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1. 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

2. 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

3. Rapid evolution in plant–microbe interactions – a molecular genomics perspective

Author

Frantzeskakis, Lamprinos, Di Pietro, Antonio, Rep, Martijn, Schirawski, Jan, Wu, Chih‐Hang, and Panstruga, Ralph

Subjects
Infectious Diseases, Biotechnology, Genetics, Emerging Infectious Diseases, Evolution, Molecular, Genomics, Host-Pathogen Interactions, RNA, Plant, Secondary Metabolism, Virulence, adaptation, dispensable chromosome, genome evolution, phytopathogens, virulence factors, Biological Sciences, Agricultural and Veterinary Sciences, Plant Biology & Botany
Abstract

Rapid (co-)evolution at multiple timescales is a hallmark of plant-microbe interactions. The mechanistic basis for the rapid evolution largely rests on the features of the genomes of the interacting partners involved. Here, we review recent insights into genomic characteristics and mechanisms that enable rapid evolution of both plants and phytopathogens. These comprise fresh insights in allelic series of matching pairs of resistance and avirulence genes, the generation of novel pathogen effectors, the recently recognised small RNA warfare, and genomic aspects of secondary metabolite biosynthesis. In addition, we discuss the putative contributions of permissive host environments, transcriptional plasticity and the role of ploidy on the interactions. We conclude that the means underlying the rapid evolution of plant-microbe interactions are multifaceted and depend on the particular nature of each interaction.

Published
2020

4. The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes.

Author

Zhang, Yong, Yang, He, Turra, David, Zhou, Shiguo, Ayhan, Dilay Hazal, DeIulio, Gregory A, Guo, Li, Broz, Karen, Wiederhold, Nathan, Coleman, Jeffrey J, Donnell, Kerry O', Youngster, Ilan, McAdam, Alexander J, Savinov, Sergey, Shea, Terrance, Young, Sarah, Zeng, Qiandong, Rep, Martijn, Pearlman, Eric, Schwartz, David C, Di Pietro, Antonio, Kistler, H Corby, and Ma, Li-Jun

Abstract

Fusarium oxysporum is a cross-kingdom fungal pathogen that infects plants and humans. Horizontally transferred lineage-specific (LS) chromosomes were reported to determine host-specific pathogenicity among phytopathogenic F. oxysporum. However, the existence and functional importance of LS chromosomes among human pathogenic isolates are unknown. Here we report four unique LS chromosomes in a human pathogenic strain NRRL 32931, isolated from a leukemia patient. These LS chromosomes were devoid of housekeeping genes, but were significantly enriched in genes encoding metal ion transporters and cation transporters. Homologs of NRRL 32931 LS genes, including a homolog of ceruloplasmin and the genes that contribute to the expansion of the alkaline pH-responsive transcription factor PacC/Rim1p, were also present in the genome of NRRL 47514, a strain associated with Fusarium keratitis outbreak. This study provides the first evidence, to our knowledge, for genomic compartmentalization in two human pathogenic fungal genomes and suggests an important role of LS chromosomes in niche adaptation.

Published
2020

13. Specific members of the TOPLESS family are susceptibility genes for Fusarium wilt in tomato and Arabidopsis.

Author

Aalders, Thomas R., de Sain, Mara, Gawehns, Fleur, Oudejans, Nina, Jak, Yoran D., Dekker, Henk L., Rep, Martijn, van den Burg, Harrold A., and Takken, Frank L.W.

Subjects
FUSARIOSIS, FUSARIUM, WILT diseases, FUSARIUM oxysporum, ARABIDOPSIS, DISEASE susceptibility, PIGEON pea
Abstract

Summary: Vascular wilt diseases caused by Fusarium oxysporum are a major threat to many agriculturally important crops. Genetic resistance is rare and inevitably overcome by the emergence of new races. To identify potentially durable and non‐race‐specific genetic resistance against Fusarium wilt diseases, we set out to identify effector targets in tomato that mediate susceptibility to the fungus. For this purpose, we used the SIX8 effector protein, an important and conserved virulence factor present in many pathogenic F. oxysporum isolates. Using protein pull‐downs and yeast two‐hybrid assays, SIX8 was found to interact specifically with two members of the tomato TOPLESS family: TPL1 and TPL2. Loss‐of‐function mutations in TPL1 strongly reduced disease susceptibility to Fusarium wilt and a tpl1;tpl2 double mutant exerted an even higher level of resistance. Similarly, Arabidopsis tpl;tpr1 mutants became significantly less diseased upon F. oxysporum inoculation as compared to wildtype plants. We conclude that TPLs encode susceptibility genes whose mutation can confer resistance to F. oxysporum. [ABSTRACT FROM AUTHOR]

Published
2024
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15. The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes

Author

Talbi, Nacera, primary, Fokkens, Like, additional, Audran, Corinne, additional, Petit‐Houdenot, Yohann, additional, Pouzet, Cécile, additional, Blaise, Françoise, additional, Gay, Elise J., additional, Rouxel, Thierry, additional, Balesdent, Marie‐Hélène, additional, Rep, Martijn, additional, and Fudal, Isabelle, additional

Published
2023
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20. Fusarium oxysporum

Author

Kang, Seogchan, Demers, Jill, del Mar Jimenez-Gasco, Maria, Rep, Martijn, Dean, Ralph A., editor, Lichens-Park, Ann, editor, and Kole, Chittaranjan, editor

Published
2014
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26. The neighboring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes

Author

Talbi, Nacera, primary, Fokkens, Like, additional, Audran, Corinne, additional, Petit-Houdenot, Yohann, additional, Pouzet, Cécile, additional, Blaise, Françoise, additional, Gay, Elise, additional, Rouxel, Thierry, additional, Balesdent, Marie-Hélène, additional, Rep, Martijn, additional, and Fudal, Isabelle, additional

Published
2022
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28. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

Cuomo, Christina A., Güldener, Ulrich, Xu, Jin-Rong, Trail, Frances, Turgeon, B. Gillian, Di Pietro, Antonio, Walton, Jonathan D., Ma, Li-Jun, Baker, Scott E., Rep, Martijn, Adam, Gerhard, Antoniw, John, Baldwin, Thomas, Calvo, Sarah, Chang, Yueh-Long, DeCaprio, David, Gale, Liane R., Gnerre, Sante, Goswami, Rubella S., Hammond-Kosack, Kim, Harris, Linda J., Hilburn, Karen, Kennell, John C., Kroken, Scott, Magnuson, Jon K., Mannhaupt, Gertrud, Mauceli, Evan, Mewes, Hans-Werner, Mitterbauer, Rudolf, Muehlbauer, Gary, Münsterkötter, Martin, Nelson, David, O'Donnell, Kerry, Ouellet, Thérèse, Qi, Weihong, Quesneville, Hadi, Roncero, M. Isabel G., Seong, Kye-Yong, Tetko, Igor V., Urban, Martin, Waalwijk, Cees, Ward, Todd J., Yao, Jiqiang, Birren, Bruce W., and Kistler, H. Corby

Published
2007
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31. Fusarium oxysporum effector clustering version 2: An updated pipeline to infer host range.

Author

Guallar, Megan A. Brenes, Fokkens, Like, Rep, Martijn, Berke, Lidija, and van Dam, Peter

Subjects
HIERARCHICAL clustering (Cluster analysis), SEQUENCE alignment, FUSARIUM oxysporum, SCALABILITY, GENOMES
Abstract

The fungus Fusarium oxysporum is infamous for its devastating effects on economically important crops worldwide. F. oxysporum isolates are grouped into formae speciales based on their ability to cause disease on different hosts. Assigning F. oxysporum strains to formae speciales using non-experimental procedures has proven to be challenging due to their genetic heterogeneity and polyphyletic nature. However, genetically diverse isolates of the same forma specialis encode similar repertoires of effectors, proteins that are secreted by the fungus and contribute to the establishment of compatibility with the host. Based on this observation, we previously designed the F. oxysporum Effector Clustering (FoEC) pipeline which is able to classify F. oxysporum strains by forma specialis based on hierarchical clustering of the presence of predicted putative effector sequences, solely using genome assemblies as input. Here we present the updated FoEC2 pipeline which is more user friendly, customizable and, due to multithreading, has improved scalability. It is designed as a Snakemake pipeline and incorporates a new interactive visualization app. We showcase FoEC2 by clustering 537 publicly available F. oxysporum genomes and further analysis of putative effector families as multiple sequence alignments. We confirm classification of isolates into formae speciales and are able to further identify their subtypes. The pipeline is available on github: https://github.com/pvdam3/FoEC2. [ABSTRACT FROM AUTHOR]

Published
2022
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32. 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., primary, Al-Hatmi, Abdullah M. S., additional, Aoki, Takayuki, additional, Arie, Tsutomu, additional, Balmas, Virgilio, additional, Barnes, Irene, additional, Bergstrom, Gary C., additional, Bhattacharyya, Madan K., additional, Blomquist, Cheryl L., additional, Bowden, Robert L., additional, Brankovics, Balázs, additional, Brown, Daren W., additional, Burgess, Lester W., additional, Bushley, Kathryn, additional, Busman, Mark, additional, Cano-Lira, José F., additional, Carrillo, Joseph D., additional, Chang, Hao-Xun, additional, Chen, Chi-Yu, additional, Chen, Wanquan, additional, Chilvers, Martin, additional, Chulze, Sofia, additional, Coleman, Jeffrey J., additional, Cuomo, Christina A., additional, de Beer, Z. Wilhelm, additional, de Hoog, G. Sybren, additional, Del Castillo-Múnera, Johanna, additional, Del Ponte, Emerson M., additional, Diéguez-Uribeondo, Javier, additional, Di Pietro, Antonio, additional, Edel-Hermann, Véronique, additional, Elmer, Wade H., additional, Epstein, Lynn, additional, Eskalen, Akif, additional, Esposto, Maria Carmela, additional, Everts, Kathryne L., additional, Fernández-Pavía, Sylvia P., additional, da Silva, Gilvan Ferreira, additional, Foroud, Nora A., additional, Fourie, Gerda, additional, Frandsen, Rasmus J. N., additional, Freeman, Stanley, additional, Freitag, Michael, additional, Frenkel, Omer, additional, Fuller, Kevin K., additional, Gagkaeva, Tatiana, additional, Gardiner, Donald M., additional, Glenn, Anthony E., additional, Gold, Scott E., additional, Gordon, Thomas R., additional, Gregory, Nancy F., additional, Gryzenhout, Marieka, additional, Guarro, Josep, additional, Gugino, Beth K., additional, Gutierrez, Santiago, additional, Hammond-Kosack, Kim E., additional, Harris, Linda J., additional, Homa, Mónika, additional, Hong, Cheng-Fang, additional, Hornok, László, additional, Huang, Jenn-Wen, additional, Ilkit, Macit, additional, Jacobs, Adriaana, additional, Jacobs, Karin, additional, Jiang, Cong, additional, Jiménez-Gasco, María del Mar, additional, Kang, Seogchan, additional, Kasson, Matthew T., additional, Kazan, Kemal, additional, Kennell, John C., additional, Kim, Hye-Seon, additional, Kistler, H. Corby, additional, Kuldau, Gretchen A., additional, Kulik, Tomasz, additional, Kurzai, Oliver, additional, Laraba, Imane, additional, Laurence, Matthew H., additional, Lee, Theresa, additional, Lee, Yin-Won, additional, Lee, Yong-Hwan, additional, Leslie, John F., additional, Liew, Edward C. Y., additional, Lofton, Lily W., additional, Logrieco, Antonio F., additional, S. López-Berges, Manuel, additional, Luque, Alicia G., additional, Lysøe, Erik, additional, Ma, Li-Jun, additional, Marra, Robert E., additional, Martin, Frank N., additional, May, Sara R., additional, McCormick, Susan P., additional, McGee, Chyanna, additional, Meis, Jacques F., additional, Migheli, Quirico, additional, Mohamed Nor, N. M. I., additional, Monod, Michel, additional, Moretti, Antonio, additional, Mostert, Diane, additional, Mulè, Giuseppina, additional, Munaut, Françoise, additional, Munkvold, Gary P., additional, Nicholson, Paul, additional, Nucci, Marcio, additional, O’Donnell, Kerry, additional, Pasquali, Matias, additional, Pfenning, Ludwig H., additional, Prigitano, Anna, additional, Proctor, Robert H., additional, Ranque, Stéphane, additional, Rehner, Stephen A., additional, Rep, Martijn, additional, Rodríguez-Alvarado, Gerardo, additional, Rose, Lindy Joy, additional, Roth, Mitchell G., additional, Ruiz-Roldán, Carmen, additional, Saleh, Amgad A., additional, Salleh, Baharuddin, additional, Sang, Hyunkyu, additional, Scandiani, María Mercedes, additional, Scauflaire, Jonathan, additional, Schmale, David G., additional, Short, Dylan P. G., additional, Šišić, Adnan, additional, Smith, Jason A., additional, Smyth, Christopher W., additional, Son, Hokyoung, additional, Spahr, Ellie, additional, Stajich, Jason E., additional, Steenkamp, Emma, additional, Steinberg, Christian, additional, Subramaniam, Rajagopal, additional, Suga, Haruhisa, additional, Summerell, Brett A., additional, Susca, Antonella, additional, Swett, Cassandra L., additional, Toomajian, Christopher, additional, Torres-Cruz, Terry J., additional, Tortorano, Anna M., additional, Urban, Martin, additional, Vaillancourt, Lisa J., additional, Vallad, Gary E., additional, van der Lee, Theo A. J., additional, Vanderpool, Dan, additional, van Diepeningen, Anne D., additional, Vaughan, Martha M., additional, Venter, Eduard, additional, Vermeulen, Marcele, additional, Verweij, Paul E., additional, Viljoen, Altus, additional, Waalwijk, Cees, additional, Wallace, Emma C., additional, Walther, Grit, additional, Wang, Jie, additional, Ward, Todd J., additional, Wickes, Brian L., additional, Wiederhold, Nathan P., additional, Wingfield, Michael J., additional, Wood, Ana K. M., additional, Xu, Jin-Rong, additional, Yang, Xiao-Bing, additional, Yli-Mattila, Tapani, additional, Yun, Sung-Hwan, additional, Zakaria, Latiffah, additional, Zhang, Hao, additional, Zhang, Ning, additional, Zhang, Sean X., additional, and Zhang, Xue, additional

Published
2021
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