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1. 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, 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, López-Berges, Manuel S, 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, Mulè, Giuseppina, Geiser, David M, 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, López-Berges, Manuel S, 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

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

2. 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, 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, López-Berges, Manuel S, 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, Mulè, Giuseppina, Geiser, David M, 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, López-Berges, Manuel S, 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

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

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 M S, 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 J. N., 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 C Y, 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, N M I, Monod, Michel, Moretti, Antonio, Mostert, Diane, Mulè, Giuseppina, Munaut, Françoise, Munkvold, Gary P, Nicholson, Paul, Nucci, Marcio, O'Donnell, Kerry, Pasquali, Matias, Pfenning, Ludwig H, Prigitano, Anna, Proctor, Robert H, Ranque, Stéphane, Rehner, Stephen A, Rep, Martijn, Rodríguez-Alvarado, Gerardo, Rose, Lindy Joy, Roth, Mitchell G, Ruiz-Roldán, Carmen, Saleh, Amgad A, Salleh, Baharuddin, Sang, Hyunkyu, Scandiani, María Mercedes, Scauflaire, Jonathan, Schmale, David G, Short, Dylan P G, Šišić, Adnan, Smith, Jason A, Smyth, Christopher W, Son, Hokyoung, Spahr, Ellie, Stajich, Jason E, Steenkamp, Emma, Steinberg, Christian, Subramaniam, Rajagopal, Suga, Haruhisa, Summerell, Brett A, Susca, Antonella, Swett, Cassandra L, Toomajian, Christopher, Torres-Cruz, Terry J, Tortorano, Anna M, Urban, Martin, Vaillancourt, Lisa J, Vallad, Gary E, van der Lee, Theo A J, Vanderpool, Dan, van Diepeningen, Anne D, Vaughan, Martha M, Venter, Eduard, Vermeulen, Marcele, Verweij, Paul E, Viljoen, Altus, Waalwijk, Cees, Wallace, Emma C, Walther, Grit, Wang, Jie, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Wood, Ana K M, Xu, Jin-Rong, Yang, Xiao-Bing, Yli-Mattila, Tapani, Yun, Sung-Hwan, Zakaria, Latiffah, Zhang, Hao, Zhang, Ning, Zhang, Sean X, Zhang, Xue, Geiser, David M, Al-Hatmi, Abdullah M S, 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 J. N., 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 C Y, 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, N M I, Monod, Michel, Moretti, Antonio, Mostert, Diane, Mulè, Giuseppina, Munaut, Françoise, Munkvold, Gary P, Nicholson, Paul, Nucci, Marcio, O'Donnell, Kerry, Pasquali, Matias, Pfenning, Ludwig H, Prigitano, Anna, Proctor, Robert H, Ranque, Stéphane, Rehner, Stephen A, Rep, Martijn, Rodríguez-Alvarado, Gerardo, Rose, Lindy Joy, Roth, Mitchell G, Ruiz-Roldán, Carmen, Saleh, Amgad A, Salleh, Baharuddin, Sang, Hyunkyu, Scandiani, María Mercedes, Scauflaire, Jonathan, Schmale, David G, Short, Dylan P G, Šišić, Adnan, Smith, Jason A, Smyth, Christopher W, Son, Hokyoung, Spahr, Ellie, Stajich, Jason E, Steenkamp, Emma, Steinberg, Christian, Subramaniam, Rajagopal, Suga, Haruhisa, Summerell, Brett A, Susca, Antonella, Swett, Cassandra L, Toomajian, Christopher, Torres-Cruz, Terry J, Tortorano, Anna M, Urban, Martin, Vaillancourt, Lisa J, Vallad, Gary E, van der Lee, Theo A J, Vanderpool, Dan, van Diepeningen, Anne D, Vaughan, Martha M, Venter, Eduard, Vermeulen, Marcele, Verweij, Paul E, Viljoen, Altus, Waalwijk, Cees, Wallace, Emma C, Walther, Grit, Wang, Jie, Ward, Todd J, Wickes, Brian L, Wiederhold, Nathan P, Wingfield, Michael J, Wood, Ana K M, Xu, Jin-Rong, Yang, Xiao-Bing, Yli-Mattila, Tapani, Yun, Sung-Hwan, Zakaria, Latiffah, Zhang, Hao, Zhang, Ning, Zhang, Sean X, and Zhang, Xue

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

4. Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora

Author

Rhoades, Nicholas A., Harvey, Austin M., Samarajeewa, Dilini A., Svedberg, Jesper, Yusifov, Aykhan, Abusharekh, Anna, Manitchotpisit, Pennapa, Brown, Daren W., Sharp, Kevin J., Rehard, David G., Peters, Joshua, Ostolaza-Maldonado, Xavier, Stephenson, Jackson, Shiu, Patrick K. T., Johannesson, Hanna, Hammond, Thomas M., Rhoades, Nicholas A., Harvey, Austin M., Samarajeewa, Dilini A., Svedberg, Jesper, Yusifov, Aykhan, Abusharekh, Anna, Manitchotpisit, Pennapa, Brown, Daren W., Sharp, Kevin J., Rehard, David G., Peters, Joshua, Ostolaza-Maldonado, Xavier, Stephenson, Jackson, Shiu, Patrick K. T., Johannesson, Hanna, and Hammond, Thomas M.

Abstract

Sk-2 is a meiotic drive element that was discovered in wild populations of Neurospora fungi over 40 years ago. While early studies quickly determined that Sk-2 transmits itself through sexual reproduction in a biased manner via spore killing, the genetic factors responsible for this phenomenon have remained mostly unknown. Here, we identify and characterize rfk-1, a gene required for Sk-2-based spore killing. The rfk-1 gene contains four exons, three introns, and two stop codons, the first of which undergoes RNA editing to a tryptophan codon during sexual development. Translation of an unedited rfk-1 transcript in vegetative tissue is expected to produce a 102-amino acid protein, whereas translation of an edited rfk-1 transcript in sexual tissue is expected to produce a protein with 130 amino acids. These findings indicate that unedited and edited rfk-1 transcripts exist and that these transcripts could have different roles with respect to the mechanism of meiotic drive by spore killing. Regardless of RNA editing, spore killing only succeeds if rfk-1 transcripts avoid silencing caused by a genome defense process called meiotic silencing by unpaired DNA (MSUD). We show that rfk-1's MSUD avoidance mechanism is linked to the genomic landscape surrounding the rfk-1 gene, which is located near the Sk-2 border on the right arm of chromosome III. In addition to demonstrating that the location of rfk-1 is critical to spore-killing success, our results add to accumulating evidence that MSUD helps protect Neurospora genomes from complex meiotic drive elements.

Published
2019
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5. Extensive sampling of basidiomycete genomes demonstrates inadequate of the white rot/ brown rot paradigm for wood decay fungi

Author

Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, Grigoriev, Igor V., Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, and Grigoriev, Igor V.

Published
2014

6. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

Author

Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, Grigoriev, Igor V., Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, and Grigoriev, Igor V.

Abstract

Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wooddecay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Published
2014

7. Extensive sampling of basidiomycete genomes demonstrates inadequate of the white rot/ brown rot paradigm for wood decay fungi

Author

Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, Grigoriev, Igor V., Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, and Grigoriev, Igor V.

Published
2014

8. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

Author

Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, Grigoriev, Igor V., Riley, Robert, Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, and Grigoriev, Igor V.

Abstract

Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wooddecay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Published
2014

9. One Fungus, One Name: Defining the Genus Fusarium in a Scientifically Robust Way That Preserves Longstanding Use

Author

UCL - SST/ELI/ELIM - Applied Microbiology, Geiser, David M., Aoki, Takayuki, Bacon, Charles W., Baker, Scott E., Bhattacharyya, Madan K., Brandt, Mary E., Brown, Daren W., Burgess, Lester W., Chulze, Sofia, Coleman, Jeffrey J., Correll, James C., Covert, Sarah F., Crous, Pedro W., Cuomo, Christina A., De Hoog, G. Sybren, Di Pietro, Antonio, Elmer, Wade H., Epstein, Lynn, Frandsen, Rasmus J. N., Freeman, Stanley, Gagkaeva, Tatiana, Glenn, Anthony E., Gordon, Thomas R., Gregory, Nancy F., Hammond-Kosack, Kim E., Hanson, Linda E., Jímenez-Gasco, María del Mar, Kang, Seogchan, Kistler, H. Corby, Kuldau, Gretchen A., Leslie, John F., Logrieco, Antonio, Lu, Guozhong, Lysøe, Erik, Ma, Li-Jun, McCormick, Susan P., Migheli, Quirico, Moretti, Antonio, Munaut, Françoise, O'Donnell, Kerry, Pfenning, Ludwig, Ploetz, Randy C., Proctor, Robert H., Rehner, Stephen A., Robert, Vincent A. R. G., Rooney, Alejandro P., bin Salleh, Baharuddin, Scandiani, Maria Mercedes, Scauflaire, Jonathan, Short, Dylan P. G., Steenkamp, Emma, Suga, Haruhisa, Summerell, Brett A., Sutton, Deanna A., Thrane, Ulf, Trail, Francis, Van Diepeningen, Anne, VanEtten, Hans D., Viljoen, Altus, Waalwijk, Cees, Ward, Todd J., Wingfield, Michael J., Xu, Jin-Rong, Yang, Xiao-Bing, Yli-Mattila, Tapani, Zhang, Ning, UCL - SST/ELI/ELIM - Applied Microbiology, Geiser, David M., Aoki, Takayuki, Bacon, Charles W., Baker, Scott E., Bhattacharyya, Madan K., Brandt, Mary E., Brown, Daren W., Burgess, Lester W., Chulze, Sofia, Coleman, Jeffrey J., Correll, James C., Covert, Sarah F., Crous, Pedro W., Cuomo, Christina A., De Hoog, G. Sybren, Di Pietro, Antonio, Elmer, Wade H., Epstein, Lynn, Frandsen, Rasmus J. N., Freeman, Stanley, Gagkaeva, Tatiana, Glenn, Anthony E., Gordon, Thomas R., Gregory, Nancy F., Hammond-Kosack, Kim E., Hanson, Linda E., Jímenez-Gasco, María del Mar, Kang, Seogchan, Kistler, H. Corby, Kuldau, Gretchen A., Leslie, John F., Logrieco, Antonio, Lu, Guozhong, Lysøe, Erik, Ma, Li-Jun, McCormick, Susan P., Migheli, Quirico, Moretti, Antonio, Munaut, Françoise, O'Donnell, Kerry, Pfenning, Ludwig, Ploetz, Randy C., Proctor, Robert H., Rehner, Stephen A., Robert, Vincent A. R. G., Rooney, Alejandro P., bin Salleh, Baharuddin, Scandiani, Maria Mercedes, Scauflaire, Jonathan, Short, Dylan P. G., Steenkamp, Emma, Suga, Haruhisa, Summerell, Brett A., Sutton, Deanna A., Thrane, Ulf, Trail, Francis, Van Diepeningen, Anne, VanEtten, Hans D., Viljoen, Altus, Waalwijk, Cees, Ward, Todd J., Wingfield, Michael J., Xu, Jin-Rong, Yang, Xiao-Bing, Yli-Mattila, Tapani, and Zhang, Ning

Abstract

In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.

Published
2013

10. Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

Author

Brown, Daren W., Butchko, Robert A. E., Baker, Scott E., Proctor, Robert A., Brown, Daren W., Butchko, Robert A. E., Baker, Scott E., and Proctor, Robert A.

Abstract

Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain-based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, Fusarium graminearum, Fusarium oxysporum, and Fusarium solani identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted phylogenomic and functional domain analyses. The resulting geneaology suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-offunction due to nucleotide mutations. Transcriptional analysis indicates that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

Published
2012

11. Lae1 regulates expression of multiple secondary metabolite gene clusters in Fusarium verticillioides

Author

Butchko, Robert A.E., Brown, Daren W., Busman, Mark, Tudzynski, Bettina, Wiemann, Philipp, Butchko, Robert A.E., Brown, Daren W., Busman, Mark, Tudzynski, Bettina, and Wiemann, Philipp

Abstract

The filamentous fungus Fusarium verticillioides can cause disease of maize and is capable of producing fumonisins, a family of toxic secondary metabolites linked to esophageal cancer and neural tube defects in humans and lung edema in swine and leukoencephalomalacia in equines. The expression of fumonisin biosynthetic genes is influenced by broad-domain transcription factors (global regulators) and Fum21, a pathway-specific transcription factor. LaeA is a global regulator that in Aspergillus nidulans, affects the expression of multiple secondary metabolite gene clusters by modifying heterochromatin structure. Here, we employed gene deletion analysis to assess the effect of loss of a F. verticillioides laeA orthologue, LAE1, on genome-wide gene expression and secondary metabolite production. Loss of Lae1 resulted in reduced expression of gene clusters responsible for synthesis of the secondary metabolites bikaverin, fumonisins, fusaric acid and fusarins as well as two clusters for which the corresponding secondary metabolite is unknown. Analysis of secondary metabolites revealed that, in contrast to a previously described Fusarium fujikuroi lae1 mutant, bikaverin production is reduced. Fumonisin production is unchanged in the F. verticillioides lae1 mutant. Complementation of the F. verticillioides mutant resulted in increased fumonisin production.

Published
2012

12. Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioides

Author

Brown, Daren W., Butchko, Robert A. E., Busman, Mark, Proctor, Robert H., Brown, Daren W., Butchko, Robert A. E., Busman, Mark, and Proctor, Robert H.

Abstract

The genus Fusarium is of concern to agricultural production and food/feed safety because of its ability to cause crop disease and to produce mycotoxins. Understanding the genetic basis for production of mycotoxins and other secondary metabolites (SMs) has the potential to limit crop disease and mycotoxin contamination. In fungi, SM biosynthetic genes are typically located adjacent to one another in clusters of coexpressed genes. Such clusters typically include a core gene, responsible for synthesis of an initial chemical, and several genes responsible for chemical modifications, transport, and/or regulation. Fusarium verticillioides is one of the most common pathogens of maize and produces a variety of SMs of concern. Here, we employed whole genome expression analysis and utilized existing knowledge of polyketide synthase (PKS) genes, a common cluster core gene, to identify three novel clusters of co-expressed genes in F. verticillioides. Functional analysis of the PKS genes linked the clusters to production of three known Fusarium SMs, a violet pigment in sexual fruiting bodies (perithecia) and the mycotoxins fusarin C and fusaric acid. The results indicate that microarray analysis of RNA derived from culture conditions that induce differential gene expression can be an effective tool for identifying SM biosynthetic gene clusters.

Published
2012

13. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium.

Author

Ma, Li-Jun, van der Does, H Charlotte, Borkovich, Katherine A, Coleman, Jeffrey J, Daboussi, Marie-Josée, Di Pietro, Antonio, Dufresne, Marie, Freitag, Michael, Grabherr, Manfred, Henrissat, Bernard, Houterman, Petra M, Kang, Seogchan, Shim, Won-Bo, Woloshuk, Charles, Xie, Xiaohui, Xu, Jin-Rong, Antoniw, John, Baker, Scott E, Bluhm, Burton H, Breakspear, Andrew, Brown, Daren W, Butchko, Robert A E, Chapman, Sinead, Coulson, Richard, Coutinho, Pedro M, Danchin, Etienne G J, Diener, Andrew, Gale, Liane R, Gardiner, Donald M, Goff, Stephen, Hammond-Kosack, Kim E, Hilburn, Karen, Hua-Van, Aurélie, Jonkers, Wilfried, Kazan, Kemal, Kodira, Chinnappa D, Koehrsen, Michael, Kumar, Lokesh, Lee, Yong-Hwan, Li, Liande, Manners, John M, Miranda-Saavedra, Diego, Mukherjee, Mala, Park, Gyungsoon, Park, Jongsun, Park, Sook-Young, Proctor, Robert H, Regev, Aviv, Ruiz-Roldan, M Carmen, Sain, Divya, Sakthikumar, Sharadha, Sykes, Sean, Schwartz, David C, Turgeon, B Gillian, Wapinski, Ilan, Yoder, Olen, Young, Sarah, Zeng, Qiandong, Zhou, Shiguo, Galagan, James, Cuomo, Christina A, Kistler, H Corby, Rep, Martijn, Ma, Li-Jun, van der Does, H Charlotte, Borkovich, Katherine A, Coleman, Jeffrey J, Daboussi, Marie-Josée, Di Pietro, Antonio, Dufresne, Marie, Freitag, Michael, Grabherr, Manfred, Henrissat, Bernard, Houterman, Petra M, Kang, Seogchan, Shim, Won-Bo, Woloshuk, Charles, Xie, Xiaohui, Xu, Jin-Rong, Antoniw, John, Baker, Scott E, Bluhm, Burton H, Breakspear, Andrew, Brown, Daren W, Butchko, Robert A E, Chapman, Sinead, Coulson, Richard, Coutinho, Pedro M, Danchin, Etienne G J, Diener, Andrew, Gale, Liane R, Gardiner, Donald M, Goff, Stephen, Hammond-Kosack, Kim E, Hilburn, Karen, Hua-Van, Aurélie, Jonkers, Wilfried, Kazan, Kemal, Kodira, Chinnappa D, Koehrsen, Michael, Kumar, Lokesh, Lee, Yong-Hwan, Li, Liande, Manners, John M, Miranda-Saavedra, Diego, Mukherjee, Mala, Park, Gyungsoon, Park, Jongsun, Park, Sook-Young, Proctor, Robert H, Regev, Aviv, Ruiz-Roldan, M Carmen, Sain, Divya, Sakthikumar, Sharadha, Sykes, Sean, Schwartz, David C, Turgeon, B Gillian, Wapinski, Ilan, Yoder, Olen, Young, Sarah, Zeng, Qiandong, Zhou, Shiguo, Galagan, James, Cuomo, Christina A, Kistler, H Corby, and Rep, Martijn

Abstract

Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.

Published
2010
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14. The Fusarium verticillioides FUM Gene Cluster Encodes a Zn(II)2Cys6 Protein That Affects FUM Gene Expression and Fumonisin Production

Author

Brown, Daren W., Butchko, Robert A. E., Busman, Mark, Proctor, Robert H., Brown, Daren W., Butchko, Robert A. E., Busman, Mark, and Proctor, Robert H.

Abstract

Fumonisins are mycotoxins produced by some Fusarium species and can contaminate maize or maize products. Ingestion of fumonisins is associated with diseases, including cancer and neural tube defects, in humans and animals. In fungi, genes involved in the synthesis of mycotoxins and other secondary metabolites are often located adjacent to each other in gene clusters. Such genes can encode structural enzymes, regulatory proteins, and/or proteins that provide self-protection. The fumonisin biosynthetic gene cluster includes 16 genes, none of which appear to play a role in regulation. In this study, we identified a previously undescribed gene (FUM21) located adjacent to the fumonisin polyketide synthase gene, FUM1. The presence of a Zn(II)2Cys6 DNA-binding domain in the predicted protein suggested that FUM21 was involved in transcriptional regulation. FUM21 deletion (delta fum21) mutants produce little to no fumonisin in cracked maize cultures but some FUM1 and FUM8 transcripts in a liquid GYAM medium. Complementation of a delta fum21 mutant with a wild-type copy of the gene restored fumonisin production. Analysis of FUM21 cDNAs identified four alternative splice forms (ASFs), and microarray analysis indicated the ASFs were differentially expressed. Based on these data, we present a model for how FUM21 ASFs may regulate fumonisin biosynthesis.

Published
2007

15. Fusarium genomic resources: Tools to limit crop diseases and mycotoxin contamination

Author

Brown, Daren W., Butchko, Robert A. E., Proctor, Robert H., Brown, Daren W., Butchko, Robert A. E., and Proctor, Robert H.

Abstract

It has been almost 10 years since Joan Bennett suggested that fungal biologists create a ‘‘wish list’’ for fungal genome sequences (Bennett JW. White paper: Genomics for filamentous fungi. Fungal Genet Biol 1997; 21: 3–7). The availability of over 200 review papers concerning fungal genomics is a reflection of significant progress with a diversity of fungal species. Although much progress has been made, the use of genomic data to study mycotoxin synthesis and function, pathogenesis and other aspects of fungal biology is in its infancy. Here, we briefly present the status of publicly available genomic resources for Fusarium, a genus of important plant pathogenic and mycotoxin-producing fungi of worldwide concern. Preliminary examination of microarray data collected from F. verticillioides liquid cultures provides evidence of widespread differential gene expression over time.

Published
2006

16. Comparative analysis of 87,000 expressed sequence tags from the fumonisin-producing fungus Fusarium verticillioides

Author

Brown, Daren W., Cheung, Foo, Proctor, Robert H., Butchko, Robert A. E., Zheng, Li, Lee, Yuandan, Utterback, Teresa, Smith, Shannon, Feldblyum, Tamara, Green, Anthony E., Plattner, Ronald D., Kendra, David F., Town, Christopher D., Whitelaw, Catherine A., Brown, Daren W., Cheung, Foo, Proctor, Robert H., Butchko, Robert A. E., Zheng, Li, Lee, Yuandan, Utterback, Teresa, Smith, Shannon, Feldblyum, Tamara, Green, Anthony E., Plattner, Ronald D., Kendra, David F., Town, Christopher D., and Whitelaw, Catherine A.

Abstract

Fusarium verticillioides (teleomorph Gibberella moniliformis) is a pathogen of maize worldwide and produces fumonisins, a family of mycotoxins that have been associated with several animal diseases as well as cancer in humans. In this study, we sought to identify fungal genes that affect fumonisin production and/or the plant–fungal interaction. We generated over 87,000 expressed sequence tags from nine different cDNA libraries that correspond to 11,119 unique sequences and are estimated to represent 80% of the genomic complement of genes. A comparative analysis of the libraries showed that all 15 genes in the fumonisin gene cluster were differentially expressed. In addition, nine candidate fumonisin regulatory genes and a number of genes that may play a role in plant–fungal interaction were identified. Analysis of over 700 FUM gene transcripts from five different libraries provided evidence for transcripts with unspliced introns and spliced introns with alternative 3' splice sites. The abundance of the alternative splice forms and the frequency with which they were found for genes involved in the biosynthesis of a single family of metabolites as well as their differential expression suggest they may have a biological function. Finally, analysis of an EST that aligns to genomic sequence between FUM12 and FUM13 provided evidence for a previously unidentified gene (FUM20) in the FUM gene cluster.

Published
2005

17. Evolution of structural diversity of trichothecenes, a family of toxins produced by plant pathogenic and entomopathogenic fungi

Author

Microbiologia, Proctor, Robert Henry, McCormick, Susan P., Kim, Hye-Seon, Cardoza, Rosa E., Stanley, April M., Lindo Yugueros, Laura, Kelly, Amy, Brown, Daren W., Lee, Theresa, Vaughan, Martha Marie, Alexander, Nancy J., Busman, Mark, Gutiérrez Martín, Santiago, Microbiologia, Proctor, Robert Henry, McCormick, Susan P., Kim, Hye-Seon, Cardoza, Rosa E., Stanley, April M., Lindo Yugueros, Laura, Kelly, Amy, Brown, Daren W., Lee, Theresa, Vaughan, Martha Marie, Alexander, Nancy J., Busman, Mark, and Gutiérrez Martín, Santiago

Abstract

[EN] Trichothecenes are a family of terpenoid toxins produced by multiple genera of fungi, including plant and insect pathogens. Some trichothecenes produced by the fungus Fusarium are among the mycotoxins of greatest concern to food and feed safety because of their toxicity and frequent occurrence in cereal crops, and trichothecene production contributes to pathogenesis of some Fusarium species on plants. Collectively, fungi produce over 150 trichothecene analogs: i.e., molecules that share the same core structure but differ in patterns of substituents attached to the core structure. Here, we carried out genomic, phylogenetic, gene-function, and analytical chemistry studies of strains from nine fungal genera to identify genetic variation responsible for trichothecene structural diversity and to gain insight into evolutionary processes that have contributed to the variation. The results indicate that structural diversity has resulted from gain, loss, and functional changes of trichothecene biosynthetic (TRI) genes. The results also indicate that the presence of some substituents has arisen independently in different fungi by gain of different genes with the same function. Variation in TRI gene duplication and number of TRI loci was also observed among the fungi examined, but there was no evidence that such genetic differences have contributed to trichothecene structural variation. We also inferred ancestral states of the TRI cluster and trichothecene biosynthetic pathway, and proposed scenarios for changes in trichothecene structures during divergence of TRI cluster homologs. Together, our findings provide insight into evolutionary processes responsible for structural diversification of toxins produced by pathogenic fungi

18. Identification of polyketide synthase genes required for aspinolide biosynthesis in Trichoderma arundinaceum

Author

Microbiologia, Cardoza, Rosa E., McCormick, Susan P., Izquierdo-Bueno, Inmaculada, Martínez-Reyes, Natalia, Lindo, Laura, Brown, Daren W., Collado, Isidro G., Proctor, Robert H., Gutiérrez Martín, Santiago, Microbiologia, Cardoza, Rosa E., McCormick, Susan P., Izquierdo-Bueno, Inmaculada, Martínez-Reyes, Natalia, Lindo, Laura, Brown, Daren W., Collado, Isidro G., Proctor, Robert H., and Gutiérrez Martín, Santiago

Abstract

[EN] The fungus Trichoderma arundinaceum exhibits biological control activity against crop diseases caused by other fungi. Two mechanisms that likely contribute to this activity are upregulation of plant defenses and production of two types of antifungal secondary metabolites: the sesquiterpenoid harzianum A (HA) and the polyketide-derived aspinolides. The goal of the current study was to identify aspinolide biosynthetic genes as part of an effort to understand how these metabolites contribute to the biological control activity of T. arundinaceum. Comparative genomics identified two polyketide synthase genes (asp1 and asp2) that occur in T. arundinaceum and Aspergillus ochraceus, which also produces aspinolides. Gene deletion and biochemical analyses in T. arundinaceum indicated that both genes are required for aspinolide production: asp2 for formation of a 10-member lactone ring and asp1 for formation of a butenoyl subsituent at position 8 of the lactone ring. Gene expression and comparative genomics analyses indicated that asp1 and asp2 are located within a gene cluster that occurs in both T. arundinaceum and A. ochraceus. A survey of genome sequences representing 35 phylogenetically diverse Trichoderma species revealed that intact homologs of the cluster occurred in only two other species, which also produced aspinolides. An asp2 mutant inhibited fungal growth more than the wild type, but an asp1 mutant did not, and the greater inhibition by the asp2 mutant coincided with increased HA production. These findings indicate that asp1 and asp2 are aspinolide biosynthetic genes and that loss of either aspinolide or HA production in T. arundinaceum can be accompanied by increased production of the other metabolite(s).

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