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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

6. IMA genome‑F17: Draft genome sequences of an Armillaria species from Zimbabwe, Ceratocystis colombiana, Elsinoë necatrix, Rosellinia necatrix, two genomes of Sclerotinia minor, short‑read genome assemblies and annotations of four Pyrenophora teres isolates from barley grass, and a long-read genome assembly of Cercospora zeina

Author

Wingfield, Brenda D., Berger, Dave K., Coetzee, Martin P. A., Duong, Tuan A., Martin, Anke, Pham, Nam Q., van den Berg, Noelani, Wilken, P. Markus, Arun-Chinnappa, Kiruba Shankari, Barnes, Irene, Buthelezi, Sikelela, Dahanayaka, Buddhika Amarasinghe, Durán, Alvaro, Engelbrecht, Juanita, Feurtey, Alice, Fourie, Arista, Fourie, Gerda, Hartley, Jesse, Kabwe, Eugene N. K., Maphosa, Mkhululi, Narh Mensah, Deborah L., Nsibo, David L., Potgieter, Lizel, Poudel, Barsha, Stukenbrock, Eva H., Thomas, Chanel, Vaghefi, Niloofar, Welgemoed, Tanya, and Wingfield, Michael J.

Published
2022
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10. Pantoea bathycoeliae sp. nov and Sodalis sp. are core gut microbiome symbionts of the two-spotted stink bug.

Author

Fourie, Arista, Venter, Stephanus N., Slippers, Bernard, and Fourie, Gerda

Subjects
STINKBUGS, GUT microbiome, SAP (Plant), BACTERIAL diversity, BACTERIAL population, FUNCTIONAL analysis, MACADAMIA
Abstract

Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode. [ABSTRACT FROM AUTHOR]

Published
2023
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13. Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum

Author

Ioos, Renaud, Aloi, Francesco, Piškur, Barbara, Guinet, Cécile, Mullett, Martin, Berbegal, Mónica, Bragança, Helena, Cacciola, Santa Olga, Oskay, Funda, Cornejo, Carolina, Adamson, Kalev, Douanla-Meli, Clovis, Kačergius, Audrius, Martínez-Álvarez, Pablo, Nowakowska, Justyna Anna, Luchi, Nicola, Vettraino, Anna Maria, Ahumada, Rodrigo, Pasquali, Matias, Fourie, Gerda, Kanetis, Loukas, Alves, Artur, Ghelardini, Luisa, Dvořák, Miloň, Sanz-Ros, Antonio, Diez, Julio J., Baskarathevan, Jeyaseelan, and Aguayo, Jaime

Published
2019
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15. IMA genome‑F17

Author

Wingfield, Brenda D., primary, Berger, Dave K., additional, Coetzee, Martin P. A., additional, Duong, Tuan A., additional, Martin, Anke, additional, Pham, Nam Q., additional, van den Berg, Noelani, additional, Wilken, P. Markus, additional, Arun-Chinnappa, Kiruba Shankari, additional, Barnes, Irene, additional, Buthelezi, Sikelela, additional, Dahanayaka, Buddhika Amarasinghe, additional, Durán, Alvaro, additional, Engelbrecht, Juanita, additional, Feurtey, Alice, additional, Fourie, Arista, additional, Fourie, Gerda, additional, Hartley, Jesse, additional, Kabwe, Eugene N. K., additional, Maphosa, Mkhululi, additional, Narh Mensah, Deborah L., additional, Nsibo, David L., additional, Potgieter, Lizel, additional, Poudel, Barsha, additional, Stukenbrock, Eva H., additional, Thomas, Chanel, additional, Vaghefi, Niloofar, additional, Welgemoed, Tanya, additional, and Wingfield, Michael J., additional

Published
2022
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16. Reports

Author

Crous, Pedro W., Lombard, Lorenzo, Dearnaley, John, Fourie, Gerda, and Ashby, Ali

Published
2016
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19. Global geographic distribution and host range of fusarium circinatum, the causal agent of pine pitch canker

Author

European Commission, Estonian Science Foundation, Agence Nationale de la Recherche (France), Scottish Government, Office fédéral de l'environnement (Suisse), Martín-García, Jorge [0000-0002-3057-3710], Vahalík, P. [0000-0003-3404-3095], Adamson, K. [0000-0002-8810-8838], Adamčikova, K. [0000-0001-5407-5233], Ahumada, Rodrigo [0000-0002-2397-2721], Blank, Lior [0000-0002-8753-0113], Bragança, H. [0000-0002-7957-5493], Capretti, P. [0000-0002-1893-9871], Cleary, M. [0000-0002-0318-5974], Cornejo, Carolina [0000-0003-3259-6198], Davydenko, K. [0000-0001-6077-8533], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Dvorák, Milon [0000-0002-4390-4718], Enderle, R. [0000-0002-3436-9581], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Hantula, Jarkko [0000-0002-1016-0636], Ioos, Renaud [0000-0001-9359-5098], Iturritxa, Eugenia [0000-0002-6390-5873], Kanetis, Loukas [0000-0002-1869-558X], Karpun, Natalia N. [0000-0002-7696-3618], Koltay, András [0000-0001-6865-2601], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Milenkovic, Ivan [0000-0003-2792-0221], Musolin, Dmitry L. [0000-0002-3913-3674], Nowakowska, Justyna A. [0000-0001-5863-053X], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Paraschiv, Marius [0000-0001-6916-8600], Pasquali, Matias [0000-0002-9102-2066], Pecori, Francesco [0000-0002-6577-7190], Rafoss, Trond [0000-0002-8489-4771], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Robin, Cecile [0000-0002-8145-245X], Rodas, Carlos A. [0000-0002-8895-8883], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Selikhovkin, Andrey V. [0000-0003-4227-9647], Solla, A. [0000-0002-2596-1612], Soukainen, M. [0000-0001-6686-0191], Soulioti, Nikoleta [0000-0001-5011-0863], Steenkamp, Emma T. [0000-0003-0217-8219], Tsopelas, Panaghiotis [0000-0002-7853-4534], Vemic, Aleksandar [0000-0001-9195-8967], Vettraino, A. M. [0000-0003-0797-3297], Wingfield, Michael J. [0000-0001-9346-2009], Woodward, Stephen [0000-0002-6627-7702], Zamora-Ballesteros, Cristina [0000-0002-9728-5553], Mullett, M. [0000-0002-6013-0347], Drenkhan, R., Ganley, Beccy, Martín-García, Jorge, Vahalík, P., Adamson, K., Adamčikova, K., Ahumada, Rodrigo, Blank, Lior, Bragança, H., Capretti, P., Cleary, M., Cornejo, Carolina, Davydenko, K., Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Dvorák, Milon, Enderle, R., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hantula, Jarkko, Ioos, Renaud, Iturritxa, Eugenia, Kanetis, Loukas, Karpun, Natalia N., Koltay, András, Landeras, Elena, Markovskaja, S., Mesanza, Nebai, Milenkovic, Ivan, Musolin, Dmitry L., Nikolaou, Konstantinos, Nowakowska, Justyna A., Ogris, N., Oskay, F., Oszako, Tomasz, Papazova-Anakieva, Irena, Paraschiv, Marius, Pasquali, Matias, Pecori, Francesco, Rafoss, Trond, Raitelaitytė, K., Raposo Llobet, María Rosa, Robin, Cecile, Rodas, Carlos A., Santini, Alberto, Sanz-Ros, Antonio V., Selikhovkin, Andrey V., Solla, A., Soukainen, M., Soulioti, Nikoleta, Steenkamp, Emma T., Tsopelas, Panaghiotis, Vemic, Aleksandar, Vettraino, A. M., Wingfield, Michael J., Woodward, Stephen, Zamora-Ballesteros, Cristina, Mullett, M., European Commission, Estonian Science Foundation, Agence Nationale de la Recherche (France), Scottish Government, Office fédéral de l'environnement (Suisse), Martín-García, Jorge [0000-0002-3057-3710], Vahalík, P. [0000-0003-3404-3095], Adamson, K. [0000-0002-8810-8838], Adamčikova, K. [0000-0001-5407-5233], Ahumada, Rodrigo [0000-0002-2397-2721], Blank, Lior [0000-0002-8753-0113], Bragança, H. [0000-0002-7957-5493], Capretti, P. [0000-0002-1893-9871], Cleary, M. [0000-0002-0318-5974], Cornejo, Carolina [0000-0003-3259-6198], Davydenko, K. [0000-0001-6077-8533], Díez, Julio Javier [0000-0003-0558-8141], Doǧmuş-Lehtijärvi, Hatice T. [0000-0002-1050-8823], Dvorák, Milon [0000-0002-4390-4718], Enderle, R. [0000-0002-3436-9581], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0003-3165-1992], Ghelardini, L. [0000-0002-3180-4226], Hantula, Jarkko [0000-0002-1016-0636], Ioos, Renaud [0000-0001-9359-5098], Iturritxa, Eugenia [0000-0002-6390-5873], Kanetis, Loukas [0000-0002-1869-558X], Karpun, Natalia N. [0000-0002-7696-3618], Koltay, András [0000-0001-6865-2601], Markovskaja, S. [0000-0003-3111-6949], Mesanza, Nebai [0000-0002-1578-9193], Milenkovic, Ivan [0000-0003-2792-0221], Musolin, Dmitry L. [0000-0002-3913-3674], Nowakowska, Justyna A. [0000-0001-5863-053X], Ogris, N. [0000-0002-4058-9417], Oskay, F. [0000-0002-8918-5595], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Paraschiv, Marius [0000-0001-6916-8600], Pasquali, Matias [0000-0002-9102-2066], Pecori, Francesco [0000-0002-6577-7190], Rafoss, Trond [0000-0002-8489-4771], Raitelaitytė, K. [0000-0001-9753-9712], Raposo Llobet, María Rosa [0000-0002-4893-6874], Robin, Cecile [0000-0002-8145-245X], Rodas, Carlos A. [0000-0002-8895-8883], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Selikhovkin, Andrey V. [0000-0003-4227-9647], Solla, A. [0000-0002-2596-1612], Soukainen, M. [0000-0001-6686-0191], Soulioti, Nikoleta [0000-0001-5011-0863], Steenkamp, Emma T. [0000-0003-0217-8219], Tsopelas, Panaghiotis [0000-0002-7853-4534], Vemic, Aleksandar [0000-0001-9195-8967], Vettraino, A. M. [0000-0003-0797-3297], Wingfield, Michael J. [0000-0001-9346-2009], Woodward, Stephen [0000-0002-6627-7702], Zamora-Ballesteros, Cristina [0000-0002-9728-5553], Mullett, M. [0000-0002-6013-0347], Drenkhan, R., Ganley, Beccy, Martín-García, Jorge, Vahalík, P., Adamson, K., Adamčikova, K., Ahumada, Rodrigo, Blank, Lior, Bragança, H., Capretti, P., Cleary, M., Cornejo, Carolina, Davydenko, K., Díez, Julio Javier, Doǧmuş-Lehtijärvi, Hatice T., Dvorák, Milon, Enderle, R., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hantula, Jarkko, Ioos, Renaud, Iturritxa, Eugenia, Kanetis, Loukas, Karpun, Natalia N., Koltay, András, Landeras, Elena, Markovskaja, S., Mesanza, Nebai, Milenkovic, Ivan, Musolin, Dmitry L., Nikolaou, Konstantinos, Nowakowska, Justyna A., Ogris, N., Oskay, F., Oszako, Tomasz, Papazova-Anakieva, Irena, Paraschiv, Marius, Pasquali, Matias, Pecori, Francesco, Rafoss, Trond, Raitelaitytė, K., Raposo Llobet, María Rosa, Robin, Cecile, Rodas, Carlos A., Santini, Alberto, Sanz-Ros, Antonio V., Selikhovkin, Andrey V., Solla, A., Soukainen, M., Soulioti, Nikoleta, Steenkamp, Emma T., Tsopelas, Panaghiotis, Vemic, Aleksandar, Vettraino, A. M., Wingfield, Michael J., Woodward, Stephen, Zamora-Ballesteros, Cristina, and Mullett, M.

Abstract

Fusarium circinatum, the causal agent of pine pitch canker (PPC), is currently one of the most important threats of Pinus spp. globally. This pathogen is known in many pine-growing regions, including natural and planted forests, and can affect all life stages of trees, from emerging seedlings to mature trees. Despite the importance of PPC, the global distribution of F. circinatum is poorly documented, and this problem is also true of the hosts within countries that are affected. The aim of this study was to review the global distribution of F. circinatum, with a particular focus on Europe. We considered (1) the current and historical pathogen records, both positive and negative, based on confirmed reports from Europe and globally; (2) the genetic diversity and population structure of the pathogen; (3) the current distribution of PPC in Europe, comparing published models of predicted disease distribution; and (4) host susceptibility by reviewing literature and generating a comprehensive list of known hosts for the fungus. These data were collated from 41 countries and used to compile a specially constructed geo-database. A review of 6297 observation records showed that F. circinatum and the symptoms it causes on conifers occurred in 14 countries, including four in Europe, and is absent in 28 countries. Field observations and experimental data from 138 host species revealed 106 susceptible host species including 85 Pinus species, 6 non-pine tree species and 15 grass and herb species. Our data confirm that susceptibility to F. circinatum varies between different host species, tree ages and environmental characteristics. Knowledge on the geographic distribution, host range and the relative susceptibility of different hosts is essential for disease management, mitigation and containment strategies. The findings reported in this review will support countries that are currently free of F. circinatum in implementing effective procedures and restrictions and prevent further

Published
2020

20. Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

Author

Wingfield, Brenda D., Ades, Peter K., Al-Naemi, Fatima A., Beirn, Lisa A., Bihon, Wubetu, Crouch, Jo Anne, de Beer, Z. Wilhelm, De Vos, Lieschen, Duong, Tuan A., Fields, Christopher J., Fourie, Gerda, Kanzi, Aquillah M., Malapi-Wight, Martha, Pethybridge, Sarah J., Radwan, Osman, Rendon, Gloria, Slippers, Bernard, Santana, Quentin C., Steenkamp, Emma T., Taylor, Paul W. J., Vaghefi, Niloofar, van der Merwe, Nicolaas A., Veltri, Daniel, and Wingfield, Michael J.

Published
2015
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23. Sampling and detection strategies for the pine pitch canker (PPC) disease pathogen Fusarium Circinatum in Europe

Author

European Commission, Ministerio de Economía y Competitividad (España), Fundação para a Ciência e a Tecnologia (Portugal), Vainio, Eeva [0000-0002-6739-7968], Bezos, Diana [0000-0002-0423-4627], Bragança, H. [0000-0002-4554-2722], Cleary, M. [0000-0002-0318-5974], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0001-6580-4147], Ghelardini, L. [0000-0002-3180-4226], Hannunen, Salla [0000-0002-0998-4240], Ioos, Renaud [0000-0001-9359-5098], Martín-García, Jorge [0000-0002-3057-3710], Martínez-Álvarez, Pablo [0000-0002-4605-7702], Mullett, M. [0000-0002-6013-0347], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Piškur, B. [0000-0002-9914-4930], Romeralo, Carmen [0000-0002-8510-9915], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Steenkamp, Emma T. [0000-0003-0217-8219], Tubby, K. [0000-0001-6864-4185], Wingfield, Michael J. [0000-0001-9346-2009], Díez, Julio Javier [0000-0003-0558-8141], Vainio, Eeva, Bezos, Diana, Bragança, H., Cleary, M., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hannunen, Salla, Ioos, Renaud, Martín-García, Jorge, Martínez-Álvarez, Pablo, Mullett, M., Oszako, Tomasz, Papazova-Anakieva, Irena, Piškur, B., Romeralo, Carmen, Sanz-Ros, Antonio V., Steenkamp, Emma T., Tubby, K., Wingfield, Michael J., Díez, Julio Javier, European Commission, Ministerio de Economía y Competitividad (España), Fundação para a Ciência e a Tecnologia (Portugal), Vainio, Eeva [0000-0002-6739-7968], Bezos, Diana [0000-0002-0423-4627], Bragança, H. [0000-0002-4554-2722], Cleary, M. [0000-0002-0318-5974], Fourie, Gerda [0000-0003-2650-5448], Georgieva, M. [0000-0001-6580-4147], Ghelardini, L. [0000-0002-3180-4226], Hannunen, Salla [0000-0002-0998-4240], Ioos, Renaud [0000-0001-9359-5098], Martín-García, Jorge [0000-0002-3057-3710], Martínez-Álvarez, Pablo [0000-0002-4605-7702], Mullett, M. [0000-0002-6013-0347], Oszako, Tomasz [0000-0003-4688-2582], Papazova-Anakieva, Irena [0000-0002-7260-4685], Piškur, B. [0000-0002-9914-4930], Romeralo, Carmen [0000-0002-8510-9915], Sanz-Ros, Antonio V. [0000-0002-4791-8308], Steenkamp, Emma T. [0000-0003-0217-8219], Tubby, K. [0000-0001-6864-4185], Wingfield, Michael J. [0000-0001-9346-2009], Díez, Julio Javier [0000-0003-0558-8141], Vainio, Eeva, Bezos, Diana, Bragança, H., Cleary, M., Fourie, Gerda, Georgieva, M., Ghelardini, L., Hannunen, Salla, Ioos, Renaud, Martín-García, Jorge, Martínez-Álvarez, Pablo, Mullett, M., Oszako, Tomasz, Papazova-Anakieva, Irena, Piškur, B., Romeralo, Carmen, Sanz-Ros, Antonio V., Steenkamp, Emma T., Tubby, K., Wingfield, Michael J., and Díez, Julio Javier

Abstract

Fusarium circinatum Nirenberg & O'Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions-via contaminated seeds, wood material, soil and growing substrates, natural means and human activities-into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the "bridgehead effect", where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspec

Published
2019

24. Global Geographic Distribution and Host Range of Fusarium circinatum, the Causal Agent of Pine Pitch Canker

Author

Drenkhan, Rein, primary, Ganley, Beccy, additional, Martín-García, Jorge, additional, Vahalík, Petr, additional, Adamson, Kalev, additional, Adamčíková, Katarína, additional, Ahumada, Rodrigo, additional, Blank, Lior, additional, Bragança, Helena, additional, Capretti, Paolo, additional, Cleary, Michelle, additional, Cornejo, Carolina, additional, Davydenko, Kateryna, additional, Diez, Julio J., additional, Lehtijärvi, Hatice Tuğba Doğmuş, additional, Dvořák, Miloň, additional, Enderle, Rasmus, additional, Fourie, Gerda, additional, Georgieva, Margarita, additional, Ghelardini, Luisa, additional, Hantula, Jarkko, additional, Ioos, Renaud, additional, Iturritxa, Eugenia, additional, Kanetis, Loukas, additional, Karpun, Natalia N., additional, Koltay, András, additional, Landeras, Elena, additional, Markovskaja, Svetlana, additional, Mesanza, Nebai, additional, Milenković, Ivan, additional, Musolin, Dmitry L., additional, Nikolaou, Konstantinos, additional, Nowakowska, Justyna A., additional, Ogris, Nikica, additional, Oskay, Funda, additional, Oszako, Tomasz, additional, Papazova-Anakieva, Irena, additional, Paraschiv, Marius, additional, Pasquali, Matias, additional, Pecori, Francesco, additional, Rafoss, Trond, additional, Raitelaitytė, Kristina, additional, Raposo, Rosa, additional, Robin, Cecile, additional, Rodas, Carlos A., additional, Santini, Alberto, additional, Sanz-Ros, Antonio V., additional, Selikhovkin, Andrey V., additional, Solla, Alejandro, additional, Soukainen, Mirkka, additional, Soulioti, Nikoleta, additional, Steenkamp, Emma T., additional, Tsopelas, Panaghiotis, additional, Vemić, Aleksandar, additional, Vettraino, Anna Maria, additional, Wingfield, Michael J., additional, Woodward, Stephen, additional, Zamora-Ballesteros, Cristina, additional, and Mullett, Martin S., additional

Published
2020
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25. A Detection Assay to Identify Alternative Food Sources of the Two-Spotted Stink Bug, Bathycoelia distincta(Hemiptera: Pentatomidae)

Author

Fourie, Arista, Venter, Stephanus N, Slippers, Bernard, and Fourie, Gerda

Abstract

The two-spotted stink bug, Bathycoelia distinctaDistant (Hemiptera: Pentatomidae), is a serious pest in South African macadamia orchards. This pest is predominantly controlled using insecticides, thus alternative control methods are essential. The stink bugs arrive as adults in the orchards, during the early nut set season, but little is known about their alternative plant hosts before their arrival. The aim of this study was to develop a PCR-based metabarcoding assay to identify plant material in the gut of B. distincta.Thereafter, the persistence of plant DNA in the gut, after switching food sources, was determined by rearing the stink bugs on Zea maysL. (Cyperales: Poaceae), transferring them to Macadamiasp. and then collecting insects at different time points. As a proof of concept, the assay was tested on insects collected from commercial macadamia orchards to determine if it can identify alternative food sources. The chloroplast gene markers, trnLand trnF, were most successful for plant DNA amplification. The time trial suggested that plant material can be detected 24 h after switching to the alternate food source and one of the samples still contained Z. maysDNA after five days. Various plant species were detected from the orchard collected samples, including known food sources of other stink bugs, such as tea plants (Camellia sinensisL. (Ericales:Theaceae)) and sunflowers (Helianthus annuusL. (Asterales: Asteraceae)). This study provides the first indication of potential alternative food sources of B. distincta. The assay developed in this study can now be implemented for large-scale field surveys to contribute to future integrated pest management strategies.

Published
2022
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26. The synergistic effect of concatenation in phylogenomics: the case in Pantoea

Author

Palmer, Marike, primary, Venter, Stephanus N., additional, McTaggart, Alistair R., additional, Coetzee, Martin P.A., additional, Van Wyk, Stephanie, additional, Avontuur, Juanita R., additional, Beukes, Chrizelle W., additional, Fourie, Gerda, additional, Santana, Quentin C., additional, Van Der Nest, Magriet A., additional, Blom, Jochen, additional, and Steenkamp, Emma T., additional

Published
2019
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27. Evolutionary relationships among the Fusarium oxysporum f. sp. cubense vegetative compatibility groups

Author

Fourie, Gerda, Steenkamp, E.T., Gordon, T.R., and Viljoen, A.

Subjects
Fusarium -- Genetic aspects, Fusarium -- Physiological aspects, Mitochondrial DNA -- Research, Nucleotide sequencing -- Usage, Biological sciences
Abstract

Genetic relatedness among and within vegetative compatibility groups (VCGs) of Fusarium oxysporum f. sp. cubense is analyzed by sequencing two nuclear and two mitochondrial DNA regions in a collection of 70 Furasium oxysporum isolates that has included representatives of 20 VCGs of Fusarium oxysporum f. sp. cubense, other formae speciales and nonpathogens. The isolates examined have harbored one of the two mating-type idiomorphs, but never both, suggesting a heterothallic mating system should sexual reproduction occur.

Published
2009

29. The distribution and host range of the banana Fusarium wilt fungus, Fusarium oxysporum f. sp. cubense, in Asia

Author

Mostert, Diane, primary, Molina, Agustin B., additional, Daniells, Jeff, additional, Fourie, Gerda, additional, Hermanto, Catur, additional, Chao, Chih-Ping, additional, Fabregar, Emily, additional, Sinohin, Vida G., additional, Masdek, Nik, additional, Thangavelu, Raman, additional, Li, Chunyu, additional, Yi, Ganyun, additional, Mostert, Lizel, additional, and Viljoen, Altus, additional

Published
2017
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30. IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata

Author

Wingfield, Brenda D., Ades, Peter K., Al-Naemi, Fatima A., Beirn, Lisa A., Bihon, Wubetu, Crouch, Jo Anne, de Beer, Z. Wilhelm, De Vos, Lieschen, Duong, Tuan A., Fields, Christopher J., Fourie, Gerda, Kanzi, Aquillah M., Malapi-Wight, Martha, Pethybridge, Sarah J., Radwan, Osman, Rendon, Gloria, Slippers, Bernard, Santana, Quentin C., Steenkamp, Emma T., Taylor, Paul W.J., Vaghefi, Niloofar, van der Merwe, Nicolaas A., Veltri, Daniel, and Wingfield, Michael J.

Subjects
pink patch disease, ray blight, blue stain, canker pathogen, basal stalk and root rot, black scorch disease
Abstract

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms. Genomics Research Institute (University of Pretoria), Tree Protection Co-operative Programme (TPCP) and the DST-NRF Centre of Excellence in Tree Health Biotechnology (CTHB) at the Forestry and Agricultural Biotechnology Institute (FABI), together with the National Research Foundation (NRF) and the University of Pretoria, Pretoria, South Africa. The research on Stagonosporopsis tanaceti was supported by Botanical Resources Australia, Agricultural Services Pty Ltd,, and USDA-NIFA Hatch project NYG-625424, managed by The New York Agricultural Experiment Station, Cornell University (Geneva, NY). The genome sequencing of Limonomyces culmigenus (CBS661.85) was funded by the US Department of Agriculture (USDA), Agricultural Research Service (ARS). The research on Thielaviopsis punctulata was made possible by a grant from the Qatar National Research Fund (QNRF) under National Priorities Research Program (NPRP-5-1002-4-010).

Published
2015

31. Association of the pitch canker pathogen Fusarium circinatum with grass hosts in commercial pine production areas of South Africa

Author

Swett, Cassandra L, Porter, Bernice, Fourie, Gerda, Steenkamp, Emma T, Gordon, Thomas R, and Wingfield, Michael J

Abstract

The pitch canker pathogen, Fusarium circinatum, has major impacts on production in pine nurseries and plantations in South Africa. Thus far, efforts to reduce local spread have focused on rouging of infected pines and sanitation to eliminate local sources of inoculum. Although the host range of F. circinatum was thought to be limited to pines and Douglas-fir, recent studies in California indicate that this fungus is capable of infecting grasses as a symptomless endophyte. Consequently, it is possible that grasses represent a reservoir of inoculum that influences the occurrence of disease in South African pine nurseries and plantations. The objectives of this study were to survey a wide range of grass species in both nurseries and plantations in South Africa for the presence of F. circinatum. In all, 22 species of grass were sampled at a nursery in Mpumulanga and in a plantation on the Western Cape. Isolates obtained from grasses were identified based on morphological criteria and DNA sequence data. Fusarium circinatum was recovered from vegetative tissues of four grass species including Briza maxima, Ehrharta erecta var. erecta, Pentameris pallida and one species that could not be identified. All isolates were pathogenic to pines and comparable in virulence to a known F. circinatum isolate that was included as a positive control. These studies indicate that grasses may constitute inoculum reservoirs that could facilitate persistence and dissemination of the pathogen in nurseries, and provide a means for the pathogen to move between widely separated pine stands, where grass hosts occur in intervening areas.Keywords: alternate hosts, Fusarium circinatum, grasses, Pinus, pitch canker, PoaceaeSouthern Forests 2014, 76(3): 161–166

Published
2014

32. Effect on nursery and field performance of Pinus patula seedlings after inoculation with Fusarium circinatum

Author

Jones, Nicoletta B, Ford, Craig M, Light, Marnie E, Nadel, Ryan L, Greyling, Izette, Fourie, Gerda, Wingfield, Michael J, and Morris, Andrew R

Abstract

Fusarium circinatum is an important fungal pathogen of Pinus species. In South Africa, it is the most significant pathogen of Pinus patula seedlings in forestry nurseries where it presents a substantial constraint to productivity and can continue to cause mortality in-field for up to two years after establishment. This study describes the results from two trials where P. patula seedlings were inoculated with F. circinatum to determine the impact of the pathogen on nursery and field performance. Seedlings were also subjected to water stress treatments to ascertain whether this would trigger the onset of disease symptoms. Inoculum load and timing of inoculation had significant effects on seedling survival in both the nursery and field. High inoculum concentrations caused greater levels of mortality and, where seedlings were inoculated at a young age, they showed higher levels of susceptibility to F. circinatum. Temporary water-stress in the nursery produced smaller plants and improved in-field survival, but this treatment did not trigger higher mortality in inoculated treatments. On the other hand, transplant stress was a major contributor to the higher levels of mortality observed in inoculated treatments. Overall, these studies confirmed that infection in the nursery leads to the disease problems observed during early plant establishment in the field.Keywords: Fusarium circinatum, inoculation, nursery-to-field, Pinus patula, seedlings, survivalSouthern Forests 2014, 76(3): 125–136

Published
2014

33. Re-use of seedling containers and Fusarium circinatum association with asymptomatic Pinus patula planting stock

Author

Morris, Andrew R, Fourie, Gerda, Greyling, Izette, Steenkamp, Emma T, and Jones, Nicoletta B

Abstract

Fusarium circinatum is a pathogen causing serious post-planting mortality of Pinus patula seedlings in southern Africa. Containerised planting stock that is asymptomatic but associated with F. circinatum in the nursery is thought to be the cause of this problem. The aim of this study was to determine if re-use of seedling containers could be a source of inoculum resulting in asymptomatic planting stock and increased post-planting mortality of P. patula. Two experiments were conducted in successive years comparing nursery cull of symptomatic seedlings, seedling growth, association of F. circinatum with asymptomatic seedlings and post-planting mortality for crops raised in re-used containers, with and without sanitation, and factory-new containers. Each experiment consisted of a nursery production trial followed by out-planting into pots to assess post-planting mortality. Our results show that re-use of containers without sanitation increases the cull of symptomatic seedlings, incidence of F. circinatum associated with asymptomatic seedlings and post-planting mortality compared with the re-use of containers after steam sanitation or factory-new containers. Growth of asymptomatic seedlings was unaffected by container treatment or association with F. circinatum and in the absence of wilt symptoms the root system did not exhibit typical discolouration. Watering frequency did not influence post-planting mortality in pots. The comparison of two open-pollinated seed mixes of P. patula that, based on seedling stem inoculation screening, represented susceptible and tolerant material did not show differences in nursery cull or post-planting mortality. This work demonstrated that natural contamination of re-used containers can be a primary source of inoculum producing asymptomatic seedlings associated with F. circinatum that will succumb to the pathogen after field planting. The process of seedling infection, apparent latent infection in the seedling and expression of disease after planting needs greater understanding to improve nursery hygiene measures to control this disease.Keywords: containerised seedling nursery, Fusarium circinatum, Pinus patula, post-planting mortalitySouthern Forests 2014, 76(3): 177–187

Published
2014

34. Characterisation of South African isolates of Fusarium oxysporum f.sp. cubense from Cavendish bananas

Author

Visser, Marinda, Gordon, Tom, Fourie, Gerda, and Viljoen, Altus

Subjects
phylogenetics, bananas, mating types, vegetative compatibility groups, Fusarium wilt
Abstract

Fusarium wilt, caused bythe soil-borne fungusFusarium oxysporum f.sp. cubense (Foc), is a serious vascular disease of bananas in most subtropical and tropical regions of the world. Twenty-four vegetative compatibility groups (VCGs) and three pathogenic races have been identified in Foc, reflecting a relatively high genetic diversity for an asexual fungus. To characterise a South African population of Foc, a collection of 128 isolates from diverse geographic origins were isolated from diseased Cavendish bananas and subjected to VCG analysis and sequencing of the translation elongation factor 1-α (TEF) gene region. The presence of mating type genes was also determined using MAT-1 and MAT-2 specific primers. VCG 0120 was established as the only VCG of Foc present in the South African population studied. Only the MAT-2 idiomorph was present in all the local isolates of Foc. A phylogenetic analysis of DNA sequences of the TEF gene region revealed that the South African isolates grouped closely with VCG 0120 isolates from Australia and Asia. These results suggest that the South African population of Foc was most likely introduced in a limited number of events and that it had spread with infected planting material within the country. The presence of only one mating type and the limited diversity in this pathogen render it unlikely to rapidly overcome disease management strategies involving host resistance.

Published
2010

40. Mitochondrial introgression and interspecies recombination in the Fusarium fujikuroispecies complex

Author

Fourie, Gerda, Van der Merwe, Nicolaas, Wingfield, Brenda, Bogale, Mesfin, Wingfield, Michael, and Steenkamp, Emma

Abstract

The Fusarium fujikuroispecies complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization. The aim of this study was therefore to search for recombination between the mitochondrial genomes of different species in the FFSC. Using methods based on mt genome sequence similarity, five significant recombinant regions in both gene and intergenic regions were detected. Using coalescent-based methods and the sequences for individual mt genes, various ancestral recombination events between different lineages of the FFSC were also detected. These findings suggest that interspecies gene flow and introgression are likely to have played key roles in the evolution of the FFSC at both ancient and more recent time scales.

Published
2018
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42. First fungal genome sequence from Africa: A preliminary analysis

Author

Wingfield, Brenda D., primary, Steenkamp, Emma T., additional, Santana, Quentin C., additional, Coetzee, Martin P.A., additional, Bam, Stefan, additional, Barnes, Irene, additional, Beukes, Chrizelle W., additional, Chan, Wai Yin, additional, De Vos, Lieschen, additional, Fourie, Gerda, additional, Friend, Melanie, additional, Gordon, Thomas R., additional, Herron, Darryl A., additional, Holt, Carson, additional, Korf, Ian, additional, Kvas, Marija, additional, Martin, Simon H., additional, Mlonyeni, X. Osmond, additional, Naidoo, Kershney, additional, Phasha, Mmatshepho M., additional, Postma, Alisa, additional, Reva, Oleg, additional, Roos, Heidi, additional, Simpson, Melissa, additional, Slinski, Stephanie, additional, Slippers, Bernard, additional, Sutherland, Rene, additional, Van der Merwe, Nicolaas A., additional, Van der Nest, Magriet A., additional, Venter, Stephanus N., additional, Wilken, Pieter M., additional, Yandell, Mark, additional, Zipfel, Renate, additional, and Wingfield, Mike J., additional

Published
2012
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46. Culture-independent detection and quantification of Fusarium circinatum in a pine-producing seedling nursery.

Author

Fourie, Gerda, Wingfield, Michael J, Wingfield, Brenda D, Jones, Nicky B, Morris, Andrew R, and Steenkamp, Emma T

Subjects
FUSARIUM, TUBERCULARIACEAE, CYLINDROCARPON, CONIDIA, FUNGAL spores
Abstract

The primary symptoms associated withFusarium circinatuminfection in pine seedling nurseries are root and collar rot, shoot and tip die-back and seedling mortality. Management of this pathogen in nurseries usually involves the integration of various strategies relating to sanitation, insect control and fungicide treatment. The overall goal of this study was to use quantitative real-time PCR (qPCR) to detect and quantify the airborne inoculum ofF. circinatumin a commercial pine seedling nursery. For this purpose, an existing qPCR method was optimised and evaluated for its efficacy to quantify and monitor airborne conidia over a one-year period. Results showed thatF. circinatumoccurred at relatively low levels in the nursery throughout the year and that its distribution was spatially sporadic. The data suggest that standard nursery sanitation practices in the test nursery maintained the airborne inoculum ofF. circinatumat low levels. The uneven distribution of infection also suggests that airborne inoculum does not represent the primary source of inoculum for theF. circinatum-associated seedling disease. [ABSTRACT FROM AUTHOR]

Published
2014
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47. Multiple gene sequences delimit Botryosphaeria australissp. nov. from B. lutea

Author

Slippers, Bernard, Fourie, Gerda, Crous, Pedro W., Coutinho, Teresa A., Wingfield, Brenda D., and Wingfield, Michael J.

Abstract

Botryosphaeria lutea(anamorph Fusicoccum luteum) most easily is distinguished from other Botryosphaeriaspp. by a yellow pigment that is formed in young cultures. This fungus has been reported from a number of cultivated hosts in New Zealand and Portugal. During a survey of Botryosphaeriafungi that occur on native Acaciaspecies in Australia, a yellow pigment was observed in some cultures. These isolates were morphologically similar to B. lutea,but the pigment differed slightly from the one formed by authentic B. luteaisolates. Preliminary data also revealed small differences in ITS rDNA sequence data. The aim of this study was to determine whether these small differences were indicative of separate species or merely variations within B. lutea.Anamorph, teleomorph and culture morphology were compared between B. luteaand Acaciaisolates from Australia. Sequence data of two other genome regions, namely the β-tubulin and EF1-α gene and intron regions, were combined with ITS rDNA sequence data to determine the phylogenetic relationship between these isolates. Isolates of B. luteaand those from Australian Acaciaspecies were not significantly different in spore morphology. The yellow pigment, however, was much more distinct in cultures of B. luteathan in cultures from Acacia.There were only a few base pair variations in each of the analyzed gene regions, but these variations were fixed in the two groups in all regions. By combining these data it was clear that B. luteaand the isolates from Acaciawere distinct species, albeit very closely related. We, therefore, propose the new epithet B. australisfor the fungus from Australia. Botryosphaeria australisalso was isolated in this study from exotic Sequoiadendrontrees in Australia. Re-analyses of GenBank data in this study showed that B. australisalso occurs on other native Australian hosts, namely a Banksiasp. and a Eucalyptussp., as well as a native Proteasp. in South Africa and on Pistachioin Italy. These records from GenBank have been identified previously as B. lutea.The common occurrence of B. australison a variety of native hosts across Australia suggests that this fungus is native to this area.

Published
2004
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48. Sampling and Detection Strategies for the Pine Pitch Canker (PPC) Disease Pathogen Fusarium circinatum in Europe.

Author

Vainio, Eeva J., Bezos, Diana, Bragança, Helena, Cleary, Michelle, Fourie, Gerda, Georgieva, Margarita, Ghelardini, Luisa, Hannunen, Salla, Ioos, Renaud, Martín-García, Jorge, Martínez-Álvarez, Pablo, Mullett, Martin, Oszako, Tomasz, Papazova-Anakieva, Irena, Piškur, Barbara, Romeralo, Carmen, Sanz-Ros, Antonio V., Steenkamp, Emma T., Tubby, Katherine, and Wingfield, Michael J.

Subjects
FUSARIOSIS, INSECT trapping, DOUGLAS fir, PINE, SOIL sampling, PHYTOSANITATION, PINACEAE
Abstract

Fusarium circinatum Nirenberg & O'Donnel is listed among the species recommended for regulation as quarantine pests in Europe. Over 60 Pinus species are susceptible to the pathogen and it also causes disease on Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and species in genera such as Picea and Larix. The European Food Safety Authority considers the probability of new introductions—via contaminated seeds, wood material, soil and growing substrates, natural means and human activities—into the EU very likely. Due to early detection, constant surveillance and control measures, F. circinatum outbreaks have officially been eradicated in Italy and France. However, the global spread of F. circinatum suggests that the pathogen will continue to be encountered in new environments in the future. Therefore, continuous surveillance of reproductive material, nurseries and plantations, prompt control measures and realistic contingency plans will be important in Europe and elsewhere to limit disease spread and the "bridgehead effect", where new introductions of a tree pathogen become increasingly likely as new environments are invaded, must be considered. Therefore, survey programs already implemented to limit the spread in Europe and that could be helpful for other EU countries are summarized in this review. These surveys include not only countries where pitch canker is present, such as Portugal and Spain, but also several other EU countries where F. circinatum is not present. Sampling protocols for seeds, seedlings, twigs, branches, shoots, soil samples, spore traps and insects from different studies are collated and compiled in this review. Likewise, methodology for morphological and molecular identification is herein presented. These include conventional PCR with a target-specific region located in the intergenic spacer region, as well as several real-time PCR protocols, with different levels of specificity and sensitivity. Finally, the global situation and future perspectives are addressed. [ABSTRACT FROM AUTHOR]

Published
2019
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49. Architecture and Distribution of Introns in Core Genes of Four Fusarium Species.

Author

Phasha MM, Wingfield BD, Coetzee MPA, Santana QC, Fourie G, and Steenkamp ET

Subjects
Conserved Sequence, Fusarium genetics, Genes, Fungal, Introns
Abstract

Removal of introns from transcribed RNA represents a crucial step during the production of mRNA in eukaryotes. Available whole-genome sequences and expressed sequence tags (ESTs) have increased our knowledge of this process and revealed various commonalities among eukaryotes. However, certain aspects of intron structure and diversity are taxon-specific, which can complicate the accuracy of in silico gene prediction methods. Using core genes, we evaluated the distribution and architecture of Fusarium circinatum spliceosomal introns, and linked these characteristics to the accuracy of the predicted gene models of the genome of this fungus. We also evaluated intron distribution and architecture in F. verticillioides , F. oxysporum , and F. graminearum , and made comparisons with F. circinatum Results indicated that F. circinatum and the three other Fusarium species have canonical 5' and 3' splice sites, but with subtle differences that are apparently not shared with those of other fungal genera. The polypyrimidine tract of Fusarium introns was also found to be highly divergent among species and genes. Furthermore, the conserved adenosine nucleoside required during the first step of splicing is contained within unique branch site motifs in certain Fusarium introns. Data generated here show that introns of F. circinatum , as well as F. verticillioides , F. oxysporum , and F. graminearum , are characterized by a number of unique features such as the CTHAH and ACCAT motifs of the branch site. Incorporation of such information into genome annotation software will undoubtedly improve the accuracy of gene prediction methods used for Fusarium species and related fungi., (Copyright © 2017 Phasha et al.)

Published
2017
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50. IMA Genome-F 4: Draft genome sequences of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygamai, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata.

Author

Wingfield BD, Ades PK, Al-Naemi FA, Beirn LA, Bihon W, Crouch JA, de Beer ZW, De Vos L, Duong TA, Fields CJ, Fourie G, Kanzi AM, Malapi-Wight M, Pethybridge SJ, Radwan O, Rendon G, Slippers B, Santana QC, Steenkamp ET, Taylor PW, Vaghefi N, van der Merwe NA, Veltri D, and Wingfield MJ

Abstract

The genomes of Chrysoporthe austroafricana, Diplodia scrobiculata, Fusarium nygami, Leptographium lundbergii, Limonomyces culmigenus, Stagonosporopsis tanaceti, and Thielaviopsis punctulata are presented in this genome announcement. These seven genomes are from endophytes, plant pathogens and economically important fungal species. The genome sizes range from 26.6 Mb in the case of Leptographium lundbergii to 44 Mb for Chrysoporthe austroafricana. The availability of these genome data will provide opportunities to resolve longstanding questions regarding the taxonomy of species in these genera, and may contribute to our understanding of the lifestyles through comparative studies with closely related organisms.

Published
2015
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