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

Author

Geiser, David M, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Arie, Tsutomu, Balmas, Virgilio, Barnes, Irene, Bergstrom, Gary C, Bhattacharyya, Madan K, Blomquist, Cheryl L, Bowden, Robert L, Brankovics, Balázs, Brown, Daren W, Burgess, Lester W, Bushley, Kathryn, Busman, Mark, Cano-Lira, José F, Carrillo, Joseph D, Chang, Hao-Xun, Chen, Chi-Yu, Chen, Wanquan, Chilvers, Martin, Chulze, Sofia, Coleman, Jeffrey J, Cuomo, Christina A, de Beer, Z Wilhelm, de Hoog, G Sybren, Del Castillo-Múnera, Johanna, Del Ponte, Emerson M, Diéguez-Uribeondo, Javier, Di Pietro, Antonio, Edel-Hermann, Véronique, Elmer, Wade H, Epstein, Lynn, Eskalen, Akif, Esposto, Maria Carmela, Everts, Kathryne L, Fernández-Pavía, Sylvia P, da Silva, Gilvan Ferreira, Foroud, Nora A, Fourie, Gerda, Frandsen, Rasmus JN, Freeman, Stanley, Freitag, Michael, Frenkel, Omer, Fuller, Kevin K, Gagkaeva, Tatiana, Gardiner, Donald M, Glenn, Anthony E, Gold, Scott E, Gordon, Thomas R, Gregory, Nancy F, Gryzenhout, Marieka, Guarro, Josep, Gugino, Beth K, Gutierrez, Santiago, Hammond-Kosack, Kim E, Harris, Linda J, Homa, Mónika, Hong, Cheng-Fang, Hornok, László, Huang, Jenn-Wen, Ilkit, Macit, Jacobs, Adriaana, Jacobs, Karin, Jiang, Cong, Jiménez-Gasco, María Del Mar, Kang, Seogchan, Kasson, Matthew T, Kazan, Kemal, Kennell, John C, Kim, Hye-Seon, Kistler, H Corby, Kuldau, Gretchen A, Kulik, Tomasz, Kurzai, Oliver, Laraba, Imane, Laurence, Matthew H, Lee, Theresa, Lee, Yin-Won, Lee, Yong-Hwan, Leslie, John F, Liew, Edward CY, Lofton, Lily W, Logrieco, Antonio F, S López-Berges, Manuel, Luque, Alicia G, Lysøe, Erik, Ma, Li-Jun, Marra, Robert E, Martin, Frank N, May, Sara R, McCormick, Susan P, McGee, Chyanna, Meis, Jacques F, Migheli, Quirico, Mohamed Nor, NMI, Monod, Michel, Moretti, Antonio, Mostert, Diane, and Mulè, Giuseppina

Subjects
evolution, fungal pathogens, Plant Biology & Botany, Microbiology, Plant Biology, Crop and Pasture Production
Abstract

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

Published
2021

5. No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium

Author

O’Donnell, Kerry, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Brankovics, Balázs, Cano-Lira, José F, Coleman, Jeffrey J, de Hoog, G Sybren, Di Pietro, Antonio, Frandsen, Rasmus JN, Geiser, David M, Gibas, Connie FC, Guarro, Josep, Kim, Hye-Seon, Kistler, H Corby, Laraba, Imane, Leslie, John F, López-Berges, Manuel S, Lysøe, Erik, Meis, Jacques F, Monod, Michel, Proctor, Robert H, Rep, Martijn, Ruiz-Roldán, Carmen, Šišić, Adnan, Stajich, Jason E, Steenkamp, Emma T, Summerell, Brett A, van der Lee, Theo AJ, van Diepeningen, Anne D, Verweij, Paul E, Waalwijk, Cees, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Zhang, Ning, and Zhang, Sean X

Subjects
Microbiology, Biological Sciences, Infectious Diseases, Infection, Good Health and Well Being, Antifungal Agents, Fusarium, Phylogeny, clinical mycology, evolution, fungi, phylogenetics, taxonomy, Immunology
Abstract

This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold FusariumFusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the Fusarium solani species complex (FSSC), and they collectively account for approximately two-thirds of all reported Fusarium infections. Many of these species were recently given scientific names for the first time by a research group in the Netherlands, but they were misplaced in the genus Neocosmospora In this paper, we present genetic arguments that strongly support inclusion of the FSSC in Fusarium There are potentially serious consequences associated with using the name Neocosmospora for Fusarium species because clinicians need to be aware that fusaria are broadly resistant to the spectrum of antifungals that are currently available.

Published
2020

6. No to Neocosmospora: Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium.

Author

O'Donnell, Kerry, Al-Hatmi, Abdullah MS, Aoki, Takayuki, Brankovics, Balázs, Cano-Lira, José F, Coleman, Jeffrey J, de Hoog, G Sybren, Di Pietro, Antonio, Frandsen, Rasmus JN, Geiser, David M, Gibas, Connie FC, Guarro, Josep, Kim, Hye-Seon, Kistler, H Corby, Laraba, Imane, Leslie, John F, López-Berges, Manuel S, Lysøe, Erik, Meis, Jacques F, Monod, Michel, Proctor, Robert H, Rep, Martijn, Ruiz-Roldán, Carmen, Šišić, Adnan, Stajich, Jason E, Steenkamp, Emma T, Summerell, Brett A, van der Lee, Theo AJ, van Diepeningen, Anne D, Verweij, Paul E, Waalwijk, Cees, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Zhang, Ning, and Zhang, Sean X

Subjects
Fusarium, Antifungal Agents, Phylogeny, clinical mycology, evolution, fungi, phylogenetics, taxonomy, Infectious Diseases, Infection
Abstract

This article is to alert medical mycologists and infectious disease specialists of recent name changes of medically important species of the filamentous mold Fusarium Fusarium species can cause localized and life-threating infections in humans. Of the 70 Fusarium species that have been reported to cause infections, close to one-third are members of the Fusarium solani species complex (FSSC), and they collectively account for approximately two-thirds of all reported Fusarium infections. Many of these species were recently given scientific names for the first time by a research group in the Netherlands, but they were misplaced in the genus Neocosmospora In this paper, we present genetic arguments that strongly support inclusion of the FSSC in Fusarium There are potentially serious consequences associated with using the name Neocosmospora for Fusarium species because clinicians need to be aware that fusaria are broadly resistant to the spectrum of antifungals that are currently available.

Published
2020

7. Genome sequencing of Cladophialophora exuberans, a novel candidate for bioremediation of hydrocarbon and heavy metal polluted habitats

Author

Silva, Nickolas Menezes da, Reis, Guilherme Fonseca, Costa, Flávia de Fátima, Grisolia, Maria Eduarda, Geraldo, Marlon Roger, Lustosa, Bruno Paulo Rodrigues, Lima, Bruna Jacomel Favoreto de Souza, Weiss, Vinicius Almir, de Souza, Emanuel Maltempi, Li, Ruoyu, Song, Yinggai, Nascimento, Mariana Machado Fidelis, Robl, Diogo, Gomes, Renata Rodrigues, de Hoog, G. Sybren, and Vicente, Vania Aparecida

Published
2023
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9. Phylogenetic and Phylogenomic Definition of Rhizopus Species

Author

Gryganskyi, Andrii P, Golan, Jacob, Dolatabadi, Somayeh, Mondo, Stephen, Robb, Sofia, Idnurm, Alexander, Muszewska, Anna, Steczkiewicz, Kamil, Masonjones, Sawyer, Liao, Hui-Ling, Gajdeczka, Michael T, Anike, Felicia, Vuek, Antonina, Anishchenko, Iryna M, Voigt, Kerstin, de Hoog, G Sybren, Smith, Matthew E, Heitman, Joseph, Vilgalys, Rytas, and Stajich, Jason E

Subjects
Biological Sciences, Ecology, Evolutionary Biology, Genetics, Microbiology, Infectious Diseases, DNA Transposable Elements, Genes, Mating Type, Fungal, Genome Size, Genome, Fungal, Genomics, Likelihood Functions, Open Reading Frames, Phylogeny, Rhizopus, Species Specificity, Whole Genome Sequencing, zygomycete, orthologs, genome duplication, transposons, sexual reproduction, Biochemistry and cell biology, Statistics
Abstract

Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.

Published
2018

10. Global guideline for the diagnosis and management of rare mould infections: an initiative of the European Confederation of Medical Mycology in cooperation with the International Society for Human and Animal Mycology and the American Society for Microbiology

Author

Hoenigl, Martin, Salmanton-García, Jon, Walsh, Thomas J, Nucci, Marcio, Neoh, Chin Fen, Jenks, Jeffrey D, Lackner, Michaela, Sprute, Rosanne, Al-Hatmi, Abdullah M S, Bassetti, Matteo, Carlesse, Fabianne, Freiberger, Tomas, Koehler, Philipp, Lehrnbecher, Thomas, Kumar, Anil, Prattes, Juergen, Richardson, Malcolm, Revankar, Sanjay, Slavin, Monica A, Stemler, Jannik, Spiess, Birgit, Taj-Aldeen, Saad J, Warris, Adilia, Woo, Patrick C Y, Young, Jo-Anne H, Albus, Kerstin, Arenz, Dorothee, Arsic-Arsenijevic, Valentina, Bouchara, Jean-Philippe, Chinniah, Terrence Rohan, Chowdhary, Anuradha, de Hoog, G Sybren, Dimopoulos, George, Duarte, Rafael F, Hamal, Petr, Meis, Jacques F, Mfinanga, Sayoki, Queiroz-Telles, Flavio, Patterson, Thomas F, Rahav, Galia, Rogers, Thomas R, Rotstein, Coleman, Wahyuningsih, Retno, Seidel, Danila, and Cornely, Oliver A

Published
2021
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13. Feline Sporotrichosis

Author

Rodrigues, Anderson Messias, de Hoog, G. Sybren, de Camargo, Zoilo Pires, Seyedmousavi, Seyedmojtaba, editor, de Hoog, G. Sybren, editor, Guillot, Jacques, editor, and Verweij, Paul E., editor

Published
2018
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19. Fungal Communities in Hydrocarbon Degradation

Author

Prenafeta-Boldú, Francesc X., de Hoog, G. Sybren, Summerbell, Richard C., Timmis, Kenneth N., Editor-in-Chief, Boll, Matthias, Series Editor, Geiger, Otto, Series Editor, Goldfine, Howard, Series Editor, Krell, Tino, Series Editor, Lee, Sang Yup, Series Editor, McGenity, Terry J., Series Editor, Rojo, Fernando, Series Editor, Sousa, Diana Z., Series Editor, Stams, Alfons J. M., Series Editor, Steffan, Robert, Series Editor, and Wilkes, Heinz, Series Editor

Published
2019
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20. Commentaries: Name Changes in Medically Important Fungi and Their Implications for Clinical Practice

Author

de Hoog, G Sybren, Chaturvedi, Vishnu, Denning, David W, Dyer, Paul S, Frisvad, Jens Christian, Geiser, David, Gräser, Yvonne, Guarro, Josep, Haase, Gerhard, Kwon-Chung, Kyung-Joo, Meis, Jacques F, Meyer, Wieland, Pitt, John I, Samson, Robert A, Taylor, John W, Tintelnot, Kathrin, Vitale, Roxana G, Walsh, Thomas J, and Lackner, Michaela

Subjects
Fungi, Humans, Infectious Disease Medicine, Mycology, Mycoses, Terminology as Topic, ISHAM Working Group on Nomenclature of Medical Fungi, Biological Sciences, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology
Abstract

Recent changes in the Fungal Code of Nomenclature and developments in molecular phylogeny are about to lead to dramatic changes in the naming of medically important molds and yeasts. In this article, we present a widely supported and simple proposal to prevent unnecessary nomenclatural instability.

Published
2015

23. Correction to: Proposed nomenclature for Pseudallescheria, Scedosporium and related genera

Author

Lackner, Michaela, de Hoog, G. Sybren, Yang, Liyue, Ferreira Moreno, Leandro, Ahmed, Sarah A., Andreas, Fritz, Kaltseis, Josef, Nagl, Markus, Lass-Flörl, Cornelia, Risslegger, Brigitte, Rambach, Günter, Speth, Cornelia, Robert, Vincent, Buzina, Walter, Chen, Sharon, Bouchara, Jean-Philippe, Cano-Lira, José F., Guarro, Josep, Gené, Josepa, Fernández Silva, Fabiola, Haido, Rosa, Haase, Gerhard, Havlicek, Vladimir, Garcia-Hermoso, Dea, Meis, Jacques F., Hagen, Ferry, Kirchmair, Martin, Rainer, Johannes, Schwabenbauer, Katharina, Zoderer, Mirjam, Meyer, Wieland, Gilgado, Felix, Schwabenbauer, Katharina, Vicente, Vania A., Piecková, Elena, Regenermel, Monika, Rath, Peter-Michael, Steinmann, Joerg, de Alencar, Xisto Wellington, Symoens, Françoise, Tintelnot, Kathrin, Ulfig, Krzysztof, Velegraki, Aristea, Tortorano, Anna Maria, Giraud, Sandrine, Mina, Sara, Rigler-Hohenwarter, Kinga, Hernando, Fernando L., Ramirez-Garcia, Andoni, Pellon, Aize, Kaur, Jashanpreet, Bergter, Eliana Barreto, de Meirelles, Jardel Vieira, da Silva, Ingrid Dutra, Delhaes, Laurence, Alastruey-Izquierdo, Ana, Li, Ruo-yu, Lu, Qiaoyun, Moussa, Tarek, Almaghrabi, Omar, Al-Zahrani, Hassan, Okada, Gen, Deng, Shuwen, Liao, Wangqing, Zeng, Jingsi, Issakainen, Jouni, and Liporagi Lopes, Livia Cristina

Published
2022
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28. New Molecular Markers Distinguishing Fonsecaea Agents of Chromoblastomycosis

Author

Schneider, Gabriela X., Gomes, Renata R., Bombassaro, Amanda, Zamarchi, Kassiely, Voidaleski, Morgana F., Costa, Flávia F., Leão, Aniele C. R., Lima, Bruna J. F. S., Soley, Bruna S., Colombo, Israella R., Cândido, Giovanna Z., Najafzadeh, Mohammad J., Sun, Jiufeng, de Azevedo, Conceição M. P. S., Marques, Sirlei G., de Hoog, G. Sybren, and Vicente, Vânia A.

Published
2019
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30. Environmental prospecting of black yeast-like agents of human disease using culture-independent methodology

Author

Costa, Flávia de Fátima, da Silva, Nickolas Menezes, Voidaleski, Morgana Ferreira, Weiss, Vinicius Almir, Moreno, Leandro Ferreira, Schneider, Gabriela Xavier, Najafzadeh, Mohammad J., Sun, Jiufeng, Gomes, Renata Rodrigues, Raittz, Roberto Tadeu, Castro, Mauro Antonio Alves, de Muniz, Graciela Bolzón Inez, de Hoog, G. Sybren, and Vicente, Vania Aparecida

Published
2020
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31. Aflatoxin profiles of Aspergillus flavus isolates in Sudanese fungal rhinosinusitis.

Author

Zhou, Shaoqin, Ismail, Mawahib A I, Aimanianda, Vishukumar, de Hoog, G Sybren, Kang, Yingqian, and Ahmed, Sarah A

Abstract

Aspergillus flavus is a commonly encountered pathogen responsible for fungal rhinosinusitis (FRS) in arid regions. The species is known to produce aflatoxins, posing a significant risk to human health. This study aimed to investigate the aflatoxin profiles of A. flavus isolates causing FRS in Sudan. A total of 93 clinical and 34 environmental A. flavus i solates were studied. Aflatoxin profiles were evaluated by phenotypic (thin-layer and high-performance chromatography) and genotypic methods at various temperatures and substrates. Gene expression of aflD and aflR was also analyzed. A total of 42/93 (45%) isolates were positive for aflatoxin B1 and AFB2 by HPLC. When the incubation temperature changed from 28°C to 36°C, the number of positive isolates decreased to 41% (38/93). Genetic analysis revealed that 85% (79/93) of clinical isolates possessed all seven aflatoxin biosynthesis-associated genes, while 27% (14/51) of non-producing isolates lacked specific genes (aflD/aflR / aflS). Mutations were observed in aflS and aflR genes across both aflatoxin-producers and non-producers. Gene expression of aflD and aflR showed the highest expression between the 4th and 6th days of incubation on the Sabouraud medium and on the 9th day of incubation on the RPMI (Roswell Park Memorial Institute) medium. Aspergillus flavus clinical isolates demonstrated aflatoxigenic capabilities, influenced by incubation temperature and substrate. Dynamic aflD and aflR gene expression patterns over time enriched our understanding of aflatoxin production regulation. The overall findings underscored the health risks of Sudanese patients infected by this species, emphasizing the importance of monitoring aflatoxin exposure. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Exploring the genomic diversity of black yeasts and relatives (Chaetothyriales, Ascomycota)

Author

Teixeira, M.M., Moreno, L.F., Stielow, B.J., Muszewska, A., Hainaut, M., Gonzaga, L., Abouelleil, A., Patané, J.S.L., Priest, M., Souza, R., Young, S., Ferreira, K.S., Zeng, Q., da Cunha, M.M.L., Gladki, A., Barker, B., Vicente, V.A., de Souza, E.M., Almeida, S., Henrissat, B., Vasconcelos, A.T.R., Deng, S., Voglmayr, H., Moussa, T.A.A., Gorbushina, A., Felipe, M.S.S., Cuomo, C.A., and de Hoog, G. Sybren

Published
2017
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47. Dermatophytes and mammalian hair: aspects of the evolution of Arthrodermataceae

Author

Tang, Chao, Zhou, Xin, Guillot, Jacques, Wibbelt, Gudrun, Deng, Shuwen, Kandemir, Hazal, Gräser, Yvonne, Feng, Peiying, Kang, Yingqian, de Hoog, G. Sybren, Tang, Chao, Zhou, Xin, Guillot, Jacques, Wibbelt, Gudrun, Deng, Shuwen, Kandemir, Hazal, Gräser, Yvonne, Feng, Peiying, Kang, Yingqian, and de Hoog, G. Sybren

Published
2023

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