucia, Australia
42Toxicology
& Mycotoxin Research Unit, ARS-USDA, Athens, GA 30605
43Department
of Plant and Soil Sciences, University of Delaware, DE 19716
44Department
of Genetics, University of the Free State, Bloemfontein, South Africa
45Unitat
de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Universitat Rovira i Virgili, Reus, Spain
46Department
of Molecular Biology, Universidad de Leon, Spain
47Rothamsted
Research, Department of Biointeractions and Crop Protection, Harpenden, United Kingdom
48Ottawa
Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
49MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences—University of Szeged, Szeged, Hungary
50Institute
51Division
of Plant Protection, Szent István University, Gödöllő, Hungary
of Mycology, Faculty of Medicine, University of Çukurova, Sarıçam, Adana, Turkey
52ABiosystematics
53Department
54College
Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
of Microbiology, Stellenbosch University, Matieland, South Africa
of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, P. R. China
55Division
of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506
56Biology
Department, St. Louis University, St. Louis, MO 63101
57USDA
ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108
58Department
of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
59German
National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection
Biology – Hans-Knoell-Institute, Jena, Germany
60Australian
61Microbial
Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
Safety Team, National Institute of Agricultural Sciences, RDA, Wanju, Republic of Korea
62Department
of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
63Department
of Plant Pathology, Kansas State University, Manhattan, KS 66506
64CNR
(Research National Council), ISPA Institute of Sciences of Food Production, Bari, Italy
65Centro
de Referencia de Micología (CEREMIC) Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario,
Argentina
66Norwegian
Institute of Bioeconomy Research, Division of Biotechnology and Plant Health, Høgskoleveien, Ås, Norway
67Department
of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA 01003
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68Crop
Improvement and Protection Research Unit, ARS-USDA, Salinas, CA 93905
69Dipartimento
di Agraria and Nucleo Ricerca Desertificazione (NRD), Universita` degli Studi di Sassari, Italy
70School
of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
71Service
de Dermatologie, Laboratoire de Mycologie, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland
72Department
73Brussels,
of Plant Pathology, Stellenbosch University, Matieland, South Africa
Belgium
74Department
of Plant Pathology & Microbiology, Iowa State University, Ames, IA 50011
75Department
of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
76Hospital
Universitário, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
77Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
78Departmento
79Aix
de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais State, Brazil
Marseille University, IHU Méditerranée Infection, Marseille, France
80Mycology
and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705
81Swammerdam
Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands
82Department
of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
83Department
of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
84Department
of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
85Centre
de Recherche et de Formation Agronomie, Haute Ecole Louvain en Hainaut, Montignies-sur-Sambre, Belgium
86School
of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
87Amycel/Spawn
88Department
89School
of Forest Resources & Conservation, University of Florida, Gainesville, FL 32611
90Department
91
Mate, San Juan Bautista, CA 95045
of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902
Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521
92Agroécologie,
93Life
AgroSup Dijon, INRAE, University of Bourgogne Franche-Comté, Dijon, France
Science Research Center, Gifu University, Gifu, Japan
94LDepartment
of Plant Pathology, University of Kentucky, Lexington, KY 40546
95Department
of Biology, Indiana University, Bloomington, IN 47405
96Department
of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, South Africa
97Microbial
Biochemical and Food Biotechnology Department, University of the Free State, Bloemfontein, South Africa
98Department of Microbiology, Immunology & Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, TX
78229
99Department
of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229
100Department
of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
101Department
of Biochemistry, University of Turku, Turku, Finland
102Department
of Medical Biotechnology, Soonchunhyang University, Asan, Republic of Korea
103Department
of Plant Biology, Rutgers University, New Brunswick, NJ 08901
104Department
of Pathology, Johns Hopkins University, Baltimore, MD 21287
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Abstract
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Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the
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end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology
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103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium
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that represented a clade comprising all agriculturally and clinically important Fusarium species, including
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the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group
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(Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven
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genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims
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that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia
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41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of
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19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the
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FSSC. We reassert the practical and scientific argument in support of a Fusarium that includes the FSSC
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and several other basal lineages, consistent with the longstanding use of this name among plant
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pathologists, medical mycologists, quarantine officials, regulatory agencies, students and researchers
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with a stake in its taxonomy. In recognition of this monophyly, 40 species recently described as
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Neocosmospora were recombined in Fusarium, and nine others were renamed Fusarium. Here the
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global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains
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the best scientific, nomenclatural and practical taxonomic option available.
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Introduction
Scientific advances and new fungal nomenclatural rules have forced necessary changes in fungal
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names in recent years, many of which are inconvenient. But unlike other fungal genera where
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phylogenetics and nomenclatural conflicts forced very difficult taxonomic decisions (e.g.,
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Magnaporthe/Pyricularia; Zhang et al. 2016), there is a clear path to define Fusarium phylogenetically,
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eliminate confusing dual nomenclature/taxonomy, and maintain a generic circumscription that has been
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widely used for over a century (Bilai 1955; Booth 1971; Gams and Nirenberg 1989; Gerlach and
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Nirenberg 1982; Joffe 1974; Leslie and Summerell 2006a; Matuo 1972; Nelson et al. 1983; Raillo 1950;
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Snyder and Hansen 1941; Summerell 2019; Wollenweber 1913; Wollenweber and Reinking 1935). The
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highest impact taxonomic outcome at stake is the segregation of F. solani and the F. solani Species
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Complex (FSSC) out of Fusarium into the relatively obscure taxon Neocosmospora, the type of which
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represents a morphologically aberrant lineage within the FSSC. Here we argue that this move is
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scientifically unnecessary and impractical, and refute phylogenetic arguments that have been presented
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to support it (Sandoval-Denis and Crous 2018).
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The scientific argument for a monophyletic Fusarium in Geiser et al. (2013) was strongly
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supported by 66 authors from 17 countries representing the Fusarium community. The goal was to
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promote a generic concept of Fusarium that is scientifically (i.e., monophyletic) and nomenclaturally
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sound, and at the same time minimizes disruption by protecting scientifically valid, longstanding use.
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Fusarium is one of the most commonly used ascomycete generic names in the scientific literature
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(Geiser et al. 2013), so this practical consideration is essential due to the negative impact of
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disconnecting past, current and future uses of the name.
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The Geiser et al. (2013) phylogenetic circumscription of Fusarium precisely corresponds to a
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monophyletic group that encompassed all economically important Fusarium species, originally termed
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the Terminal Fusarium Clade (herein abbreviated TFC; Gräfenhan et al. 2011). Members of this clade
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almost always produce spores and colonies with a recognizable Fusarium morphology. The TFC included
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the type species of Fusarium, F. sambucinum, the same species in which the competing teleomorph
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genus Gibberella is typified: G. pulicaris. This overlap made it straightforward to propose unitary use of
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the name Fusarium over Gibberella (Rossman et al. 2013). That proposal, however, did not address the
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many Fusarium species within the TFC with connections to teleomorph genera other than Gibberella,
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comprising the FSSC and all other Species Complexes in Figure 1 that resolve basally with respect to the
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F. buharicum Species Complex.
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Geiser et al. (2013) proposed that all members of the TFC be included in Fusarium, not just
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those associated with Gibberella, and synonymized competing genera in the TFC under that name.
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Based on portions of two loci (the second-largest RNA polymerase II B-subunit (rpb2) and larger ATP
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citrate lyase (acl1) genes), the Gräfenhan et al. (2011) phylogenetic analysis provided only weak
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statistical support for the node associated with the TFC. The proposal in Geiser et al. (2013) was based
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on a phylogenetic analysis of a much larger set of species in the TFC that utilized more informative loci
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(rpb2, as well as the largest RNA Polymerase II B-subunit gene rpb1; O’Donnell et al. 2013). This analysis
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also resolved the TFC as monophyletic ("node F1"), with improved but still weak statistical support
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(<70% maximum parsimony bootstrap (MP-BS) and maximum likelihood bootstrap (ML-BS); 1.0 Bayesian
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posterior probability (BPP). Recognizing this uncertainty, a second node ("F2"), which received much
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stronger statistical support (87% MP-BS; 100% ML-BS; 1.0 BPP), was offered as an alternative to F1,
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should more rigorous analyses reject the monophyly of F1. F2 comprises all of F1 except its two basal-
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most clades (the F. ventricosum and F. dimerum Species Complexes; FVSC and FDSC respectively).
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Notably, both the F1 and the F2 hypotheses include the FSSC within Fusarium.
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Based on a phylogenetic analysis of nine concatenated loci and a rich sampling of nectriaceous
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taxa, Lombard et al. (2015) also resolved the same TFC node, but again with weak statistical support.
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Although the aforementioned studies all resolved the same node, with different levels of support,
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Sandoval-Denis and Crous (2018) claimed with no new phylogenetic evidence that the concept of
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Fusarium proposed by Geiser et al. (2013) is polyphyletic. However, as carefully accounted for in Geiser
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et al. (2013) and O'Donnell et al. (2013), statistical support for that node based on analyses of RPB1 and
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RPB2 was in need of a more rigorously tested phylogeny using additional genes. In this paper, we
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address this with a phylogenetic inference based on complete exonic nucleotide sequences of 19
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protein-coding genes, derived from whole-genome sequences of 89 taxa, 47 of which were generated in
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the present study (Supp. Table 1). The resulting analysis provides 100% ML-BS/1.0 BPP for the
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monophyly of Fusarium as delimited by Geiser et al. (2013; i.e., the F1 node in Fig. 1), reaffirming the
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taxonomic hypothesis that Fusarium has nomenclatural priority over all names typified in that clade,
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including Neocosmospora.
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We also present a phylogeny of 77 FSSC species based on three-loci: portions of rpb2 and tef1
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(translation elongation factor 1-α), and rDNA (a contiguous portion of the nuclear ribosomal RNA gene
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repeat comprising the internal transcribed spacer (ITS) and D1-D2 regions of the nuclear large subunit).
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Sandoval-Denis and Crous (2018) and Sandoval-Denis et al. (2019) typified and named many of the
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previously unnamed species within the FSSC. This is an extremely important advance in the taxonomy of
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this group, an effort and will greatly facilitate scientific communication about these fungi. However, we
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disagree with their placement in Neocosmospora, for reasons we outline here and in O’Donnell et al.
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(2020). Accordingly, we list the combinations of these taxa in Fusarium (Aoki et al. 2020), along with
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other FSSC species typified or previously combined in Neocosmospora.
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Materials and Methods
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Selection and extraction of marker loci. Exonic nucleotide sequences of the 19 housekeeping genes
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(Table 1) used to infer the Fusarium phylogeny in this study were selected based on (i) their use in
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previous studies for inferring phylogenetic relationships within this genus and across the Kingdom Fungi
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(Floudas et al. 2012; O'Donnell et al. 2013; Sarver et al. 2011; Villani et al. 2019; Watanabe et al. 2011);
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(ii) their utility in previous studies of the distribution and evolution of secondary metabolite genes/gene
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clusters in Fusarium (Brown and Proctor 2016; Brown et al. 2019; Busman et al. 2012; Kim et al. 2020;
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Proctor et al. 2009, 2010, 2013, 2018) and (iii) their relative lengths. Full-length exonic sequences of
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each gene were obtained from whole-genome sequences of 89 taxa, generated in-house at the USDA-
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ARS-NCAUR (n=65), or by the Beijing Genome Institute (BGI; n=4), or downloaded from the GenBank
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database at the National Center for Biotechnology Information (n=20; Suppl. Table 1).
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Genomic DNA for sequencing was extracted from mycelia grown in liquid GYP medium (2%
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glucose, 1% peptone, and 0.3% yeast extract) for 2 – 3 days, harvested by filtration, lyophilized, and
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ground to a powder. Genomic DNA was then extracted using a ZR Fungal/Bacterial DNA MiniPrep kit
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(Zymo Research, Irvine, CA), the Qiagen Genomic-Tip 20/G protocol, or a previously described
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chloroform-phenol-based method (Raeder and Broda 1985). For data generated in-house, sequence
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reads were generated using the MiSeq systems (Illumina) and processed using CLC Genomics
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Workbench (CLC) versions 8 – 20 (Qiagen) as previously described (Laraba et al. 2020a, b; Proctor et al.
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2018). Sequence reads were imported into CLC and then screened against genome sequences of 84
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bacterial species to remove contaminating DNA introduced during library preparation and/or the
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sequencing process. Reads were trimmed to remove low-quality data and assembled using the following
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parameter settings in CLC: word size = 20; bubble size = 50; minimum contig length = 500; auto-detect
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paired distances = checked; and perform scaffolding = checked.
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Protein coding genes were predicted with the program AUGUSTUS (Stanke and Morgenstern
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2005) using F. graminearum genes as a reference and the fgenesh algorithm (Solovyev et al. 2006)
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implemented online in Softberry (http://www.softberry.com). Gene sequences were retrieved from
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coding region databases of each strain using the BLASTn function in CLC Genomics Workbench and
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query sequences from F. fujikuroi, F. graminearum and F. vanettenii (formerly reported as Nectria
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haematococca mating population MPVI; Coleman et al. 2009). Sequences of each gene were aligned
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with the query sequences using MUSCLE (Edgar 2004) as implemented in MEGA7 (Kumar et al. 2016),
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and the resulting alignments were examined for differences between predicted coding regions and the
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query sequences. When necessary, genes were manually annotated using genome sequence data to
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correct errors introduced by the automated annotation, particularly with respect to predicted intron-
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splicing sites. The three loci utilized for phylogenetic analysis of the FSSC were those utilized in previous
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studies (O’Donnell et al. 2008; Sandoval-Denis and Crous 2019).
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Molecular phylogenetics. Two multilocus datasets were assembled and analyzed using partitioned
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maximum likelihood bootstrapping (ML-BS, 5000 replicates) with IQ-TREE 1.6.12 for MacOS (Nguyen et
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al. 2015; http://www.iqtree.org/) and Bayesian inference with MrBayes v.3.2.7 (Ronquist et al. 2019). A
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partitioned 19-gene 55.1 kb dataset was assembled to assess Fusarium monophyly (Table 1). It
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contained complete exonic nucleotide sequences for 84 fusaria, a putative sister group comprising three
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Neonectria species, and sequences of two non-nectriaceous hypocrealean taxa, Beauveria bassiana
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(Cordycipitaceae) and Trichoderma brevicompactum (Hypocreaceae), which were used to root the
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phylogeny. A partitioned 3-locus 3.2 kb dataset was constructed to infer evolutionary relationships
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among 77 species within the FSSC, derived from previous studies (O’Donnell et al. 2008; Sandoval-Denis
275
and Crous 2019). Sequences were aligned with MUSCLE and then manually edited using TextPad 8
276
(https://www.textpad.com) to improve the alignment. ModelFinder (Kalyaanamoorthy et al. 2017) was
277
used to identify the best-fit model of molecular evolution for each partition based on the Bayesian
278
information criterion (BIC) scores (Chernomor et al. 2016). Bayesian inference was conducted using
279
1,000,000 generations in four chains (3 cold, and one hot, with 25% burnin), using the GTR+Γ+I
280
evolutionary model. To assess compatibility of individual loci in the phylogenetic inference, gene
281
compatibility factors (gCF) were calculated using IQ-TREE v.2.1.2 (Minh et al. 2020a,b); gCF values,
282
representing the proportion of gene partitions that resolve a particular node, were translated into
283
numerals representing the number of supporting loci out of 19. In addition, Internode Certainty (IC), IC-
284
All (ICA),Tree Certainty (TC) and relative TC values (Salichos and Rokas 2013; Salichos et al. 2014) were
285
calculated for the IQ-TREE partitioned ML tree in RAxML v.8.2.12 (Stamakis 2014; Kobert et al. 2016).
286
Aligned 19- and 3-locus datasets and best ML trees in NEXUS format, with genes partitioned as charsets,
287
are included as Supplemental Materials, and also deposited in TreeBASE (Study S27101;
288
http://purl.org/phylo/treebase/phylows/study/TB2:S27101).
289
290
Results
291
Fusarium phylogenetics.— The 19-gene nucleotide alignment of full-length exons totalled 55,140 sites,
292
23,668 of which were parsimony informative (Table 1). Individual genes provided a range of 0.5% (cal1)
293
to 12.7% (dpe1) of the total parsimony informative sites in the concatenated character set. In the best
294
ML phylogeny (Fig. 1), 72/86 inferred nodes were supported at the 100% level by ML bootstrapping (BS)
295
as well as 1.0 Bayesian Posterior Probability (BPP), with only two nodes receiving <80% BS/<0.99 BPP
296
support (highlighted in magenta in Fig. 1). The F1/TFC node, upon which the Geiser et al. (2013)
297
circumscription was based (O’Donnell et a. 2013), received 100% BS/1.0 BPP, as did the previously
298
proposed alternate node F2. The ML and Bayesian (Suppl. Fig. 1) trees were topologically identical
299
except for placement of F. ventricosum within node F1 (see discussion below), which neither method
300
resolved with statistical confidence (BS <50%; 0.88 BPP for an alternative topology; see Fig. 1 and Suppl.
301
Fig. 1).
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Based on gCF values, 53/86 internodes in the ML tree were supported by at least 16/19 loci in
303
the dataset, while 71/86 were supported by at least half (Suppl. Fig. 3). Nodes F1 and F2 were
304
supported by 12 and 14 individual loci. The most poorly supported node in the ML tree (unresolved in
305
the majority-rule boostrap consensus tree and by Bayesian analysis) placed F. ventricosum as a sister to
306
the F. dimerum Species Complex, within the F1 node. In 7/19 individual gene trees (act1, cal1, dpe1,
307
ku70, pgk1, tef1, tub2; Suppl. Fig. 2), ingroup taxa (usually F. ventricosum) resolved among outgroup
308
taxa. These genes tend to be shorter and have lower PIC/bp values than those that resolve F1 (Table 1).
309
However, the F1/TFC,inclusive of F. ventricosum was supported in each of the remaining 12 individual
310
gene trees, with bootstrap values between 78-100%. Three loci, fas1, fas2, and ku70, representing
311
24.6% of the parsimony-informative characters in the matrix, are co-located within ~30kb on the same
312
contig (FFUJ_scaffold03) of the F. fujikuroi genome sequence. Removal of these linked loci and
313
reanalysis using IQ-TREE resolved the F1/TFC node with 100% ML bootstrap support (result not shown).
314
The IC and ICA values for the F1 node were 0.19 and 0.33, respectively (Suppl. Fig. 3), indicating that
315
roughly 70% of the genes support the bipartition (see Fig. 2 in Salichos et al., 2014). This value is similar
316
to the proportion of 12/19 (~63%) indicated by gCF, and evident by visual inspection of individual gene
317
trees (Suppl. Figs. 2 and 3). TC, representing the sum of IC values across trees, was 48.41, and relative
318
TC, representing TC normalized to the maximum TC for the phylogeny, was 0.563.
319
Three additional Species Complexes recognized within Fusarium since the publication of the
320
rpb1 + rpb2 phylogeny (O’Donnell et al. 2013) are represented in the dataset: the F. torreyae Species
321
Complex (FtorSC; Zhou et al. 2018 ), the F. newnesense Species Complex (FnewSC; Laurence et al. 2016)
322
and F. burgessii Species Complex (FburSC, here represented by F. beomiforme; Laraba et al. 2018;
323
Laurence et al. 2011; Nelson and Toussoun 1987), bringing the total to 23 Species Complexes recognized
324
within the genus. Each of these Species Complexes received at least 95% ML-BS, except for the F.
325
concolor Species Complex (FconSC), which received 69% ML-BS/0.98 BPP support. This lack of resolution
326
appears to be due to FconSC’s sister taxon, the F. babinda Species Complex, being represented by a
327
single taxon in the dataset. When F. babinda was removed, FconSC received 100% BS support (result not
328
shown). Similarly, the F. ventricosum Species Complex (FVSC) is represented by a single taxon on a long
329
branch, which likely explains the failure to resolve its placement (Felsenstein 1978). However, it does
330
resolve within the FTC/F1 node with 100% ML-BS and 1.0 BPP support, as it did with weaker support in
331
previous studies (Gräfenhan et al. 2011; Lombard et al. 2015; O’Donnell et al. 2013).
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FSSC phylogenetics. The 3-locus DNA alignment for the FSSC comprised 3209 sites (665 for TEF1, 956 for
333
rDNA, 1588 for RPB2), 655 of which were parsimony-informative (164 for TEF1, 131 for rDNA, 360 for
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RPB2). In the best ML cladogram, the previously identified major clades 1, 2 and 3 (O’Donnell 2000)
335
were resolved with 100% bootstrap support. Three clades with unique morphologies and host
336
associations were also resolved within the FSSC: (i) the subclade within Clade 3 that is morphologically
337
associated with Neocosmospora’s type (Smith 1899); (ii) the Ambrosia Fusarium Clade (AFC; Kasson et
338
al. 2013; O’Donnell et al. 2015); and (iii) the Soybean Sudden Death Syndrome (SDS) and Bean Root Rot
339
(BRR) pathogen clade nested in Clade 2 (Aoki et al. 2012).
340
Taxonomy. Recognizing that Neocosmospora sensu Lombard et al. (2015), Sandoval-Denis and Crous
341
(2018) and Sandoval-Denis et al. (2018, 2019) represents a later synonym of Fusarium under this
342
taxonomic hypothesis, species combinations (Aoki et al. 2020) are listed in Appendix A.
343
Importantly, we retained as distinct species the important soybean sudden death (SDS) and
344
bean root rot (BRR) pathogens in the FSSC, F. phaseoli, F. tucumaniae, F. virguliforme, F. brasiliense, F.
345
cuneirostrum, F. crassistipitatum and F. azukicola, which were synonymized under F. phaseoli by
346
Sandoval-Denis et al. (2019). The latter authors performed a split graph analysis and interpreted
347
reticulate patterns as evidence that these groups are conspecific. This is in contrast to previous work
348
providing evidence that they were genealogically exclusive (Aoki et al. 2005, 2012). However, the split
349
graph analysis was based on tef1, rpb2 and rDNA, with only twelve parsimony informative sites among
350
these taxa, and they did not analyze the more phylogenetically informative loci that indicated
351
genealogical exclusivity among these species (Aoki et al. 2012). While the levels of sequence divergence
352
among these species were very small, and scrutiny of the species boundaries based on information-rich
353
phylogenomic datasets is encouraged, the reticulate pattern illustrating homoplasy could be due to
354
processes other than intraspecific genetic exchange, including incomplete lineage sorting and
355
convergence. The synonymization by Sandoval-Denis et al. (2019) also does not account for the
356
morphological differences among these species, nor reported distinctions in their symptomology and
357
host range (Aoki et al. 2005, 2012).
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359
Discussion
360
The rationale for a phylogenetic delimitation of Fusarium outlined by Geiser et al. (2013), reaffirmed
361
here, can be considered on its own merit. However, we emphasize that the 166 scientists from 30
362
countries (aka core global Fusarium community) who co-authored the present publication
363
enthusiastically support it as the best scientifically and nomenclaturally valid taxonomic option. We
364
argue that the alternative posed by Lombard et al. (2015) is based on a taxonomic viewpoint that binds
365
the concept of Fusarium to a teleomorph name, Gibberella. This approach was first hinted at (Gräfenhan
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et al. 2011; Schroers et al. 2011), and later manifested in a proposal (Lombard et al. 2015) to split
367
Fusarium into seven genera within the TFC: Fusarium (Gibberella’s de facto replacement), Albonectria,
368
Bisifusarium, Cyanonectria, Geejayessia, Neocosmospora, and Rectifusarium. Although the generic
369
concepts proposed by Lombard et al. (2015) are monophyletic and nomenclaturally valid, they fail on
370
the practicality criterion because they exclude species with a longstanding place in Fusarium. We see no
371
benefit in splitting Fusarium in favor of competing names that are largely tied to rarely observed sexual
372
stages.
373
The most important exclusion by Lombard et al. (2015) is that of the FSSC, which was moved to
374
the genus Neocosmospora in their taxonomic proposal. The type species, Neocosmospora vasinfecta,
375
which was recombined in Fusarium as F. neocosmosporiellum (Geiser et al. 2013), represents an atypical
376
morphological lineage derived within the FSSC (Figs. 1 and 2). Fusarium neocosmosporiellum and
377
related species produce an asexual stage that, unlike most FSSC species, lacks the fusiform sporodochial
378
macroconidia that are the hallmark of Fusarium, and a homothallic sexual stage consisting of smooth,
379
thin-walled perithecia and ascospores that are mostly single-celled (Smith 1899; Wollenweber and
380
Reinking 1935). However, F. neocosmosporiellum produces microconidiophores typical of the FSSC
381
(Domsch et al. 1980). Viewed within a robust phylogenetic framework, F. neocosmosporiellum clearly
382
represents a morphologically aberrant FSSC lineage whose species have lost the ability to produce the
383
iconic multiseptate macroconidia and only occasionally produce two-celled ascospores (O’Donnell 2000;
384
O’Donnell et al. 2013). Similarly, most of the 19 species in the Ambrosia Fusarium Clade are
385
morphologically unique within the FSSC in that they produce club-shaped macroconidia that are
386
hypothesized to be adaptive to roles associated with the ambrosia beetle symbiosis (Kasson et al. 2013).
387
While Neocosmospora works nomenclaturally as an available genus name typified within the
388
FSSC, it would be unfortunate if its aberrant morphology were to replace Fusarium, which represents
389
the dominant morphology of the group. Because Neocosmospora is the oldest teleomorph name
390
associated with the FSSC, this awkward nomenclatural option seemed reasonable when it was applied
391
under dual nomenclature (e.g., Nalim et al. 2011). However, the demise of dual nomenclature as of 01
392
Jan 2013 opened the door to a much more practical and attractive option: Fusarium, an older name, and
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the dominant longstanding generic concept associated with the FSSC. Highlighting that status, ‘Fusarium
394
solani’ generated over 100 times more Google hits than ‘Neocosmospora’ (3,000,000 to 27,600; search
395
conducted on 09 July 2020). In summary, we argue that the practical and most scientifically attractive
396
option is to combine Neocosmospora species under Fusarium (Geiser et al. 2013), not the other way
397
around.
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We refute the argument that inclusion of the FSSC in Fusarium “implies a denial of the current
399
phenotypic ... evidence” (Sandoval-Denis et al. 2019), and, to the contrary, argue that the name
400
‘Neocosmospora’ is an atypical phenotypic fit for the FSSC. Sandoval-Denis et al. (2019) do not apply a
401
rigorous test or accounting of phenotypic synapomorphies that invalidate the Geiser et al. (2013)
402
circumscription. Iconic Fusarium multiseptate macroconidia are observed in a majority of FSSC species,
403
as they are in members of every other Fusarium Species Complex. In addition to the aforementioned F.
404
neocosmosporiellum, occasional isolates within multiple FSSC species appear to lack macroconidium
405
production (Gams 1971; O’Donnell 2000; Short et al. 2013; Summerbell and Schroers 2002). However,
406
the vast majority of isolates in the FSSC do produce these spores, and a lack of macroconidia is
407
occasionally observed in Fusarium sensu Lombard et al. (2015) as well (e.g., F. xyrophilum: Laraba et al.
408
2020a). While the FSSC is morphologically distinguishable from other Fusarium Species Complexes, we
409
do not accept that these differences are sufficiently significant to require recognition as a separate
410
genus. To wit, the concept of Fusarium in existence for over a century has consistently accommodated
411
this level of phenotypic diversity in the recognition of taxonomic subgroups within the genus
412
(Wollenweber 1913; Wollenweber and Reinking 1935).
413
While there are indeed morphological and ecological trends associated with the phylogenetic
414
structure within our circumscription of Fusarium, there are no convincing nomenclatural, scientific or
415
practical criteria that obligate splitting it into multiple genera. Illustrating similarities between the FSSC
416
and other Fusarium clades, FSSC species share many morphological, ecological and genomic
417
characteristics with the F. oxysporum Species Complex (FOSC), which Lombard et al. (2015) retain in
418
Fusarium. FSSC and FOSC often are co-isolated from the same soil and plant samples, and while they can
419
be resolved morphologically, misidentification of one as the other is common. FSSC and the FOSC are
420
cosmopolitan residents of soil and the rhizosphere, and of decaying and living plant material, where
421
they may act as parasites and/or endophytes. Interestingly, their ecological similarities are reflected in
422
their genomes, with both having significantly expanded accessory genomes that include supernumerary,
423
conditionally dispensable chromosomes that harbor niche adaptive genes (Coleman et al. 2009; Ma et
424
al. 2010; Waalwijk et al. 2018). While these two groups occupy different clades within Fusarium, and
425
placing them in separate genera is a discretionary option, plant pathologists and medical mycologists
426
have treated them as congeneric for the past century. International Fusarium Laboratory Workshops,
427
which have been held regularly since the 1970s, (Leslie and Summerell 2006b) present the FSSC and the
428
FOSC, which is retained in Fusarium by Lombard et al. (2015), together in lectures and the laboratory,
429
reflecting the shared ecological, morphological and genomic characteristics that are relevant to
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clinicians and researchers. In short, we argue that the individual lineages that comprise the
431
monophyletic Fusarium sensu Geiser et al. (2013) share more in common than not.
432
In support of splitting Fusarium into seven genera and promoting the FSSC as Neocosmospora,
433
additional claims were made about the status of the TFC as a monophyletic group (Sandoval-Denis and
434
Crous 2018), including: (i) the Geiser et al. (2013) concept of Fusarium is “polyphyletic,” and (ii) moving
435
it to Neocosmospora represents a “more natural classification.” To correct the record, there are no
436
published phylogenies known to the authors of this paper with appropriate taxon sampling and
437
resolving power showing the TFC to be anything but monophyletic, including the Lombard et al. (2015)
438
phylogeny. Comparisons of the phylogeny in Lombard et al. (2015) with those in Geiser et al. (2013),
439
O’Donnell et al. (2013) and Gräfenhan et al. (2011) reveal that a monophyletic TFC is resolved in all of
440
them. Certainly, as has been shown in many publications, there is phylogenetic structure within
441
Fusarium, but phylogenetic structure is not synonymous with polyphyly (i.e., having multiple distinct
442
evolutionary origins (Farris 1990)); a strongly supported monophyletic genus can encompass strongly
443
supported monophyletic subgroups. Nor would it be reasonable to argue that a genus can
444
accommodate only a certain degree of phylogenetic structure, particularly when its well-studied
445
taxonomy has unanimously accommodated substructure, in the form of Sections (Wollenweber 1913)
446
and now phylogenetic lineages referred to as Species Complexes (O’Donnell et al. 2013).
447
We also reject the assertion that splitting the FSSC off as Neocosmospora represents a “more
448
natural classification.” Given that Neocosmospora sensu Sandoval-Denis et al. (2019) and the
449
circumscription of Fusarium in Geiser et al. (2013) are both monophyletic, the two concepts are of equal
450
status regarding scientific support. In fact, Geiser et al. (2013) openly critiqued the phylogenetic
451
evidence underlying their taxonomic hypothesis and presented an alternative circumscription of
452
Fusarium in case additional data did not support this hypothesis. Although the concept proposed by
453
Geiser et al. (2013) is based on phylogenetics, it is rooted in the first taxonomic synthesis of Fusarium
454
(Wollenweber and Reinking, 1935), and subsequent modifications based on modern morphological (e.g.,
455
moving ‘F. nivale’ into Microdochium; Samuels and Hallett 1983) and phylogenetic (Gräfenhan et al.
456
2011; O’Donnell et al. 2013) information. It retains all agriculturally, medically and economically
457
important species in Fusarium. In contrast to the claim that Neocosmospora is the more natural
458
classification for the FSSC, we find its transfer to Neocosmospora unnatural in light of this historical and
459
practical context. It is a morphologically counterintuitive, unnecessarily disruptive solution to a
460
taxonomic problem that does not exist.
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461
Our phylogenetic circumscription of Fusarium mirrors that of Aspergillus in several ways
462
(Samson et al. 2014). Aspergillus is also one of the most commonly used generic names in Fungi, and it
463
corresponds to a strongly supported clade (Kocsubé et al. 2016; Steenwyk et al. 2019). Both genera
464
harbor great species diversity, with new species being discovered at high rates. However, the Aspergillus
465
clade encompasses much greater morphological diversity than Fusarium, including sexual stages varying
466
from asci enclosed within wefts of hyphal elements (Neosartorya, associated with A. fumigatus) to
467
cleistothecia enclosed in sclerotial ascostromata (Petromyces, associated with A. flavus). While the
468
familiar Aspergillus conidiophore morphology dominates, the clade also includes aberrant anamorph
469
forms such as Phialosimplex. In the case of Aspergillus, it was decided that the broader circumscription
470
was the most reasonable solution among nomenclaturally and scientifically valid options (Samson et al.
471
2014), and all competing generic concepts have been subsumed under Aspergillus. While molecular
472
phylogenetic studies over the past three decades have revealed Aspergillus and Fusarium are much
473
larger than documented using morphology alone, it is important to note that both are monophyletic as
474
presently circumscribed.
475
The strong statistical support presented in the 19-locus phylogeny solidifies the taxonomic
476
hypothesis assigning the name Fusarium to all descendants of node F1 in Geiser et al. (2013) and
477
O’Donnell et al. (2013), and the “Terminal Fusarium Clade” sensu Gräfenhan et al. (2011). This finding
478
further negates the unsupported claim that Fusarium sensu Geiser et al. (2013) is polyphyletic, and it
479
eliminates any remaining doubt regarding the robustness of the TFC/F1 node. As a result, all competing
480
generic names typified in this clade, including Albonectria, Bisifusarium, Cyanonectria, Geejayessia,
481
Gibberella, Neocosmospora, and Rectifusarium, are recognized as Fusarium. With taxon discovery and
482
phylogenomic datasets rapidly accumulating, we will continue to scrutinize and refine our taxonomic
483
hypothesis and promote a scientifically robust and practical, user-friendly generic concept. As shown
484
here, consideration of additional data has significantly strengthened the inference that the present
485
circumscription of Fusarium is monophyletic (Geiser et al. 2013).
486
Taxonomy’s purpose is to foster clear scientific communication, and the job of taxonomists is to
487
refine it with that in mind. In doing so, taxonomists must not only recommend improved communication
488
going forward, but also weigh the costs of altering longstanding, effective communication (Booth 1978).
489
This communication underlies international trade and agricultural biosecurity, pesticide and crop
490
cultivar registration, and accurate identification and reporting of etiological agents essential for plant,
491
animal and human disease management. In some cases, scientific evidence and practical merit require
492
inconvenient disruptions of and changes in taxonomic usage to accommodate nomenclatural rules and
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scientific rigor. As spelled out here and in Geiser et al. (2013), we assert that inclusion of the FSSC in
494
Neocosmospora rather than Fusarium is not such a case. In this age, when molecular phylogenetics is
495
informing a vastly improved taxonomy, the Fusarium community is fortunate that the genus-level
496
taxonomy is supported by a phylogenetically rigorous, nomenclaturally sound and user-friendly solution
497
allowing undisrupted unitary use of the name Fusarium. In the interest of a robust taxonomy that
498
facilitates communication, we welcome cogent, data-driven alternative taxonomic hypotheses that fully
499
consider the scientific, nomenclatural and practical ramifications.
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ACKNOWLEDGMENTS
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The authors thank Crystal Probyn and Amy McGovern for skilled technical assistance in various aspects
504
of this study, and suggestions and comments on the manuscript from Antonis Rokas, Edward Kaiser and
505
two anonymous reviewers. This research was funded by the US Department of Agriculture’s Agricultural
506
Research Service (USDA-ARS) National Program for Food Safety, NSF grant DEB-1655980, and the
507
Pennsylvania State Agricultural Experiment Station Project 4655. This is contribution no. 21-022-J from
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the Kansas Agricultural Experiment Station. IL was supported through the ORISE program.
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DISCLAIMER
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The mention of company names or trade products does not imply that they are endorsed or
513
recommended by the US Department of Agriculture over other companies or similar products not
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mentioned. USDA is an equal opportunity provider and employer.
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Appendix A
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A list of taxonomic changes follows (Aoki et al. 2020):
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Fusarium acutisporum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1.
2020. [IF 557667]
≡ Neocosmospora acutispora Sand.-Den. & Crous, Persoonia 43: 108. 2019. [MB 831170]
Fusarium ambrosium (Gadd & Loos) Agnihothr. & Nirenberg, Stud. Mycol. 32: 98. 1990. [MB 130225]
≡ Monacrosporium ambrosium Gadd & Loos, Trans. Br. mycol. Soc. 30: 13. 1947. [MB 288427]
≡ Neocosmospora ambrosia (Gadd & Loos) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015.
[MB 810957]
Note: Also known as FSSC 19.
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570
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Fusarium amplum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1.
2020. [IF 557668]
≡ Neocosmospora ampla Sand.-Den. & Crous, Persoonia 43: 110. 2019. [MB 831171]
Fusarium bataticola (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1.
2020. [IF 557670]
≡ Neocosmospora bataticola Sand.-Den. & Crous, Persoonia 43: 112 2019. [MB 831172]
Note: Also known as FSSC 23.
= Neocosmospora striata Udagawa & Y. Horie, Trans. Mycol. Soc. Japan 16: 340. 1975. [MB 318599]
(non Fusarium striatum Sherb. 1915 [MB240201])
= Neocosmospora parva Mahoney, Mycologia 68: 1111. 1976. [MB 318598]
= Fusarium solani f. batatas T.T. McClure, Phytopathology 41: 75. 1951. [MB 537090] (non Fusarium
batatas Wollenw. 1914. [MB 175963])
Note: Also known as Nectria haematococca Mating Population II (NhMPII).
Fusarium bomiense (Z.Q. Zeng & W.Y. Zhuang) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440:
1. 2020. [IF 557671
≡ Neocosmospora bomiensis Z.Q. Zeng & W.Y. Zhuang, Phytotaxa 319(2): 177. 2017. [MB 570412]
Fusarium borneense (Petr.) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1. 2020. [IF
557672]
≡ Neocosmospora borneensis (Petr.) Sand.-Den. & Crous, Persoonia 43: 115. 2019. [MB 831173]
≡ Nectria borneensis Petr., Sydowia 8: 20. 1954. [MB 301755]
Note: Also known as FSSC 30.
Fusarium bostrycoides Wollenw. & Reinking, Phytopathology 15(3): 166. 1925. [MB 258714]
≡ Neocosmospora bostrycoides (Wollenw. & Reinking) Sand.-Den. & Crous, Persoonia 43: 115.
2019. [MB 831174]
Note: Also known as FSSC 25.
Fusarium breve (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1. 2020.
[IF 557673]
≡ Neocosmospora brevis Sand.-Den. & Crous, Persoonia 43: 119. 2019. [MB 831176]
Note: Also known as FSSC 15.
Fusarium breviconum (Wollenw.) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1. 2020. [IF
557674]
≡ Hypomyces haematococcus var. breviconus Wollenw., Fusaria autographice delineata 3: no. 828.
1930. [MB 373029]
≡ Neocosmospora brevicona (Wollenw.) Sand.-Den. & Crous, Persoonia 43: 117. 2019. [MB 831175]
≡ Nectria haematococca var. brevicona (Wollenw.) Gerlach, Fusarium: Disease, Biology, and
Taxonomy (State College), p. 422. 1981. [MB 117167]
= Fusarium solani var. minus Wollenw., Die Fusarien, ihre Beschreibung, Schadwirkung und
Bekämpfung (Berlin). p. 134. 1935. [MB 185066]
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615
616
617
618
619
620
Fusarium catenatum (Sand.-Den. & Crous) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 1. 2020. [IF
557675]
≡ Neocosmospora catenata Sand.-Den. & Crous, Persoonia 41: 115. 2018. [MB 822898]
Note: Also known as FSSC 43.
Fusarium crassum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 1.
2020. [IF 557676]
≡ Neocosmospora crassa Sand.-Den. & Crous, Persoonia 43: 122. 2019. [MB 831177])
Note: Also known as FSSC 34.
Fusarium croci (Guarnaccia, Sand.-Den. & Crous) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 1.
2020. [IF 557677]
≡ Neocosmospora croci Guarnaccia, Sand.-Den. & Crous, Persoonia 40: 17. 2017. [MB 820251]
Fusarium cryptoseptatum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum
440: 1. 2020. [IF 557678]
≡ Neocosmospora cryptoseptata Sand.-Den. & Crous, Persoonia 43: 122. 2019. [MB 831178]
Fusarium cucurbiticola O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2. 2020. [IF 557679]
≡ Neocosmospora cucurbitae Sand.-Den., L. Lombard & Crous, Persoonia 43: 125. 2019. [MB
831179]
(non Fusarium cucurbitae Taubenh. 1920 [MB 509348])
= Fusarium solani f. cucurbitae W.C. Snyder & H.N. Hansen, Amer. J. Bot. 28: 740. 1941. [MB 346145]
= Fusarium solani f. sp. cucurbitae W.C. Snyder & H.N. Hansen, Root rots caused by Phycomycetes
28: 740. 1941. [MB 434083]
= Hypomyces solani f. cucurbitae W.C. Snyder & H.N. Hansen, Amer. J. Bot. 28: 741. 1941. [MB
346179]
≡ Nectria haematococca var. cucurbitae (W.C. Snyder & H.N. Hansen) Dingley, New Zealand J. Agric.
Res. 4: 337. 1961. [MB 349909]
≡Nectria solani f. cucurbitae (W.C. Snyder & H.N. Hansen) G.R.W. Arnold, Z. Pilzk. 37: 193. 1972.
[MB 348526]
Note: Also known as Nectria haematococca Mating Population I (NhMPI) and FSSC 10.
Fusarium cyanescens (G.A. de Vries, de Hoog & Bruyn) O’Donnell, Geiser & T. Aoki, Index Fungorum 440:
2. 2020. [IF 557680]
≡ Phialophora cyanescens G.A. de Vries, de Hoog & Bruyn, Antonie van Leeuwenhoek 50(2): 150.
1984. [MB 107121]
≡ Neocosmospora cyanescens (G.A. de Vries, de Hoog & Bruyn) Summerbell, Schroers & Scott,
Biology of Microfungi (Cham) 183. 2016. [MB 813864]
≡ Cylindrocarpon cyanescens (G.A. de Vries, de Hoog & Bruyn) Sigler, J. Clin. Microbiol. 29: 1858.
1991. [MB 499349]
Note: Also known as FSSC 27.
Fusarium diminutum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2.
2020. [IF 557681]
≡ Neocosmospora diminuta Sand.-Den. & Crous, Persoonia 43: 127. 2019. [MB 831180]
Note: Also known as FSSC 39.
Page 18 of 64
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629
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642
643
644
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647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
Fusarium euwallaceae S. Freeman, Z. Mendel, T. Aoki & O'Donnell, Mycologia 105(6): 1599. 2013. [MB
803293]
≡ Neocosmospora euwallaceae (S. Freeman, Z. Mendel, T. Aoki & O'Donnell) Sand.-Den., L.
Lombard & Crous, Persoonia 43: 129. 2019. [MB 831181]
Fusarium falciforme (Carrión) Summerb. & Schroers, J. Clin. Microbiol. 40(8): 2872. 2002. [MB 483950]
≡ Cephalosporium falciforme Carrión, Mycologia 43: 523. 1951. [MB 294124]
≡ Acremonium falciforme (Carrión) W. Gams, Cephalosporium-artige Schimmelpilze (Stuttgart):
139. 1971. [MB 308145]
≡ Neocosmospora falciformis (Carrión) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB
810958]
Note: Also known as FSSC 3+4.
Fusarium ferrugineum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2.
2020. [IF 557682]
≡ Neocosmospora ferruginea Sand.-Den. & Crous, Persoonia 43: 130. 2019. [MB 831182]
Fusarium haematococcum Nalim, Samuels & Geiser, Mycologia 103(6): 1322. 2011. [MB 519837]
= Nectria haematococca Berk. & Broome var. haematococca, J. Linn. Soc. Bot. 14: 116. 1875. [MB
417425]
≡ Neocosmospora haematococca (Berk. & Broome) Nalim, Samuels & Geiser, Mycologia 103 (6):
1322. 2011. [MB 519835]
Note: Also known as FSSC 28.
Fusarium helgardnirenbergiae O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2. 2020. [IF
557683]
≡ Neocosmospora nirenbergiana Sand.-Den. & Crous, Persoonia 43: 143. 2019. [MB 831189] (non
Fusarium nirenbergiae L. Lombard & Crous 2018. [MB 826845])
Etymology: In honor of Dr. Helgard Nirenberg.
Fusarium hengyangense (Z.Q. Zeng & W.Y. Zhuang) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum
440: 2. 2020. [IF 557684]
≡ Neocosmospora hengyangensis Z.Q. Zeng & W.Y. Zhuang, Phytotaxa 319: 179. 2017. [MB 570411]
Fusarium hypothenemi (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440:
2. 2020. [IF 557685]
≡ Neocosmospora hypothenemi Sand.-Den. & Crous, Persoonia 43: 132. 2019. [MB 831183]
Note: Also known as FSSC 38.
Fusarium illudens C. Booth, The genus Fusarium: 54. 1971. [MB 314215]
= Neocosmospora illudens (Berk.) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB 810959]
≡ Nectria illudens Berk., The botany of the Antarctic Voyage II, Flora Novae-Zealandiae 2: 203. 1855.
[MB 170632]
Fusarium kelerajum Samuels, Nalim & Geiser, Mycologia 103(6): 1326. 2011. [MB 519856]
= Neocosmospora keleraja Samuels, Nalim & Geiser, Mycologia 103(6): 1326. 2011. [MB 519854]
Page 19 of 64
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669
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671
672
673
674
675
676
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678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
Fusarium keratoplasticum Geiser, O'Donnell, D.P.G. Short & Ning Zhang, Fungal Genetics Biol. 53: 68.
2013 [MB 802390]
≡ Neocosmospora keratoplastica (Geiser, O'Donnell, D.P.G. Short & Ning Zhang) Sand.-Den. &
Crous, Persoonia 41: 120. 2017 [MB 822900]
Note: Also known as FSSC 2.
Fusarium kuroshium (F. Na, J.D. Carrillo & A. Eskalen ex Sand.-Denis & Crous) O’Donnell, Geiser, Kasson
& T. Aoki, Index Fungorum 440: 2. 2020. [IF 557669]
≡ Neocosmospora kuroshio F. Na, J.D. Carrillo & A. Eskalen ex Sand.-Den. & Crous, Persoonia 41:
137. 2018. [MB 831184]
(≡ Fusarium kuroshium F. Na, J.D. Carrillo & A. Eskalen, Plant Disease 102: 1159. 2018. Nom. inval.,
Art. 40.7 [MB 821907])
Fusarium kurunegalense Samuels, Nalim & Geiser, Mycologia 103(6): 1323. 2011. [MB 519848]
= Neocosmospora kurunegalensis Samuels, Nalim & Geiser, Mycologia 103(6): 1324. 2011. [MB
519847]
Fusarium lichenicola C. Massal., Annales Mycologici 1(3): 223. 1903. [MB 200576]
≡ Neocosmospora lichenicola (C. Massal.) Sand.-Den. & Crous, Persoonia 41: 120. 2018. [MB
822901]
≡ Bactridium lichenicola (C. Massal.) Wollenw. [as 'lichenicolum'], Fusaria autographica delineata 1:
no. 456 (1916). [MB 101879]
≡ Cylindrocarpon lichenicola (C. Massal.) D. Hawksw., Bull. Br. Mus. Nat. Hist., Bot. 6(3): 273. 1979.
[MB 312456]
Note: Also known as FSSC 16.
Fusarium liriodendri (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2.
2020. [IF 557686]
≡ Neocosmospora liriodendri Sand.-Den. & Crous, Persoonia 43: 139. 2019. [MB 831185]
Note: Also known as FSSC 24.
Fusarium macrosporum (Sand.-Den., Guarnaccia & Polizzi) O’Donnell, Geiser & T. Aoki, Index Fungorum
440: 2. 2020. [IF 557687]
≡ Neocosmospora macrospora Sand.-Den., Guarnaccia & Polizzi, Persoonia 40: 21. 2017. [MB
820253]
Fusarium mahasenii Samuels, Nalim & Geiser, Mycologia 103(6): 1325. 2011. [MB 519853]
= Neocosmospora mahasenii Samuels, Nalim & Geiser, Mycologia 103(6): 1325. 2011. [MB 519852]
Fusarium martii Appel & Wollenw., Arbeiten Kaiserl. Biol. Anst. Land- u. Forstw. 8: 83. 1910. [MB
249096]
≡ Neocosmospora martii (Appel & Wollenw.) Sand.-Den. & Crous, Persoonia 41: 121. 2018. [MB
831187]
Fusarium metavorans Al-Hatmi, S.A. Ahmed & de Hoog, Med. Mycol. 56: S147. 2018. [MB 821742]
≡ Neocosmospora metavorans (Al-Hatmi, S.A. Ahmed & de Hoog) Sand.-Den. & Crous, Persoonia
41: 121. 2018. [MB 823687]
Page 20 of 64
20
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
Note: Also known as FSSC 6.
Fusarium mori (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 2. 2020.
[IF 557688]
≡ Neocosmospora mori Sand.-Den. & Crous, Persoonia 43: 143. 2019. [MB 831188]
(= Fusarium solani f. mori Sawada, Special Publication College of Agriculture, National Taiwan
University 8: 222. 1959. Nom. inval., Art. 39.1 [MB 353476])
(= Hypomyces solani f. mori Y. Sakurai & Matuo, Ann. Phytophathol. Soc. Japan 24: 222. 1959. Nom.
inval., Art. 39.1 [MB 353542])
Note: Also known as Nectria haematococca Mating Population III (NhMPIII) and FSSC 17.
Fusarium neocosmosporiellum O'Donnell & Geiser, Phytopathology 103(5): 405. 2013. [MB 800615]
≡ Neocosmospora vasinfecta E.F. Sm., Bulletin U.S. Dept. Agri. 17: 45. 1899. [MB 241907]
(non Fusarium vasinfectum G.F. Atk. 1892. [MB 225413])
Typification (for N. vasinfecta): Lectotype: USA: Pl. V, figs 1-2 as collected on 8 Oct. 1895 (Smith,
Bull. U.S. Dept Agric. 17, 1899); Sandoval-Denis et al. 2019)[MBT 387252]; Neotype: USA, SOUTH
CAROLINA: Cameron, a dried specimen on cotton (Gossypium hirsutum), collected on Oct. 1902,
William A. Orton (BPI 630336, Cannon & Hawksworth 1984)[IF 596775]; Epitype: USA, ILLINOIS:
southern area, isolated from a cyst of Heterodera glycines in a soil sample from soybean field, 6 Apr.
1983, Lori M. Carris, CARRIS E-8-8 (BPI 910920, a dried culture of NRRL 22166, Aoki et al. 2020 [IF
557666]; Carris and Glawe 1989). Ex-epitype culture NRRL 22166 = ATCC 62199.
= Neocosmospora vasinfecta E.F. Sm. var. africana (Arx) P.F. Cannon & D. Hawksw. Trans. Br. Mycol.
Soc. 82(4): 676. 1984. [MB 116939]
≡ Neocosmospora africana Arx, Antonie van Leeuwenhoek 21(2): 161. 1955. [MB 301806]
Note: Also known as FSSC 8.
Fusarium ngaiotongaense O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 3. 2020. [IF 557689]
≡ Neocosmospora longissima Sand.-Den. & Crous, Persoonia 43: 141. 2019. [MB 831186] (non
Fusarium longissimum Sacc. & P. Syd. 1899. [MB 229470])
Etymology: Ngaiotonga + -ensis from the name of its type locality.
Fusarium noneumartii (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 3.
2020. [IF 557690]
≡ Neocosmospora noneumartii Sand.-Den. & Crous, Persoonia 43: 145. 2019. [MB 831190]
Note: Also known as FSSC 42.
Fusarium oblongum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 3.
2020. [IF 557691]
≡ Neocosmospora oblonga Sand.-Den. & Crous, Persoonia 43: 148. 2019. [MB 831191]
Note: Also known as FSSC 29.
Fusarium oligoseptatum T. Aoki, M.T. Kasson, S. Freeman, D.M. Geiser & K. O’Donnell, Fungal
Systematics and Evolution 1: 29. 2018. [MB 822305]
≡ Neocosmospora oligoseptata (T. Aoki et al.) Sand.-Den. & Crous, Persoonia 43: 149. 2019. [MB
831192]
Page 21 of 64
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762
763
764
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766
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768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
Fusarium ornamentatum (M.A.F. Barbosa) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 3. 2020. [IF
557692]
≡ Neocosmospora ornamentata M.A.F. Barbosa, Garcia de Orta, Revista da Junta de Investigações
do Ultramar (Ministério de Ultramar, Lisboa), Série de Estudos Agrónomicos 13(1): 17. 1965. [MB
335130]
Fusarium paraeumartii (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440:
3. 2020. [IF 557693]
≡ Neocosmospora paraeumartii Sand.-Den. & Crous, Persoonia 43: 149. 2019. [MB 831193]
Fusarium parceramosum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440:
3. 2020. [IF 557694]≡ Neocosmospora parceramosa Sand.-Den. & Crous, Persoonia 43: 151. 2019.
[MB 831194]
Note: Also known as FSSC 18.
Fusarium perseae (Sand.-Den. & Guarnaccia) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 3. 2020.
[IF 557695]
≡ Neocosmospora perseae Sand.-Den. & Guarnaccia, Fungal Syst. Evol. 1: 136. 2018. [MB 824587]
Fusarium petroliphilum (Q.T. Chen & X.H. Fu) Geiser, O'Donnell, D.P.G. Short & N. Zhang, Fungal Genet.
Biol. 53: 70. 2013. [MB 802539]
≡ Fusarium solani var. petroliphilum Q.T. Chen & X.H. Fu, Acta Mycol. Sinica, Suppl.: 330. 1987. [MB
127720]
≡ Neocosmospora petroliphila (Q.T. Chen & X.H. Fu) Sand.-Den. & Crous, Persoonia 41: 121. 2018.
[MB 822902]
Note: Also known as Nectria haematococca Mating Population V (NhMPV) and FSSC 1
Fusarium phaseoli (Burkh.) T. Aoki & O'Donnell, Mycologia 95(4): 671. 2003. [MB 488914]
≡ Fusarium martii f. phaseoli Burkh., Mem. Cornell U. Agr. Exp. Station 26: 1007. 1919. [MB
489076]
≡ Neocosmospora phaseoli (Burkh.) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB 810962]
Also, we recognize the following valid existing species as distinct from F. phaseoli:
Fusarium tucumaniae T. Aoki, O'Donnell, Yosh. Homma & Lattanzi, Mycologia 95(4): 664. 2003. [MB
489463]
≡ Neocosmospora tucumaniae (T. Aoki et al.) L. Lombard & Crous, Stud. Mycol. 80: 228. 2015. [MB
810966]
Fusarium virguliforme O’Donnell & T. Aoki, Mycologia 95: 667. 2003. [MB 489315]
≡ Neocosmospora virguliformis (O’Donnell & T. Aoki) L. Lombard & Crous, Stud. Mycol. 80: 228.
2015. [MB 810967]
Fusarium brasiliense T. Aoki & O’Donnell, Mycoscience 46: 166. 2005. [MB 338753]
Fusarium cuneirostrum O’Donnell & T. Aoki, Mycoscience 46: 170. 2005. [MB 341392]
Fusarium crassistipitatum Scandiani et al., Mycoscience 53: 171. 2011. [MB 561257]
Fusarium azukicola T. Aoki et al., Mycologia 104: 1075. 2012. [MB 563147]
Fusarium piperis (F.C. Albuq.) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 3. 2020. [IF
557696]
Page 22 of 64
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808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
≡ Neocosmospora piperis (F.C. Albuq.) Sand.-Den. & Crous, Persoonia 43: 152. 2019. [MB 831195]
≡ Fusarium solani f. piperis F.C. Albuq., Circular do Instituto Agronómico do Norte 5: 19. 1961. [MB
349447]
Note: Also known as FSSC 31.
Fusarium plagianthi (Dingley) O'Donnell & Geiser, Phytopathology 103(5): 404. 2013. [MB 800613]
≡ Nectria plagianthi Dingley, Trans. Proc. Royal Soc. New Zealand 79: 196. 1951. [MB 301780]
≡ Neocosmospora plagianthi (Dingley) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB
810963]
Fusarium protoensiforme (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum
440: 3. 2020. [IF 557697]
≡ Neocosmospora protoensiformis Sand.-Den. & Crous, Persoonia 43: 156. 2019. [MB 831197]
Note: Also known as FSSC 32.
Fusarium pseudensiforme Samuels, Nalim & Geiser, Mycologia 103(6): 1323. 2011. [MB 519839]
= Neocosmospora pseudensiformis Samuels, Nalim & Geiser, Mycologia 103(6): 1323. 2011. [MB
519838]
Note: Also known as FSSC 33.
Fusarium pseudoradicicola (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum
440: 3. 2020. [IF 557698]
≡ Neocosmospora pseudoradicicola Sand.-Den. & Crous, Persoonia 43: 157. 2019. [MB 831198]
Note: Also known as FSSC 37.
Fusarium pseudotonkinense (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum
440: 3. 2020. [IF 557699]
≡ Neocosmospora pseudotonkinensis Sand.-Den. & Crous, Persoonia 43: 159. 2019. [MB 831199]
Fusarium quercinum O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4. 2020. [IF 557700]
≡ Neocosmospora quercicola Sand.-Den. & Crous, Persoonia 43: 159. 2019. [MB 831200]
(non Fusarium quercicola Oudem. 1902 [MB 204737])
Etymology: quercinus (of oak), from the name of the original host plant, Quercus cerris.
Note: Also known as FSSC 14.
Fusarium ramosum (Batista & H. Maia) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 4. 2020. [IF
557701]
≡ Hyaloflorea ramosa Batista & H. Maia, Anais Soc. Biol. Pernambuco 13(1): 155. 1955. [MB
298527]
≡ Neocosmospora ramosa (Batista & H. Maia) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB
810242]
Fusarium rectiphorus Samuels, Nalim & Geiser, Mycologia 103(6): 1324. 2011. [MB 519851]
= Neocosmospora rectiphora Samuels, Nalim & Geiser, Mycologia 103(6): 1324. 2011. [MB 519850]
= Neocosmospora bomiensis Z.Q. Zeng & W.Y. Zhuang, Phytotaxa 319: 177. 2017. [MB 570412]
Page 23 of 64
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854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
Fusarium regulare (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4.
2020. [IF 557702]
≡ Neocosmospora regularis Sand.-Den. & Crous, Persoonia 43: 162. 2019. [MB 831201]
Fusarium rhizophorae (Dayarathne) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4. 2020.
[IF 557703]
≡ Neocosmospora rhizophorae Dayarathne, in Dayarathne, Jones, Maharachchikumbura,
Devadatha, Sarma, Khongphinitbunjong, Chomnunti & Hyde, Mycosphere 11(1): 112. 2020. [MB
556595]
Fusarium riograndense Dallé Rosa, Ramirez-Castrillón, P. Valente, Fuent., van Diepeningen & Goldani, J.
Mycol. Med. 28: 33. [MB 814515]
≡ Neocosmospora riograndensis (Dallé Rosa et al.) Sand.-Den. & Crous, Persoonia 43: 165. 2019.
[MB 831202]
Fusarium samuelsii (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4.
2020. [IF 557704]
≡ Neocosmospora samuelsii Sand.-Den. & Crous, Persoonia 43: 165. 2019. [MB 831204]
Fusarium silvicola (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4.
2020. [IF 557705]
≡ Neocosmospora silvicola Sand.-Den. & Crous, Persoonia 43: 167. 2019. [MB 831205]
= Fusarium solani f. robiniae Matuo & Y. Sakurai, Ann. Phytopathol. Soc. Japan 30: 35. 1965. [MB
348448](non Fusarium robiniae Pass. 1891. [MB 203747])
= Hypomyces solani f. robiniae Matuo & Y. Sakurai, Ann. Phytophathol. Soc. Japan 30: 35. 1965. [MB
349586]
Note: Also known as FSSC 13.
≡ Nectria solani f. robiniae (Matuo & Y. Sakurai) G.R.W. Arnold, Z. Pilzk. 37(1-4): 193. 1972. [MB
348527]
Note: Also known as Nectria haematococca Mating Population VII (NhMPVII)
Fusarium solani (Mart.) Sacc., Michelia 2(7): 296. 1881. [MB 190352]
≡ Fusisporium solani Mart., Die Kartoffel-Epidemie der letzten Jahre oder die Stockfäule und Räude
der Kartoffeln: 20. 1842. [MB 194746]
≡ Neocosmospora solani (Mart.) L. Lombard & Crous, Stud. Mycol. 80: 228. 2015. [MB 810964]
= Neocosmospora rubicola L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB 810243]
Note: Also known as FSSC 5.
Fusarium solani-melongenae O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4. 2020. [IF
557706]
≡ Neocosmospora ipomoeae (Halst.) L. Lombard & Crous, Stud. Mycol. 80: 227. 2015. [MB 810960]
≡ Nectria ipomoeae Halst., Report of the New Jersey State Agricultural Experimental Station 12: 281
(1891) [MB 210931] (non Fusarium ipomoeae M.M. Wang, Qian Chen & L. Cai 2019 [MB 829538],
non Fusarium batatas Wollenw. 1914 [MB 175963])
≡ Hypomyces ipomoeae (Halst.) Wollenw., Phytopathology 3(1): 34. 1913. [MB 212639]
Page 24 of 64
24
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
≡ Haematonectria ipomoeae (Halst.) Samuels & Nirenberg, in Rossman, Samuels, Rogerson &
Lowen, Stud. Mycol. 42: 136. 1999. [MB 460446]
Etymology: From the correct name of its original plant host, Solanum melongena (Halstead 2015),
represented by its holotype, BPI 552416 (Sandoval-Denis et al. 2019).
Fusarium spathulatum (Sand.-Den. & Crous) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440:
4. 2020. [IF 557707]
≡ Neocosmospora spathulata Sand.-Den. & Crous, Persoonia 43: 171. 2019. [MB 831206]
Note: Also known as FSSC 26.
Fusarium sphaerosporum Q.T. Chen & X.H. Fu, Acta Mycol. Sin., Suppl. 1: 331. 1987 [MB 127721]
≡ Neocosmospora sphaerospora (Q.T. Chen & X.H. Fu) Sand.-Den. & Crous, Persoonia 43: 173. 2019.
[MB 832096]
Fusarium spinulosum (Pfenning) O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 4. 2020. [IF
557708]
≡ Neocosmospora spinulosa Pfenning, Sydowia 47: 66. 1995. [MB 413567]
Fusarium stercicola Šišić, Al-Hatmi, Baćanović-Šišić, S.A. Ahmed & Finckh, Antonie van Leeuwenhoek
111: 1793. 2018. [MB 823581]
≡ Neocosmospora stercicola (Šišić et al.) Sand.-Den. & Crous, Persoonia 43: 173. 2019. [MB 831207]
= Fusarium witzenhausenense Šišić et al., Antonie van Leeuwenhoek 111: 1795. 2018. [MB 823582]
Fusarium suttonianum (Sand.-Den. & Crous) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 4. 2020.
[IF 557709]
≡ Neocosmospora suttoniana Sand.-Den. & Crous, Persoonia 41: 123. 2018. [MB 822903]
Note: Also known as FSSC 20.
Fusarium tenuicristatum (S. Ueda & Udagawa) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 4.
2020. [IF 557710]
≡ Neocosmospora tenuicristata S. Ueda & Udagawa, Mycotaxon 16(2): 387. 1983. [MB 109113]
= Neocosmospora boninensis Udagawa, Y. Horie & P.F. Cannon, Sydowia 41: 350. 1989. [MB
125987]
Fusarium theobromae Appel & Strunk, Centralbl. Bakteriol. Parasitenk., 1. Abth. 13: 685. 1904. [MB
235605]
≡ Neocosmospora theobromae (Appel & Strunk) Sand.-Den. & Crous, Persoonia 43: 174. 2019. [MB
831208]
Fusarium tonkinense (Bugnic.) O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 4. 2020. [IF 557711]
≡ Cylindrocarpon tonkinense Bugnic., Encyclopédie Mycologique 11: 181. 1939. [MB 255134]
≡ Neocosmospora tonkinensis (Bugnic.) Sand.-Den. & Crous, Persoonia 41: 126. 2018. [MB 822904]
≡ Fusarium ershadii Papizadeh, van Diepeningen & Zamanizadeh, Europ. J. Plant Pathol. 151: 693.
2018. (nom. illegit. as a superfluous name, Art 52.1). [MB 817602]
Note: Also known as FSSC 9.
Fusarium vanettenii O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 5. 2020. [IF 557712]
Page 25 of 64
25
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
≡ Neocosmospora pisi (F.R. Jones) Sand.-Den. & Crous, Persoonia 43: 143. 2019. [MB 831189]
≡ Fusarium martii var. pisi F.R. Jones, J. Agric. Res. 26: 459. 1923. [MB 270614].
≡ Fusarium solani f. pisi (F.R. Jones) W.C. Snyder & H.N. Hansen, Amer. J. Bot. 28: 740. 1941. [MB
351714]
(≡ Fusarium pisi (F.R. Jones) A. Šišić et al., Sci. Rep. 8: 2. 2018. Nom. inval., Art. 42.1 [MB 824719])
Note: Also known as Nectria haematococca Mating Population VI (NhMPVI) and FSSC 11.
Etymology: In honor of the late Hans D. Van Etten, whose laboratory conducted extensive studies on this
species, making the first connection between plant pathogenicity and the fungal accessory genome.
Fusarium venezuelense O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 5. 2020. [IF 557713]
≡ Neocosmospora robusta Sand.-Den. & Crous, Persoonia 43: 165. 2019. [MB 831203]
(non Fusarium robustum Gerlach 1977 [MB 314220])
Etymology: Venezuela + -ensis from the name of its type locality.
Fusarium waltergamsii O’Donnell, Geiser & T. Aoki, Index Fungorum 440: 5. 2020. [IF 557714]
≡ Neocosmospora gamsii Sand.-Den. & Crous, Persoonia 41: 116. 2018. [MB 822899] (non Fusarium
gamsii Torbati, Arzanlou, Sand.-Den. 2019 [MB 825228])
Etymology: In honor of the late Dr. Walter Gams.
Note: Also known as FSSC 7.
Fusarium yamamotoi O’Donnell, Geiser, Kasson & T. Aoki, Index Fungorum 440: 5. 2020. [IF 557715]
≡ Nectria elegans W. Yamam. & Maeda, Sci. Rep. Hyogo Univ. Agric. 3: 15. 1957. [MB 301759] (non
Fusarium elegans Appel & Wollenw. 1910 [MB 451612])
≡ Neocosmospora elegans (W. Yamam. & Maeda) Sand.-Den. & Crous, Persoonia 43: 127. 2019.
[MB 831226]
(≡ Fusarium elegans W. Yamam. & Maeda, Trans. Mycol. Soc. Japan 3: 115. 1962. Nom. illegit., Art
53.1 [MB 330986])
(= Fusarium solani f. xanthoxyli Y. Sakurai & Matuo, Ann. Phytopathol. Soc. Japan 26: 117. 1961.
Nom. inval., Art. 39.1 [MB 350973])
(= Hypomyces solani f. xanthoxyli Y. Sakurai & Matuo, Ann. Phytopathol. Soc. Japan 26: 117. 1961.
Nom. inval., Art. 39.1 [MB 350974])
Note: Also known as Nectria haematococca Mating Population IV (NhMPIV) and FSSC 22.
Etymology: in honor of the late Dr. Wataro Yamamoto who originally found Nectria elegans and studied
trunk blight of Zanthoyxlum piperitum.
982
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Page 37 of 64
37
1315
Figure 1. Partitioned maximum likelihood bootstrapped (ML-BS) phylogram of Fusarium, based on full-
1316
length exonic nucleotide (nt) sequences of 19 protein-coding genes (Table 1), inferred using IQ-TREE
1317
(Nguyen et al. 2015). Nodes supported by 100% ML bootstrap (5000 replicates; BS) and 1.0 Bayesian
1318
posterior probability (BPP), including F1 and F2, are indicated with asterisks; ML-BS/BPP values are
1319
shown for nodes receiving less than 100%/1.0 support. Two branches highlighted in magenta received
1320
BS <70 and BPP < 0.99. Two shades of blue highlight 23 species complexes within Fusarium. Numerals
1321
situated adjacent to nodes represent gene concordance factors (gCFs) calculated by IQ-TREE 2 for that
1322
node, expressed as the number of loci that resolve it out of 19. PIC = parsimony informative characters;
1323
TC = Tree credibility.
1324
1325
Figure 2. Partitioned maximum likelihood boostrapped (ML-BS) cladogram of the F. solani Species
1326
Complex (FSSC) based on tef1, rpb2 and rDNA, inferred using IQ-TREE (Nguyen et al. 2015). Clades 1, 2
1327
and 3 represent designations proposed in O'Donnell (2000). Numerical designations corresponding to an
1328
informal ad hoc nomenclature for phylogenetic species in the FSSC (e.g., FSSC 1) are provided in
1329
brackets. The Ambrosia Fusarium Clade (Kasson et al. 2013), the clade that encompasses species with
1330
typical Neocosmospora morphology, and the clade consisting of soybean sudden death syndrome (SDS)
1331
and bean root rot (BRR) pathogens, are indicated. ML-BS values, based on 5000 replicates, are shown for
1332
each node. + = medically important species, bp, base pairs; PIC = parsimony informative characters; ET =
1333
epitype isolate; IT = isotype isolate; T = type isolate. *the type of N. striata, combined under F.
1334
bataticola. †the type of N. boninensis, combined under F. tenuicristatum (see Appendix A).
1335
1336
Supplemental Figure 1. Cladogram of Fusarium 19-locus dataset based on Bayesian inference. Numbers
1337
below nodes indicate Bayesian posterior probability on a 0-100 scale.
1338
1339
Supplemental Figure 2. Individual maximum likelihood boostrap phylograms of 19 individual gene trees.
1340
Locus names and molecular evolutionary models used in IQ-TREE are as listed in Table 1. Numbers
1341
above or adjacent to nodes indicate bootstrap values (5000 replicates).
1342
1343
Supplemental Figure 3. Cladogram of Fusarium inferred using IQ-TREE, with Internode Credibility (IC)
1344
and Internode Credibility-All (ICA) values presented below nodes.
1345
Page 38 of 64
Table 1. Phylogenetic data summary of 19 genes analyzed in the present study.
Locus
Protein encoded
Identifier1
Chr2
nt sites
AA3
PIC4
PIC/
site
% total
PICs
Model5
acl1
ATP citrate lyase large subunit
FFUJ_13230
4
1473
490
505
0.34
2.13%
TN+F+I+G4
act1*
Actin
FFUJ_00687
1
1425
474
641
0.45
2.71%
TIM2+F+I+G4
cal1*
Calmodulin
FFUJ_12207
8
450
149
117
0.26
0.49%
TNe+I+G4
cpr1
Cytochrome P450 reductase
FFUJ_04716
2
2085
694
949
0.46
4.01%
TIM2+F+I+G4
dpa1
DNA polymerase alpha subunit
FFUJ_08551
7
4491
1498
2233
0.50
9.43%
GTR+F+I+G4
dpe*1
DNA polymerase epsilon subunit
FFUJ_13258
4
6699
2232
3005
0.45
12.70%
GTR+F+I+G4
fas1
Fatty acid synthase alpha subunit
FFUJ_04562
2
5622
1880
2191
0.39
9.26%
TIM2+F+I+G4
fas2
Fatty acid synthase beta subunit
FFUJ_04563
2
6330
2109
2608
0.41
11.02%
TN+F+I+G4
ku70*
ATP-dependent DNA helicase II
FFUJ_04557
2
1959
652
1020
0.52
4.31%
SYM+I+G4
lcb2
Sphinganine palmitoyl transferase subunit
FFUJ_09546
9
2121
706
910
0.42
3.84%
TIM2+F+I+G4
mcm7
DNA replication licensing factor
FFUJ_02741
3
2526
841
1211
0.48
5.12%
GTR+F+I+G4
pgk1*
Phosphoglycerate kinase
FFUJ_09403
9
1257
418
447
0.36
1.89%
TIM2+F+I+G4
rpb1
RNA polymerase largest subunit
FFUJ_00736
1
5382
1793
2348
0.44
9.92%
TIM2+F+I+G4
rpb2
RNA polymerase 2nd largest subunit
FFUJ_07996
5
3882
1293
1667
0.43
7.04%
TIM2e+F+I+G4
tef1*
Translation elongation factor 1-alpha
FFUJ_05795
6
1383
460
299
0.22
1.26%
GTR+F+I+G4
top1
Topoisomerase
FFUJ_02999
3
2859
952
1505
0.53
6.36%
TIM2+F+I+G4
tsr1
Ribosomal biogenesis protein
FFUJ_09872
9
2493
830
1261
0.51
5.33%
GTR+F+I+G4
tub1
Tubulin alpha subunit
FFUJ_00614
1
1350
449
383
0.28
1.62%
TIM+F+I+G4
tub2*
Tubulin beta subunit
FFUJ_04397
2
1353
450
368
0.27
1.55%
TN+F+I+G4
TOTAL:
55140
18370
23668
*Individual gene tree does not resolve F1
1
Gene identifier in the Fusarium fujikuroi genome (Wiemann et al. 2013)
2
Chromosomal location as mapped to the Fusarium fujikuroi genome (Wiemann et al. 2013)
3
Amino acid count, which does not account for in-frame insertions/deletions
4
Parsimony-informative characters in the nucleotide alignment
5
Best evolutionary model as determined by Bayesian Information Criterion estimated in IQ-Tree
100.00%
Page 39 of 64
Supplemental Table 1. GenBank accessions for genome sequences.
Species
F. albidum
F. albosuccineum
F. ambrosium
F. anguioides
F. armeniacum
F. asiaticum
F. avenaceum
F. aywerte
F. babinda
F. buharicum
F. beomiforme
F. buxicola
F. chlamydosporum
F. circinatum
F. commune
F. compactum
F. concolor
F. continuum
F. culmorum
F. cyanostoma
F. decemcellulare
F. dimerum
F. domesticum
F. equiseti
F. falciforme
F. foetens
F. fujikuroi
F. gaditjirrii
F. graminearum
F. graminum
F. guttiforme
F. hainanense
F. heterosporum
F. hostae
F. illudens
F. irregulare
F. langsethiae
F. lateritium
F. longipes – 4***
F. longipes – 1***
Isolate
NRRL 22152
NRRL 20459
NRRL 62606
NRRL 25385
NRRL 6227
NRRL 26156
NRRL 54939 = Fa05001
NRRL 25410
NRRL 25539
NRRL 13371
NRRL 25174
NRRL 36148
NRRL 13444
NRRL 25331
NRRL 28387
NRRL 13829
NRRL 13459
NRRL 66286
NRRL 25475
NRRL 53998
NRRL 13412
NRRL 20691
NRRL 29976
NRRL 66338
NRRL 43529
NRRL 38302
NRRL 5538 = IMI 58289
NRRL 45417
NRRL 31084 = PH-1
NRRL 20692
NRRL 22945
NRRL 66475
NRRL 20693
NRRL 29888
NRRL 22090
NRRL 31160
NRRL 53436 = Fl201059
NRRL 13362
NRRL 13317
NRRL 13368
GenBank Accession
JABFEP000000000
JAADYS000000000
NKCL00000000*
JAALXK000000000**
JABFEC000000000
JABFEQ000000000
JPYM00000000*
JABCQV000000000**
JABCKA000000000
JAATHB000000000
PVQB00000000*
JAAVUK000000000
JAAVUD00000000
JAAQPE000000000
JABFES000000000
JABFET000000000
JABCJY000000000**
JABCKB000000000**
JABFEU000000000
JABCKW000000000
JAAGWO000000000**
JABGLY000000000
JABFEV000000000
QGEB00000000*
JABEEK000000000**
JABFMM000000000
GCF_900079805.1*
JABFAI000000000**
GCA_900044135.1*
JAAGWP000000000**
JAAQRL000000000
JABFEW000000000
JAAGWQ000000000**
JABCJX000000000**
JABFEX000000000
QGEA00000000*
JXCE00000000.1*
JAAVTZ000000000
JABFEY000000000
JABFEZ000000000
Page 40 of 64
F. lyarnte
F. mangiferae
F. miscanthi
F. nelsonii
F. nematophilum
F. neocosmosporiellum
F. newnesense
F. nisikadoi
F. nurragi
F. oxysporum
F. oxysporum
F. penzigii
F. poae
F. praegraminearum
F. pseudograminearum
F. redolens
F. rusci
F. sacchari
F. sambucinum
F. sarcochroum
F. scirpi
F. setosum
F. sporotrichioides
F. staphyleae
F. stilboides
F. subglutinans
F. sublunatum
F. thapsinum
F. torreyae
F. torulosum
F. transvaalense
F. tricinctum
F. vanettenii
F. venenatum
F. ventricosum
F. verrucosum
F. verticillioides
F. virguliforme
F. xylarioides
F. zanthoxyli
F. zealandicum
Fusarium sp.
Fusarium sp.
NRRL 54252
NRRL25226
NRRL 26231
NRRL 13338
NRRL 54600
NRRL 22166
NRRL 66241
NRRL 25179
NRRL 36452
NRRL 32931
NRRL 34936 = Fo4827
NRRL 20711
NRRL 26941
NRRL 39664
NRRL 28062
NRRL 22901
NRRL 22134
NRRL 66326
NRRL 13708
NRRL 20472
NRRL 66328
NRRL 36526
NRRL 3299
NRRL 22316
NRRL 20429
NRRL 66333
NRRL 13384
NRRL 22049
NRRL 54149
NRRL 22747
NRRL 31008
NRRL 25481
NRRL 45880 = 77-13-4
NRRL 66329
NRRL 25729
NRRL 22566
NRRL 20956 = FGSC 7600
NRRL 31041
NRRL 25486
NRRL 66285
NRRL 22465
NRRL 25184
NRRL 52700
JAAVUB000000000
FCQH00000000*
JAAVUA000000000
JAAVUC000000000
JABFFA000000000
SSHR00000000*
JABCJW000000000**
JABFFB000000000
JAALXI000000000**
AFML00000000*
AAXH00000000*
JABFFC000000000
JABFFD000000000
LXHY00000000*
GCA_000974265.2*
JAAVUJ000000000
JADBHU000000000
JABSTH000000000** †
JAAVUG000000000
JABEXW000000000**
QHHJ00000000*
JABFFE000000000
PXOF00000000*
JADDON000000000
JAASAY000000000
JAAOAV000000000** †
JABFFF000000000
JAAOAX000000000** †
JABEET000000000
JABFMN000000000
JABFFG000000000
JAALXJ000000000**
ACJF00000000*
JABFFH000000000
JABFFI000000000
JABFFJ000000000
AAIM00000000*
JABEEP000000000**
JABFFK000000000
JABFFL000000000
JABEYC000000000**
JABSSZ000000000
JAAQPE000000000** †
Page 41 of 64
Fusarium sp. [AF-6]
Beauveria bassiana
Neonectria ditissima
Neonectria sp.
Neonectria coccinea
Trichoderma brevicompactum
NRRL 62590
ARSEF 2860
NRRL 20485
NRRL 22505
NRRL 20487
IBT 40841
NKCJ00000000*
GCA_000280675.1*
JABSTC000000000
JABSTB000000000
JABSTD000000000
PXNZ00000000.1*
1 NRRL = USDA/ARS/NCAUR culture collection; IMI = CABI culture collection; FGSC = Fungal Genetics Stock Center;
ARSEF = ARS Collection of Entomopathogenic Fungal Cultures; IBT = IBT Culture Collection of Fungi at Danish
Technical University. All other strain numbers refer to published non-accession designations.
* Genome sequence data previously reported and deposited in GenBank from other studies
** Genome sequence data produced at USDA-ARS-NCAUR and reported in Kim et al. (2020)
***Representing undescribed species 1 and 4 within the morphospecies F. longipes
† Sequence data generated at the Beijing Genome Institute-Hong Kong for USDA-ARS-NCAUR and reported in Kim et
al. (2020)
Page 42 of 64
Species Complex
F. langsethiae 53436
18
F. sporotrichioides 3299
19
F. armeniacum 6227
84/1.0
9
F. poae 26941
19
F. sambucinum 13708
18
18
F. venenatum 66329
F. praegraminearum 39664
F. pseudograminearum 28062
16
* F. culmorum 25475
16
* F. asiaticum 26156
17
18
18
* F. graminearum 31084
F compactum 13829
F. transvaalense 31008
13
11
F. longipes - 4 13317
*
16
F. longipes - 1 13368
F. aywerte 25410
F. chlamydosporum 13444
17
17
19
F. nelsonii 13338
F.
scirpi 66328
16
F. equiseti 66338
19
irregulare 31160
94/1.0 7
* F.
15
F. hainanense 66475
F. graminum 20692
18
F. heterosporum 20693
18
F. nurragi 36452
7
F. torulosum 22747
99/1.0
F. avenaceum 54939
19
18
19
F. tricinctum 25481
F.
anguioides 25385
69/0.98 7 18
F. concolor 13459
F. verrucosum 22566
17
F. babinda 25539
F. beomiforme 25174
17
F. hostae 29888
18 F. redolens 22901
16
F. newnesense 66241
19
Fusarium sp. 25184
19
F. oxysporum 34936
* * 18 F. oxysporum 32931
16
F. foetens 38302
17
F. gaditjirrii 45417
19
17
* 16 F. lyarnte 54252
18F. miscanthi 26231
99/1.0
96/1.0 4 F. niskadoi 25179
F. commune 28387
F. fujikuroi 5538
15
2
F. mangiferae 25226
89/1.0
17
F. sacchari 66326
F. thapsinum 22049
17
17
F.
verticillioides 20956
13
17
* 5 F. xylarioides 25486
Fusarium sp. 52700
86/1.0
F. guttiforme 22945
90/1.0 18 F. circinatum 25331
14
* F. subglutinans 66333
F. torreyae 54149
F. continuum 66286
19
18
12
F. zanthoxyli 66285
*
F. stilboides 20429
15
F. lateritium 13622
*
14
F. sarcochroum 20472
F. buharicum 13371
15
F. sublunatum 13384
F. buxicola 36148
F. cyanostoma 53998
F. rusci 22134
F. staphyleae 22316
19
F. zealandicum 22465
F. albosuccineum 20459
19
F. decemcellulare 13412
F. setosum 36526
F. illudens 22090 Clade 1
9
F. virguliforme 31041 Clade 2
F. neocosmosporiellum 22166
F. ambrosium 62606
19
19
Clade 3
Fusarium sp. 62590 AF-6
*
15
F.
falciforme 43529
*
15
F. vanettenii 45880
F. albidum 22152
F. nematophilum 54600
F. ventricosum 25729
F. domesticum 29976
F. dimerum 20691
19
F. penzigii 20711
N. ditissima 20485
Neonectria sp. 22505
10
N .coccinea 20487
Beauveria bassiana
Trichoderma brevicompactum
**
Fusarium
Phylogeny
19 genes
55,140 nt
23,668 PIC
**
*
*
sambucinum
*
*
*
TC = 48.41
relative TC = 0.563
best ML tree:
-927514.615
*
*
* *
*
*
*
*
* *
*
*
*
*
*
*
*
*
*
*
*
*
**
**
*
chlamydosporum
incarnatum-equiseti
heterosporum
tricinctum
concolor
babinda
burgessii
redolens
newnesense
oxysporum
nisikadoi
fujikuroi
*
*
*
100/0.99
*
81/0.99
*18
*15
*10
*
*
*12
7
F2
F1
*14
*19
91/0.99
*12
*19
0
12
*18
<50/<0.50
*18
*18
0.05
*
99/0.98
torreyae
lateritium
buharicum
buxicola
staphyleae
decemcellulare
*
* *
*
solani
albidum
ventricosum
dimerum
Neonectria
(sister taxon)
outgroups
Page 43 of 64
FSSC Clade 3 100
98
3-loci
99
3209 bp
655 PIC 99
67
NRRL 37625 F. cyanescens [FSSC 27] T
NRRL 28541 F. spathulatum [FSSC 26] T
+
+
79
100
+
NRRL 32437 F. ferrugineum [FSSC 28] T
NRRL 54722 F. euwallaceae AF-2 T
67
Ambrosia
Fusarium
Clade
NRRL 62579 F. oligoseptatum AF-4 T
87
NRRL 22231 F. tuaranense AF-5 T
CBS 126407 F. ngaiotongaense T
+
NRRL 22268 F. petroliphilum [FSSC 1] +
NRRL 28008 F. oblongum [FSSC 29] T
94
53
100
91
NRRL 62945 F. kuroshium AF-12
100
NRRL 62611 F. obliquiseptatum AF-7 T
NRRL 46517 F. pseudensiforme [FSSC 33] T
99
56
NRRL 25137 F. pseudoradicicola [FSSC 37] T
81
CBS 115695 F. parceramosum [FSSC 18] T
CBS 143038 F. pseudotonkinense T
58
100
74
NRRL 22399 F. cucurbiticola [FSSC 10] T
98
NRRL 28030 F. lichenicola [FSSC 16]
100
CBS 190.35 F. regulare
100
‘Neocosmospora’
morphology
99
+
100
100
+
NRRL 45880 F. vanettenii [FSSC 11] T
NRRL 43489 F. metavorans [FSSC 6]
100
CBS 119600 F. haematococcum ET
CBS 125727 F. rectiphorus T
+
+
52
SDS and
BRR
pathogens
NRRL 13997 F. paraeumartii T
78
56
53
70
94
+
+
NRRL 22661 F. keratoplasticum [FSSC 2 ] T +
NRRL 66304 F. solani [FSSC 5] ET +
NRRL 32858 F. suttonianum [FSSC 20] T
CBS 475.67 F. falciforme [FSSC 3+4] T
100
81
100
98
NRRL 22276 F. phaseoli
NRRL 31096 F. tucumaniae T
76
67
NRRL 31041 F. virguliforme T
NRRL 31757 F. brasiliense T
NRRL 54364 F. azukicola T
100
100
NRRL 31104 F. cuneirostrum
CBS 202.32 F. amplum T
NRRL 31949 F. crassistipitatum
100
NRRL 22659 F. breviconum ET
98
NRRL 22470 F. tenuicristatum†
NRRL 22166 F. neocosmosporiellum [FSSC 8] +
+
NRRL 32323 F. waltergamsii [FSSC 7] T
65
NRRL 22155 F. tenuicristatum T
NRRL 22438 F. ornamentatum T
CBS 144390 F. diminutum [FSSC 39] T
97
CBS 114067 F. samuelsii T
96
NRRL 22427 F. bataticola*
NRRL 22412 F. cryptoseptatum T
NRRL 22402 F. bataticola [FSSC 23] T
52
NRRL 22387 F. helgardnirenbergiae T
NRRL 22277 F. yamamatoi [FSSC 22] ET
100
87
88
100
FSSC Clade 2
CPC 27186 F. croci Italy T
CBS 119599 F. kurunegalense T
100
99
CBS 115659 F. martii ET
100
CBS 115658 F. noneumartii [FSSC 42] T
70
NRRL 22657 F. solani-melongenae [FSSC 21]
86
NRRL 53586 F. tonkinense [FSSC 9] T
100
NRRL 22574 F. acutisporum T
NRRL 22395 F. venezuelense T
FRC S 1836 F. kelerajum T
FRC S 1845 F. mahasenii T
+
CBS 144386 F. crassum [22277FSSC 34] T
CBS 142481 F. stercicola T
+
CBS 509.63 F. ramosum T
CBS 123846 F. silvicola [FSSC 13] T
CBS 144387 F. breve [FSSC 15] T
+
NRRL 22570 F. piperis [FSSC 31] ET
+
NRRL 22230 F. mori [FSSC 17] T
100
NRRL 22178 F. protoensiforme [FSSC 32] T
CM F12570 F. riograndense T
100
+
NRRL 22652 F. quercinum [FSSC 14] T
99
58
+
CBS 144.25 F. bostrycoides [FSSC 25] NT
99
100
+
NRRL 22579 F. borneense [FSSC 30] ET
CPC 26829 F. perseae T
NRRL 52782 F. hypothenemi [FSSC 38] T
54
50
100
86
NRRL 22389 F. liriodendri [FSSC 24] T
90
68
85
NRRL 62628 F. floridanum AF-3 T
89
NRRL 54993 F. catenatum [FSSC 43] T
74
89
CBS 142424 F. macrosporum T
NRRL 22346 F. ambrosium [FSSC 19] AF-1 ET
+
FSSC Clade 1
NRRL 22090 F. illudens
NRRL 22632 F. plagianthi IT
Page 44 of 64
MrBayes Consensus Cladogram
100
98
100
100
100
100
99
100
100
100
100
100
100
98
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
99
100
100
100
100
100
100
100
100
100
88
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
99
100
99
100
100
100
100
100
Neonectria ditissima 20485
Neonectria sp. 22505
Neonectria coccinea 20487
F albida 22152
F nematophilum 54600
F albosuccineum 20459
F decemcellulare 13412
F setosum 36526
F ambrosium 62606
Fusarium sp 62590 AF-6
F falciforme 43529
F vanettenii 45880
F neocosmosporiellum 22166
F illudens 22090
F virguliforme 31041
F anguioides 25385
F concolor 13459
F verrucosum 22566
F babinda 25539
F beomiforme 25174
F circinatum 25331
F subglutinans 66333
F guttiforme 22945
Fusarium sp 52700
F thapsinum 22049
F verticillioides 20956
F xylarioides 25486
F fujikuroi 5538
F mangifera 25226
F sacchari 66326
F commune 28387
F gaditjirrii 45417
F lyarnte 54252
F miscanthi 26231
F niskadoi 25179
F foetens 38302
F oxysporum 34936 Fol4287
F oxysporum 32931 FOSC3a
F newnesense 66241
Fusarium sp 25184
F hostae 29888
F redolens 22901
F asiaticum 26156
F graminearum 31084
F culmorum 25475
F pseudograminearum 28062
F praegraminearum 39664
F langsethiae 53436
F sporotrichioides 3299
F armeniacum 6227
F poae 26941
F sambucinum 13708
F venenatum 66329
F compactum 13829
F transvaalense 31008
F longipes 13317
F longipes 13368
F aywerte 25410
F chlamydosporum 13444
F nelsonii 13338
F scirpi 66328
F equiseti 66338
F irregulare 31160
F hainanense 66475
F avenaceum 54939
F tricinctum 25481
F torulosum 22747
F nurragi 36452
F graminum 20692
F heterosporum 20693
F continuum 66286
F zanthoxyli 66285
F torreyae 54149
F lateritium 13622
F sarcochroum 20472
F stilbioides 20429
F buharicum 13371
F sublunatum 13384
F buxicola 36148
F cyanostoma 53998
F rusci 22134
F staphyleae 22316
F zealandicum 22465
F ventricosum 25729
F dimerum 20691
F penzigii 20711
F domesticum 29976
Trichoderma brevicompactum
Beauveria bassiana
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
F_anguoides_25385
99
F_concolor_13459
98
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
100
F_circinatum_25331
F_guttiforme_22945
96
94
F_subglutinans_66333
94
100
F_thapsinum_22049
F_verticillioides_20956
87
66
F_xylarioides_25486
99
F_fujikuroi_5538
100100
F_mangiferae_25226
100
F_sacchari_6632
Fusarium_sp_52700
81
F_commune_28387
74
F_foetens_38302
99
F_oxysporum_34936
99
100
F_oxysporum_32931
93
F_newnesense_66241
100
Fusarium_sp_25184
100
F_gaditjirrii_45417
99
F_lyarnte_54252
100
100
96
F_miscanthi_26231
F_niskadoi_25179
100
F_hostae_29888
F_redolens_22901
F_asiaticum_26156
99
F_culmorum_25475
99
51
F_graminearum_31084
100
F_pseudograminearum_28062
F_praegraminearum_39664
98
100
F_langsethiae_53436
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
F_poae_26941
90 89 97
100
F_sambucinum_13708
100
F_venenatum_66329
100
F_compactum_13829
Fusarium_transvaalense_31008
100
100
74
F_longipes_13317
F_longipes_13368
85
F_aywerte_25410
100
F_chlamydosporum_13444
80
F_nelsonii_13338
F_scirpi_66328
100
F_equiseti_66338
86
F_irregulare_31160
83
F_hainanense_66475
98
95
F_avenaceum_54939
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_graminum_20692
89
90
F_heterosporum_20693
F_nurragi_36452
100
F_continuum_66286
100
F_torreyae_54149
100
F_zanthoxyli_66285
98
F_lateritium_13622
100
F_sarcochroum_20472
F_stilbioides_20429
98
F_buharicum_13371
F_sublunatum_13384
86
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
100
F_ambrosium_62606
93
Fusarium_sp_62590_AF6
94
F_falciforme_43529
70
F_vanettenii_45880
56
97
F_neocosmosporiellum_22166
94
F_illudens_22090
37
F_virguliforme_31041
100
F_dimerum_20691
100
F_penzigii_20711
66
F_domesticum_29976
F_ventricosum_25729
100
17
F_albosuccineum_20459
73
F_decemcellulare_13412
100
F_buxicola_36148
86
F_cyanostoma_53998
51
F_setosum_36526
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
99
Page 45 of 64
acl1
99
91
99
0.04
100
100
92
100
66
43
100
10
100
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
82
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
85
Fusarium_sp_62590_AF6
91
F_vanettenii_45880
99
F_falciforme_43529
F_neocosmosporiellum_22166
67
F_illudens_22090
F_virguliforme_31041
F_buxicola_36148
F_cyanostoma_53998
38
88
87
56
100
100
100
act1
F_anguoides_25385
F_concolor_13459
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
100
100
F_subglutinans_66333
100
F_guttiforme_22945
94
F_thapsinum_22049
100
F_verticillioides_20956
96 100
F_xylarioides_25486
100
Fusarium_sp_52700
F_fujikuroi_5538
100
100
F_mangiferae_25226
100
F_sacchari_6632
99 94 F_foetens_38302
F_oxysporum_34936
57 48
F_oxysporum_32931
F_miscanthi_26231
100
100
F_niskadoi_25179
95
F_gaditjirrii_45417
100
F_lyarnte_54252
99
F_commune_28387
100
F_newnesense_66241
94
Fusarium_sp_25184
100
F_hostae_29888
86
F_redolens_22901
F_asiaticum_26156
100
100
F_graminearum_31084
97
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
96
F_poae_26941
100
F_sambucinum_13708
99 100
F_venenatum_66329
F_compactum_13829
87
F_longipes_13317
100
100
100
F_longipes_13368
81
Fusarium_transvaalense_31008
F_aywerte_25410
97
100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
99
74
92
100
F_equiseti_66338
F_irregulare_31160
96
F_hainanense_66475
F_avenaceum_54939
98
99
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_graminum_20692
F_heterosporum_20693
88
F_nurragi_36452
100
F_continuum_66286
100
F_torreyae_54149
97
F_zanthoxyli_66285
F_lateritium_13622
95
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
95
100
78
Page 46 of 64
0.09
Page 47 of 64
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
85
F_ventricosum_25729
F_staphyleae_22316
F_zealandicum_22465
100
F_dimerum_20691
F_penzigii_20711
67
F_domesticum_29976
99
68
73
cal1
Beauveria_bassiana
100
F_albosuccineum_20459
F_decemcellulare_13412
100
F_anguoides_25385
76
F_concolor_13459
85
74
F_verrucosum_22566
F_babinda_25539
F_circinatum_25331
97
97
F_subglutinans_66333
39
F_guttiforme_22945
Fusarium_sp_52700
F_fujikuroi_5538
22
99
F_sacchari_6632
15 99
F_mangiferae_25226
80 99 F_thapsinum_22049
38
F_verticillioides_20956
70
F_xylarioides_25486
10
F_commune_28387
77 11 F_foetens_38302
7
F_niskadoi_25179
66 F_miscanthi_26231
31
F_oxysporum_34936
69
87
F_gaditjirrii_45417
93
F_lyarnte_54252
99 7 F_oxysporum_32931
F_newnesense_66241
87
100
Fusarium_sp_25184
77
F_hostae_29888
99
F_redolens_22901
F_beomiforme_25174
F_continuum_66286
90
81
F_zanthoxyli_66285
95
F_torreyae_54149
F_avenaceum_54939
100
99
F_tricinctum_25481
F_torulosum_22747
99
66
F_graminum_20692
100
86
F_heterosporum_20693
F_nurragi_36452
F_asiaticum_26156
80 F_graminearum_31084
96
F_culmorum_25475
100
F_langsethiae_53436
98
76
F_sporotrichioides_3299
95
93
Fusarium_armeniacum_6227
F_poae_26941
62
42 89 93 F_sambucinum_13708
F_venenatum_66329
F_praegraminearum_39664
26
35
F_pseudograminearum_28062
99
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
99
42
99
98
20
F_equiseti_66338
100
F_irregulare_31160
F_hainanense_66475
99
68
F_compactum_13829
94
Fusarium_transvaalense_31008
42
100
F_longipes_13317
F_longipes_13368
F_aywerte_25410
F_buharicum_13371
F_lateritium_13622
93
68 31
F_sarcochroum_20472
74
F_sublunatum_13384
F_stilbioides_20429
60
F_cyanostoma_53998
F_buxicola_36148
68
F_rusci_22134
F_ambrosium_62606
100
57
Fusarium_sp_62590_AF6
67
F_falciforme_43529
75
F_neocosmosporiellum_22166
94 60
F_vanettenii_45880
F_illudens_22090
86
81
F_virguliforme_31041
F_setosum_36526
100
F_albida_22152
F_nematophilum_54600
Trichoderma_brevicompactum
0.05
N_ditissima_20485
N_coccinea_20487
Neonectria_sp_22505
100
F_albosuccineum_20459
F_decemcellulare_13412
100
F_ambrosium_62606
64
Fusarium_sp_62590_AF6
100
F_neocosmosporiellum_22166
96
F_falciforme_43529
100
F_vanettenii_45880
100
F_illudens_22090
F_virguliforme_31041
F_anguoides_25385
100
93
F_concolor_13459
99
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
F_circinatum_25331
99
100
F_subglutinans_66333
100
F_guttiforme_22945
91
F_xylarioides_25486
99
F_thapsinum_22049
100
89
F_verticillioides_20956
Fusarium_sp_52700
100
F_fujikuroi_5538
100
100
F_mangiferae_25226
100
F_sacchari_6632
54
F_commune_28387
78
F_gaditjirrii_45417
100
F_lyarnte_54252
100
F_miscanthi_26231
100 29 100 F_niskadoi_25179
F_foetens_38302
F_oxysporum_34936
97
100
F_oxysporum_32931
100
F_newnesense_66241
100
Fusarium_sp_25184
F_hostae_29888
100
F_redolens_22901
100
F_asiaticum_26156
100
100
F_graminearum_31084
64
100
F_culmorum_25475
100
F_pseudograminearum_28062
98
F_praegraminearum_39664
F_poae_26941
100 100 F_sambucinum_13708
F_venenatum_66329
100
F_langsethiae_53436
100
F_sporotrichioides_3299
100
100
Fusarium_armeniacum_6227
F_compactum_13829
100
F_longipes_13317
83 81
F_longipes_13368
45
99
Fusarium_transvaalense_31008
F_aywerte_25410
100 98 100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
92
F_equiseti_66338
100
74
F_hainanense_66475
F_irregulare_31160
88
34
100
F_avenaceum_54939
99
100
F_tricinctum_25481
99
F_torulosum_22747
F_graminum_20692
100
100
F_heterosporum_20693
F_nurragi_36452
F_continuum_66286
100
100
F_torreyae_54149
95
F_zanthoxyli_66285
100
F_lateritium_13622
100
F_stilbioides_20429
66
F_sarcochroum_20472
39
F_buharicum_13371
100
F_sublunatum_13384
100
F_dimerum_20691
100
F_penzigii_20711
100
F_domesticum_29976
F_ventricosum_25729
100
F_buxicola_36148
55
F_cyanostoma_53998
F_setosum_36526
49 99
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
100
F_albida_22152
F_nematophilum_54600
100
97
78
97
97
Page 48 of 64
cpr1
Beauveria_bassiana
Trichoderma_brevicompactum
0.1
Page 49 of 64
97
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
100
36
100
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
98
59
100
100
81
85
100
44
100
100
92
41
100
100
100
96
100
69
100
100
100
F_anguoides_25385
F_concolor_13459
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
100 F_circinatum_25331
100
F_subglutinans_66333
100
F_guttiforme_22945
100
F_fujikuroi_5538
100
100 F_mangiferae_25226
F_sacchari_6632
99
Fusarium_sp_52700
100
83 100
F_thapsinum_22049
F_verticillioides_20956
97
F_xylarioides_25486
100
F_commune_28387
99 100 F_gaditjirrii_45417
F_lyarnte_54252
100
100F_miscanthi_26231
96
F_niskadoi_25179
100
100 F_newnesense_66241
93
Fusarium_sp_25184
F_foetens_38302
100 F_oxysporum_34936
100 F_oxysporum_32931
100
F_hostae_29888
F_redolens_22901
100
100 F_asiaticum_26156
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
100
F_langsethiae_53436
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
84 100
97
F_poae_26941
F_sambucinum_13708
100
F_venenatum_66329
100
100
F_longipes_13317
F_longipes_13368
100
99
F_compactum_13829
Fusarium_transvaalense_31008
F_aywerte_25410
100
100
100
F_chlamydosporum_13444
F_nelsonii_13338
99
F_scirpi_66328
100
F_equiseti_66338
F_irregulare_31160
100
F_hainanense_66475
95
100
F_avenaceum_54939
100
F_tricinctum_25481
96
F_torulosum_22747
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
66
F_continuum_66286
100
F_torreyae_54149
F_zanthoxyli_66285
95
F_lateritium_13622
100
F_sarcochroum_20472
F_stilbioides_20429
F_buharicum_13371
F_sublunatum_13384
F_buxicola_36148
F_cyanostoma_53998
100
F_ambrosium_62606
100
Fusarium_sp_62590_AF6
F_falciforme_43529
100
100
F_vanettenii_45880
F_neocosmosporiellum_22166
F_virguliforme_31041
F_illudens_22090
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
0.08
dpa1
100
100
64
100
84
80
100
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
N_ditissima_20485
100
Neonectria_sp_22505
N_coccinea_20487
100
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
F_ambrosium_62606
100
Fusarium_sp_62590_AF6
100
100
100
F_falciforme_43529
F_vanettenii_45880
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
83
100
97
100
68
98
100
100
74
80
76
100
100
100
100
0.09
Page 50 of 64
dpe1
F_anguoides_25385
F_concolor_13459
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
81
F_circinatum_25331
100
F_guttiforme_22945
100
100
F_subglutinans_66333
Fusarium_sp_52700
93
F_thapsinum_22049
100
F_verticillioides_20956
100 98
F_xylarioides_25486
F_fujikuroi_5538
100
100
98
F_mangiferae_25226
100
F_sacchari_6632
F_foetens_38302
99 100 F_oxysporum_34936
100
F_oxysporum_32931
100
F_commune_28387
F_newnesense_66241
100 100
Fusarium_sp_25184
F_gaditjirrii_45417
100
100
F_lyarnte_54252
F_miscanthi_26231
100
100
F_niskadoi_25179
100 F_hostae_29888
F_redolens_22901
100
100
F_asiaticum_26156
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
98
F_poae_26941
92 100
F_sambucinum_13708
100
F_venenatum_66329
100
F_compactum_13829
Fusarium_transvaalense_31008
100
F_longipes_13317
100
100
100
F_longipes_13368
97
F_aywerte_25410
100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
100
76
100
98
F_equiseti_66338
F_irregulare_31160
100
F_hainanense_66475
100
F_avenaceum_54939
100
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_graminum_20692
F_heterosporum_20693
96
F_nurragi_36452
99
F_continuum_66286
100
F_zanthoxyli_66285
F_torreyae_54149
87
F_lateritium_13622
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_buxicola_36148
F_cyanostoma_53998
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
Page 51 of 64
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
F_ventricosum_25729
100
98
100
100
100
85
100
100
100
65
100
100
100
89
F_ambrosium_62606
Fusarium_sp_62590_AF6
F_falciforme_43529
F_vanettenii_45880
F_neocosmosporiellum_22166
F_virguliforme_31041
F_illudens_22090
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
100
95
100
84
100
77
44
100
92
fas1
F_anguoides_25385
F_concolor_13459
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
100
100
F_subglutinans_66333
100
71
F_guttiforme_22945
Fusarium_sp_52700
F_fujikuroi_5538
100 100
F_mangiferae_25226
100
F_sacchari_6632
54
F_thapsinum_22049
100
100
90
F_verticillioides_20956
80
F_xylarioides_25486
F_commune_28387
92 100 F_foetens_38302
F_oxysporum_34936
100
100
F_oxysporum_32931
59
97
F_newnesense_66241
100
Fusarium_sp_25184
100
F_gaditjirrii_45417
100
F_lyarnte_54252
100 100
F_miscanthi_26231
F_niskadoi_25179
100
F_hostae_29888
F_redolens_22901
F_avenaceum_54939
100
100
F_tricinctum_25481
92
F_torulosum_22747
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
F_asiaticum_26156
100
94
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
F_poae_26941
100 100
100
F_sambucinum_13708
100
F_venenatum_66329
F_compactum_13829
95
100
Fusarium_transvaalense_31008
69
100
F_longipes_13317
97
F_longipes_13368
F_scirpi_66328
99
100
100
F_equiseti_66338
F_irregulare_31160
100
F_hainanense_66475
93
F_aywerte_25410
100
F_chlamydosporum_13444
100
F_nelsonii_13338
F_continuum_66286
98
100
F_zanthoxyli_66285
F_torreyae_54149
100
F_lateritium_13622
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
F_buxicola_36148
F_cyanostoma_53998
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
68
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
100
100
100
0.06
100
59
Page 52 of 64
fas2
100
88
100
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
F_dimerum_20691
100
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
100
F_albosuccineum_20459
100
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
Fusarium_sp_62590_AF6
100
F_falciforme_43529
100
100
F_vanettenii_45880
100
F_neocosmosporiellum_22166
100
F_illudens_22090
F_virguliforme_31041
100
F_anguoides_25385
57
F_concolor_13459
100
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
98
F_circinatum_25331
100
F_subglutinans_66333
F_guttiforme_22945
100
87100
F_thapsinum_22049
96
F_verticillioides_20956
100
F_xylarioides_25486
100 66
Fusarium_sp_52700
100
F_fujikuroi_5538
100
100
F_mangiferae_25226
62
F_sacchari_6632
100
F_gaditjirrii_45417
F_lyarnte_54252
100
72 100
F_miscanthi_26231
F_niskadoi_25179
68
F_newnesense_66241
100
100
Fusarium_sp_25184
F_commune_28387
F_foetens_38302
100
F_oxysporum_34936
100
100
F_oxysporum_32931
F_hostae_29888
100
F_redolens_22901
78
100
F_asiaticum_26156
100
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
79
F_langsethiae_53436
100
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
100
F_poae_26941
100
100
F_sambucinum_13708
81
F_venenatum_66329
F_compactum_13829
97
100
Fusarium_transvaalense_31008
100
F_longipes_13317
99
F_longipes_13368
100
F_aywerte_25410
100
100
F_chlamydosporum_13444
92
F_nelsonii_13338
F_scirpi_66328
100
F_equiseti_66338
100
F_irregulare_31160
80
100
F_hainanense_66475
F_avenaceum_54939
100
100
F_tricinctum_25481
100
100
F_torulosum_22747
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
F_continuum_66286
100
100
F_zanthoxyli_66285
78
F_torreyae_54149
100
F_buharicum_13371
F_sublunatum_13384
F_lateritium_13622
99
96
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buxicola_36148
F_cyanostoma_53998
100
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
97
0.07
F_ventricosum_25729
N_ditissima_20485
77
Neonectria_sp_22505
N_coccinea_20487
100
Page 53 of 64
100
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
100
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
Fusarium_sp_62590_AF6
93
F_falciforme_43529
100
79
F_vanettenii_45880
72
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
100
80
100
100
100
98
100
88
81
90
85
99
100
82
99
100
100
100
100
100
99
99
100
90
100
100
100
99
ku70
F_anguoides_25385
F_concolor_13459
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
100
F_circinatum_25331
100
F_subglutinans_66333
100
F_guttiforme_22945
78
F_thapsinum_22049
100
F_verticillioides_20956
100
F_xylarioides_25486
100
F_fujikuroi_5538
100
F_mangiferae_25226
100
100
F_sacchari_6632
66 80
Fusarium_sp_52700
F_commune_28387
F_foetens_38302
45 100 F_oxysporum_34936
100
F_oxysporum_32931
100
98
F_gaditjirrii_45417
100
F_lyarnte_54252
92
F_miscanthi_26231
100
100
F_niskadoi_25179
F_newnesense_66241
100
Fusarium_sp_25184
F_hostae_29888
100
F_redolens_22901
F_avenaceum_54939
100
100
F_tricinctum_25481
100
F_torulosum_22747
F_graminum_20692
100
F_heterosporum_20693
98
F_nurragi_36452
99
F_asiaticum_26156
100
F_graminearum_31084
99
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
97
100
F_poae_26941
100
F_sambucinum_13708
100
F_venenatum_66329
F_compactum_13829
97
Fusarium_transvaalense_31008
100
100
96
F_longipes_13317
F_longipes_13368
F_aywerte_25410
93
100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
100
73
100
F_equiseti_66338
F_irregulare_31160
100
F_hainanense_66475
F_continuum_66286
F_zanthoxyli_66285
F_torreyae_54149
F_lateritium_13622
F_sarcochroum_20472
F_stilbioides_20429
F_buharicum_13371
F_sublunatum_13384
F_buxicola_36148
F_cyanostoma_53998
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
0.2
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
F_ventricosum_25729
100
97
100
100
100
95
100
100
100
98
99
100
90
99
54
77
100
51
100
100
100
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ambrosium_62606
Fusarium_sp_62590_AF6
F_falciforme_43529
F_vanettenii_45880
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
76
79
100
91
62
Page 54 of 64
100
lcb2
F_anguoides_25385
F_concolor_13459
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
98
100
F_subglutinans_66333
100
F_guttiforme_22945
96 100 F_fujikuroi_5538
F_mangiferae_25226
100
F_sacchari_6632
74
100
F_xylarioides_25486
47
F_thapsinum_22049
100
100
93
F_verticillioides_20956
Fusarium_sp_52700
86
F_commune_28387
F_foetens_38302
73 100 F_oxysporum_34936
100
F_oxysporum_32931
F_newnesense_66241
100 100
Fusarium_sp_25184
100
F_gaditjirrii_45417
100
F_lyarnte_54252
100
F_miscanthi_26231
100
F_niskadoi_25179
98
100
F_hostae_29888
F_redolens_22901
F_asiaticum_26156
100
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
98
F_poae_26941
100
F_sambucinum_13708
100
100
F_venenatum_66329
91
F_compactum_13829
98
97
Fusarium_transvaalense_31008
100
98
F_longipes_13317
F_longipes_13368
F_aywerte_25410
100
100
F_chlamydosporum_13444
91
F_nelsonii_13338
100
F_scirpi_66328
100
F_equiseti_66338
100
F_irregulare_31160
F_hainanense_66475
100
100
F_avenaceum_54939
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_graminum_20692
99
F_heterosporum_20693
91
F_nurragi_36452
F_continuum_66286
98
100
F_zanthoxyli_66285
78
F_torreyae_54149
100
F_lateritium_13622
F_sarcochroum_20472
F_stilbioides_20429
94
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_buxicola_36148
F_cyanostoma_53998
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
0.1
100
Page 55 of 64
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
91
100
85
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
100
F_ambrosium_62606
99
Fusarium_sp_62590_AF6
100
100
F_falciforme_43529
F_vanettenii_45880
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
100
F_anguoides_25385
F_concolor_13459
100
F_babinda_25539
F_verrucosum_22566
98
F_beomiforme_25174
F_circinatum_25331
100 91 F_subglutinans_66333
100
F_guttiforme_22945
F_fujikuroi_5538
100 100
F_mangiferae_25226
100
F_sacchari_6632
63
100
F_thapsinum_22049
100
F_verticillioides_20956
88
F_xylarioides_25486
100 56
Fusarium_sp_52700
F_commune_28387
F_foetens_38302
81 100
F_oxysporum_34936
98
100
F_oxysporum_32931
77
F_newnesense_66241
100
100
76
Fusarium_sp_25184
F_gaditjirrii_45417
100
F_lyarnte_54252
100
F_miscanthi_26231
F_niskadoi_25179
100
F_hostae_29888
100
F_redolens_22901
F_avenaceum_54939
100
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_graminum_20692
99
F_heterosporum_20693
F_nurragi_36452
F_asiaticum_26156
98
100 52 F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
81
F_praegraminearum_39664
F_poae_26941
100
F_sambucinum_13708
100
100
F_venenatum_66329
F_langsethiae_53436
100
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
F_compactum_13829
100
100
Fusarium_transvaalense_31008
99
82
F_longipes_13317
100
F_longipes_13368
100
F_scirpi_66328
100
100
F_equiseti_66338
F_irregulare_31160
F_hainanense_66475
100
97
F_aywerte_25410
99
F_chlamydosporum_13444
100
F_nelsonii_13338
F_continuum_66286
68
100
F_zanthoxyli_66285
F_torreyae_54149
F_lateritium_13622
95
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
F_buxicola_36148
F_cyanostoma_53998
100
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
mcm7
99
100
100
85
100
100
91
100
85
100
59
39
62
100
0.07
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
72
N_ditissima_20485
100
N_coccinea_20487
Neonectria_sp_22505
100
F_albosuccineum_20459
59
F_decemcellulare_13412
F_setosum_36526
F_ambrosium_62606
100
98
69
Fusarium_sp_62590_AF6
100
F_vanettenii_45880
98
F_falciforme_43529
91
F_neocosmosporiellum_22166
100
F_illudens_22090
F_virguliforme_31041
100
100
pgk1
100
95
96
80
43
53
65
46
100
42
94
100
100
100
Page 56 of 64
F_anguoides_25385
F_concolor_13459
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
97
F_circinatum_25331
100
F_subglutinans_66333
100
F_guttiforme_22945
100
F_fujikuroi_5538
56
Fusarium_sp_52700
26
F_mangiferae_25226
F_sacchari_6632
81 39
F_thapsinum_22049
36 94
98
F_xylarioides_25486
98
F_verticillioides_20956
87
F_gaditjirrii_45417
98
F_lyarnte_54252
84
F_commune_28387
80
100
F_miscanthi_26231
F_niskadoi_25179
91 90
F_newnesense_66241
100
Fusarium_sp_25184
F_foetens_38302
100
F_oxysporum_34936
76
99
F_oxysporum_32931
F_hostae_29888
62
F_redolens_22901
83
F_scirpi_66328
100
F_equiseti_66338
99
F_irregulare_31160
67
F_hainanense_66475
93
F_asiaticum_26156
98
F_graminearum_31084
99
F_culmorum_25475
F_pseudograminearum_28062
100
F_langsethiae_53436
100
99
F_sporotrichioides_3299
Fusarium_armeniacum_6227
35
F_praegraminearum_39664
26
F_poae_26941
77
F_sambucinum_13708
100
72
100
F_venenatum_66329
100
F_compactum_13829
72
Fusarium_transvaalense_31008
75
F_longipes_13317
100
F_longipes_13368
100
F_aywerte_25410
F_chlamydosporum_13444
96
100
F_nelsonii_13338
F_avenaceum_54939
100
99
F_tricinctum_25481
99
F_torulosum_22747
100
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
100
F_stilbioides_20429
F_lateritium_13622
96
F_sarcochroum_20472
89
99
F_continuum_66286
100
F_zanthoxyli_66285
100
F_torreyae_54149
F_sublunatum_13384
F_buharicum_13371
F_buxicola_36148
F_cyanostoma_53998
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
0.06
Page 57 of 64
89
100
100
86
rpb1
100
64
100
97
46
99
100
92
94
100
100
N_ditissima_20485
N_coccinea_20487
Neonectria_sp_22505
F_dimerum_20691
100
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
100
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
100
Fusarium_sp_62590_AF6
100
F_falciforme_43529
73
F_vanettenii_45880
100
F_neocosmosporiellum_22166
100
F_virguliforme_31041
F_illudens_22090
100
F_anguoides_25385
80
F_concolor_13459
100
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
100
F_guttiforme_22945
91
100
F_subglutinans_66333
98 100
F_fujikuroi_5538
F_mangiferae_25226
98
F_sacchari_6632
88
F_thapsinum_22049
100
100
F_verticillioides_20956
100
100
F_xylarioides_25486
Fusarium_sp_52700
42
100 F_foetens_38302
F_oxysporum_34936
43 99 F_oxysporum_32931
F_newnesense_66241
28
100
Fusarium_sp_25184
100 100
F_gaditjirrii_45417
F_lyarnte_54252
100
F_miscanthi_26231
100
100
F_niskadoi_25179
F_commune_28387
F_hostae_29888
F_redolens_22901
100
100
F_asiaticum_26156
100 100 F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
87
100
F_langsethiae_53436
100 100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
100
F_poae_26941
99
F_sambucinum_13708
F_venenatum_66329
100
100
F_compactum_13829
Fusarium_transvaalense_31008
100
100
F_longipes_13317
100
100
F_longipes_13368
F_aywerte_25410
100
F_chlamydosporum_13444
100
100
F_nelsonii_13338
F_scirpi_66328
100
100
F_equiseti_66338
88
F_irregulare_31160
F_hainanense_66475
100
100
F_avenaceum_54939
100
100
F_tricinctum_25481
92
F_torulosum_22747
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
100
F_continuum_66286
100
F_torreyae_54149
F_zanthoxyli_66285
89
97
F_lateritium_13622
100
F_sarcochroum_20472
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
100
F_buxicola_36148
F_cyanostoma_53998
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
0.07
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
99
100
Page 58 of 64
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
100
100
100
100
93
100
F_anguoides_25385
F_concolor_13459
F_babinda_25539
96
F_verrucosum_22566
F_beomiforme_25174
F_circinatum_25331
95
100
F_subglutinans_66333
100
88
F_guttiforme_22945
100
F_xylarioides_25486
F_thapsinum_22049
94
F_verticillioides_20956
100
F_fujikuroi_5538
89
F_sacchari_6632
100
100
99 85
F_mangiferae_25226
Fusarium_sp_52700
F_commune_28387
F_gaditjirrii_45417
100
93 98
F_lyarnte_54252
100
F_miscanthi_26231
98
100
F_niskadoi_25179
100 100
F_newnesense_66241
Fusarium_sp_25184
100
100
F_foetens_38302
F_oxysporum_34936
100
F_oxysporum_32931
F_hostae_29888
100
F_redolens_22901
88
F_avenaceum_54939
100
F_tricinctum_25481
77
F_torulosum_22747
100
100
F_graminum_20692
F_heterosporum_20693
53
F_nurragi_36452
F_asiaticum_26156
100
100
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
84
F_praegraminearum_39664
F_poae_26941
100
100
F_sambucinum_13708
100
F_venenatum_66329
100
F_langsethiae_53436
100
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
F_compactum_13829
100
100
93
Fusarium_transvaalense_31008
97
100
F_longipes_13317
F_longipes_13368
100
F_aywerte_25410
100
100
F_chlamydosporum_13444
F_nelsonii_13338
100
F_scirpi_66328
96
100
F_equiseti_66338
F_irregulare_31160
100
F_hainanense_66475
99
F_continuum_66286
100
100
F_zanthoxyli_66285
F_torreyae_54149
100
F_lateritium_13622
F_sarcochroum_20472
82
86
F_stilbioides_20429
99
F_buharicum_13371
F_sublunatum_13384
100
F_buxicola_36148
F_cyanostoma_53998
100
F_albosuccineum_20459
50
100
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
74
99
Fusarium_sp_62590_AF6
F_falciforme_43529
100
100
F_vanettenii_45880
100
F_neocosmosporiellum_22166
40
F_illudens_22090
94
F_virguliforme_31041
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
99
48
100
100
rpb2
0.09
F_ventricosum_25729
Page 59 of 64
97
F_anguoides_25385
F_concolor_13459
F_asiaticum_26156
100
F_graminearum_31084
100
F_avenaceum_54939
F_tricinctum_25481
F_torulosum_22747
97
F_nurragi_36452
84
100
F_graminum_20692
76
F_heterosporum_20693
F_langsethiae_53436
100
92
63
100 F_sporotrichioides_3299
Fusarium_armeniacum_6227
90
F_pseudograminearum_28062
68
F_praegraminearum_39664
F_culmorum_25475
F_poae_26941
51
F_sambucinum_13708
97
100
F_venenatum_66329
F_chlamydosporum_13444
100
F_nelsonii_13338
69
Fusarium_transvaalense_31008
94
F_aywerte_25410
100
F_scirpi_66328
100
94
100
F_equiseti_66338
99
88
F_irregulare_31160
85
F_hainanense_66475
100
F_longipes_13317
85
F_longipes_13368
F_compactum_13829
F_babinda_25539
F_circinatum_25331
100
99
F_guttiforme_22945
63
F_subglutinans_66333
80
F_xylarioides_25486
98
F_fujikuroi_5538
65 75
F_sacchari_6632
F_mangiferae_25226
F_verticillioides_20956
75
96
Fusarium_sp_52700
58
48 84
F_foetens_38302
100
F_oxysporum_34936
F_oxysporum_32931
F_gaditjirrii_45417
95
94
61
F_lyarnte_54252
97
81
F_miscanthi_26231
100
F_niskadoi_25179
55
F_newnesense_66241
100
Fusarium_sp_25184
45
F_commune_28387
92
61
F_hostae_29888
100
F_redolens_22901
61
F_thapsinum_22049
F_beomiforme_25174
83
F_verrucosum_22566
100
F_continuum_66286
61
F_torreyae_54149
97
F_zanthoxyli_66285
F_stilbioides_20429
95
F_sarcochroum_20472
100
F_lateritium_13622
F_sublunatum_13384
F_buharicum_13371
100
F_dimerum_20691
100
F_penzigii_20711
87
F_domesticum_29976
46
N_ditissima_20485
100
N_coccinea_20487
Neonectria_sp_22505
84
F_rusci_22134
100
F_staphyleae_22316
F_zealandicum_22465
99
F_buxicola_36148
F_cyanostoma_53998
58
F_ambrosium_62606
Fusarium_sp_62590_AF6
84
59
F_falciforme_43529
76
78
F_vanettenii_45880
F_neocosmosporiellum_22166
F_illudens_22090
76
90
F_virguliforme_31041
100
F_albosuccineum_20459
97
F_decemcellulare_13412
92
F_setosum_36526
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
67
tef1
100
61
58
99
84
100
0.02
91
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
F_ventricosum_25729
Page 60 of 64
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
100
F_albosuccineum_20459
100
F_decemcellulare_13412
F_setosum_36526
100
F_ambrosium_62606
85
Fusarium_sp_62590_AF6
100
100
F_falciforme_43529
88
F_vanettenii_45880
94
100
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
F_anguoides_25385
100
100
F_concolor_13459
100
F_verrucosum_22566
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
100
100
F_subglutinans_66333
96
F_guttiforme_22945
100
Fusarium_sp_52700
96
F_thapsinum_22049
100
F_verticillioides_20956
100 93
F_xylarioides_25486
F_fujikuroi_5538
100
100
F_mangiferae_25226
98
100
F_sacchari_6632
100 F_gaditjirrii_45417
F_lyarnte_54252
100
76
F_miscanthi_26231
100
F_niskadoi_25179
85
93
F_newnesense_66241
100
Fusarium_sp_25184
F_commune_28387
100
F_foetens_38302
100
98 100 F_oxysporum_34936
F_oxysporum_32931
F_hostae_29888
100
F_redolens_22901
F_avenaceum_54939
100
100
F_tricinctum_25481
59
59
F_torulosum_22747
100
100
F_graminum_20692
F_heterosporum_20693
F_nurragi_36452
F_asiaticum_26156
100
100
100
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
96
F_langsethiae_53436
100
100 100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
100
F_poae_26941
100
100
F_sambucinum_13708
F_venenatum_66329
100
F_compactum_13829
100
98
Fusarium_transvaalense_31008
100
85
F_longipes_13317
F_longipes_13368
100
F_aywerte_25410
100
100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
99
100
F_irregulare_31160
100
100
F_hainanense_66475
F_equiseti_66338
100
F_continuum_66286
100
F_zanthoxyli_66285
100
F_torreyae_54149
100
F_lateritium_13622
100
F_sarcochroum_20472
51
F_stilbioides_20429
100
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
100
43 80
F_staphyleae_22316
F_zealandicum_22465
100
F_buxicola_36148
F_cyanostoma_53998
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
100
top1
99
100
66
99
99
0.07
100
Page 61 of 64
93
100
92
100
99
56
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
100
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
F_ventricosum_25729
F_albosuccineum_20459
F_decemcellulare_13412
F_setosum_36526
F_buxicola_36148
F_cyanostoma_53998
98
F_anguoides_25385
F_concolor_13459
F_babinda_25539
94
F_verrucosum_22566
F_beomiforme_25174
88
F_circinatum_25331
100
F_subglutinans_66333
100
100
F_guttiforme_22945
Fusarium_sp_52700
98 100
F_fujikuroi_5538
F_mangiferae_25226
100
F_sacchari_6632
100 98
F_thapsinum_22049
100
100
F_verticillioides_20956
97
F_xylarioides_25486
F_commune_28387
100
F_gaditjirrii_45417
100
97
F_lyarnte_54252
100
F_miscanthi_26231
71
100
F_niskadoi_25179
100
F_foetens_38302
55
F_oxysporum_34936
100
F_oxysporum_32931
100
F_newnesense_66241
100
Fusarium_sp_25184
F_hostae_29888
100
F_redolens_22901
F_avenaceum_54939
100
100
F_tricinctum_25481
91
F_torulosum_22747
100
F_nurragi_36452
100
F_graminum_20692
F_heterosporum_20693
F_asiaticum_26156
100
100
99
F_graminearum_31084
100
F_culmorum_25475
100
F_pseudograminearum_28062
F_praegraminearum_39664
100
F_langsethiae_53436
95
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
93 100
F_poae_26941
100
F_sambucinum_13708
100
F_venenatum_66329
F_compactum_13829
100
100
80
Fusarium_transvaalense_31008
100
98
F_longipes_13317
F_longipes_13368
F_aywerte_25410
100
100
F_chlamydosporum_13444
98
F_nelsonii_13338
F_scirpi_66328
98
100
F_equiseti_66338
100
100
F_irregulare_31160
F_hainanense_66475
98
F_continuum_66286
100
F_zanthoxyli_66285
F_torreyae_54149
F_lateritium_13622
83
100
F_stilbioides_20429
F_sarcochroum_20472
100
F_buharicum_13371
F_sublunatum_13384
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
100
F_ambrosium_62606
89
Fusarium_sp_62590_AF6
94
F_vanettenii_45880
F_falciforme_43529
F_neocosmosporiellum_22166
F_illudens_22090
F_virguliforme_31041
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
100
98
91
72
100
52
98
62
100
100
100
55
100
100
tsr1
0.08
100
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
F_ventricosum_25729
100
100
94
Page 62 of 64
F_dimerum_20691
F_penzigii_20711
F_domesticum_29976
100
F_albosuccineum_20459
F_decemcellulare_13412
F_ambrosium_62606
98
Fusarium_sp_62590_AF6
99
F_falciforme_43529
93
98
F_vanettenii_45880
99
F_neocosmosporiellum_22166
98
F_virguliforme_31041
F_illudens_22090
100
100
95
84
95
tub1
F_anguoides_25385
F_concolor_13459
F_babinda_25539
F_verrucosum_22566
F_beomiforme_25174
F_circinatum_25331
F_graminum_20692
100
100
F_subglutinans_66333
96
F_fujikuroi_5538
100
99
F_mangiferae_25226
100
F_sacchari_6632
100
Fusarium_sp_52700
100
F_thapsinum_22049
100
F_verticillioides_20956
100
F_xylarioides_25486
F_commune_28387
99
97
F_foetens_38302
F_oxysporum_34936
98 81
F_oxysporum_32931
96
99
F_gaditjirrii_45417
100
F_lyarnte_54252
100
F_miscanthi_26231
70 99
F_niskadoi_25179
100
F_newnesense_66241
53
Fusarium_sp_25184
98
F_heterosporum_20693
F_redolens_22901
70
100
F_asiaticum_26156
90
F_culmorum_25475
98
86
F_graminearum_31084
83
F_pseudograminearum_28062
F_praegraminearum_39664
97
F_langsethiae_53436
100
100
F_sporotrichioides_3299
99
Fusarium_armeniacum_6227
100
F_poae_26941
89
78
F_sambucinum_13708
F_venenatum_66329
98
93
F_compactum_13829
Fusarium_transvaalense_31008
100
86
F_longipes_13317
89
F_longipes_13368
98
F_aywerte_25410
100
100
F_chlamydosporum_13444
F_nelsonii_13338
100
F_scirpi_66328
100
34
92
F_equiseti_66338
98
F_irregulare_31160
88
F_hainanense_66475
100
F_avenaceum_54939
89
100
F_tricinctum_25481
100
F_torulosum_22747
100
F_guttiforme_22945
F_hostae_29888
86
F_nurragi_36452
100
F_lateritium_13622
100
F_sarcochroum_20472
19
33
F_stilbioides_20429
96
F_continuum_66286
100
F_zanthoxyli_66285
F_torreyae_54149
94
F_buharicum_13371
F_sublunatum_13384
82
F_rusci_22134
99
F_staphyleae_22316
F_zealandicum_22465
100
F_buxicola_36148
77
F_cyanostoma_53998
F_setosum_36526
100
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
100
86
94
0.03
Page 63 of 64
100
F_albosuccineum_20459
F_decemcellulare_13412
F_anguoides_25385
F_babinda_25539
F_beomiforme_25174
F_circinatum_25331
F_subglutinans_66333
96
F_guttiforme_22945
F_fujikuroi_5538
100
99
F_mangiferae_25226
95 98
95
F_sacchari_6632
Fusarium_sp_52700
96
99
F_thapsinum_22049
99
69
F_verticillioides_20956
100
F_xylarioides_25486
F_gaditjirrii_45417
100
F_lyarnte_54252
98
97
F_miscanthi_26231
100
97
F_niskadoi_25179
100
F_commune_28387
66
F_foetens_38302
99
100
F_oxysporum_34936
98
F_oxysporum_32931
67
F_newnesense_66241
100
Fusarium_sp_25184
99
F_hostae_29888
F_redolens_22901
F_concolor_13459
F_verrucosum_22566
100
F_asiaticum_26156
99
F_graminearum_31084
100
F_culmorum_25475
42
F_praegraminearum_39664
58
87
88
F_pseudograminearum_28062
100
F_poae_26941
100
100
F_sambucinum_13708
F_venenatum_66329
100
F_langsethiae_53436
76
100
F_sporotrichioides_3299
Fusarium_armeniacum_6227
98
F_compactum_13829
77
Fusarium_transvaalense_31008
100
98
F_longipes_13317
92
F_longipes_13368
100
F_aywerte_25410
97
100
F_chlamydosporum_13444
F_nelsonii_13338
F_scirpi_66328
95
F_equiseti_66338
94
61
F_hainanense_66475
100
F_irregulare_31160
34
F_avenaceum_54939
98
100
F_tricinctum_25481
97
F_torulosum_22747
100
F_nurragi_36452
100
84
F_graminum_20692
F_heterosporum_20693
F_continuum_66286
84
100
F_torreyae_54149
97
F_zanthoxyli_66285
F_stilbioides_20429
97
F_buharicum_13371
41
74
F_sublunatum_13384
49
F_lateritium_13622
88
F_sarcochroum_20472
60
100
F_dimerum_20691
100
F_penzigii_20711
F_domesticum_29976
F_setosum_36526
85
F_rusci_22134
100
F_staphyleae_22316
61
F_zealandicum_22465
96
F_buxicola_36148
F_cyanostoma_53998
F_ambrosium_62606
100
100
Fusarium_sp_62590_AF6
F_falciforme_43529
99
100
F_vanettenii_45880
72
F_neocosmosporiellum_22166
100
F_virguliforme_31041
53
F_illudens_22090
F_ventricosum_25729
59
93
N_ditissima_20485
100
N_coccinea_20487
Neonectria_sp_22505
98
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
100
100
98
98
tub2
Trichoderma_brevicompactum
0.03
Page 64 of 64
0.70,0.70
0.08,0.07
0.70,0.70
1.00,1.00
0.70,0.70
Internode Credibility Values (IC,ICA)
0.33,0.40
0.69,0.69
0.69,0.63
0.68,0.61
0.30,0.32
0.69,0.63
0.35,0.42
0.69,0.63
1.00,1.00
0.68,0.56
0.70,0.70
0.70,0.70
0.69,0.63
0.70,0.70
0.50,0.51
1.00,1.00
0.70,0.70
0.69,0.63
0.70,0.70
0.50,0.51
Node F1
0.68,0.61
0.70,0.70
0.70,0.70
0.70,0.70
1.00,1.00
0.70,0.70
0.70,0.70
0.19,0.33
0.69,0.63
1.00,1.00
0.70,0.70
1.00,1.00
0.16,0.26
0.21,0.35
0.68,0.61
0.69,0.63
0.69,0.69
1.00,1.00
0.50,0.51
0.48,0.40
1.00,1.00
0.68,0.61
1.00,1.00
0.70,0.70
0.50,0.50
1.00,1.00
0.70,0.70
0.70,0.70
0.19,0.17
1.00,1.00
0.66,0.60
0.46,0.38
0.48,0.49
1.00,1.00
1.00,1.00
0.22,0.25
1.00,1.00
0.48,0.49
0.35,0.42
0.41,0.34
1.00,1.00
0.65,0.44
0.48,0.47
0.70,0.70
1.00,1.00
1.00,1.00
N_ditissima_20485
Neonectria_sp_22505
N_coccinea_20487
F_ventricosum_25729
F_domesticum_29976
F_dimerum_20691
F_penzigii_20711
F_beomiforme_25174
F_commune_28387
Fusarium_sp_52700
F_guttiforme_22945
F_circinatum_25331
F_subglutinans_66333
F_sacchari_66326
F_fujikuroi_5538
F_mangiferae_25226
F_xylarioides_25486
F_thapsinum_22049
F_verticillioides_20956
F_gaditjirrii_45417
F_lyarnte_54252
F_miscanthi_26231
F_niskadoi_25179
F_foetens_38302
F_oxysporum_34936
F_oxysporum_32931
F_newnesense_66241
Fusarium_sp_25184
F_hostae_29888
F_redolens_22901
F_verrucosum_22566
F_babinda_25539
F_anguoides_25385
F_concolor_13459
F_praegraminearum_39664
F_pseudograminearum_28062
F_culmorum_25475
F_asiaticum_26156
F_graminearum_31084
F_armeniacum_6227
F_langsethiae_53436
F_sporotrichioides_3299
F_poae_26941
F_sambucinum_13708
F_venenatum_66329
F_longipes_13317
F_longipes_13368
F_compactum_13829
F_transvaalense_31008
F_aywerte_25410
F_chlamydosporum_13444
F_nelsonii_13338
F_irregulare_31160
F_hainanense_66475
F_scirpi_66328
F_equiseti_66338
F_nurragi_36452
F_torulosum_22747
F_avenaceum_54939
F_tricinctum_25481
F_graminum_20692
F_heterosporum_20693
F_torreyae_54149
F_continuum_66286
F_zanthoxyli_66285
F_stilbioides_20429
F_lateritium_13622
F_sarcochroum_20472
F_buharicum_13371
F_sublunatum_13384
F_illudens_22090
F_virguliforme_31041
F_neocosmosporiellum_22166
F_ambrosium_62606
Fusarium_sp_62590_AF_6
F_falciforme_43529
F_vanettenii_45880
F_setosum_36526
F_albosuccineum_20459
F_decemcellulare_13412
F_rusci_22134
F_staphyleae_22316
F_zealandicum_22465
F_buxicola_36148
F_cyanostoma_53998
F_albida_22152
F_nematophilum_54600
Beauveria_bassiana
Trichoderma_brevicompactum
Lindy Rose