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262 results on '"Brown, Daren W."'

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

9. A Fusarium verticillioides MAT1-2 Strain near Isogenic to the Sequenced FGSC7600 Strain for Producing Homozygous Multigene Mutants.

Author

Gold, Scott E., Brown, Daren W., Williams, Felicia N., Nadon, Brian D., Vo, Vivian T., and Miller, Christine E.

Subjects
*SEXUAL cycle, *FUNGAL genetics, *GIBBERELLA fujikuroi, *SINGLE nucleotide polymorphisms, *ASEXUAL reproduction
Abstract

Fungal genetic systems ideally combine molecular tools for genome manipulation and a sexual reproduction system to create an informative assortment of combinations of genomic modifications. When employing the sexual cycle to generate multi-mutants, the background genotype variations in the parents may result in progeny phenotypic variation obscuring the effects of combined mutations. Here, to mitigate this variation in Fusarium verticillioides, we generated a MAT1-2 strain that was near isogenic to the sequenced wild-type MAT1-1 strain, FGSC7600. This was accomplished by crossing FGSC7600 with the divergent wild-type MAT1-2 strain FGSC7603 followed by six sequential backcrosses (e.g., six generations) of MAT1-2 progeny to FGSC7600. We sequenced each generation and mapped recombination events. The parental cross involved twenty-six crossovers on nine of the eleven chromosomes. The dispensable chromosome 12, found in FGSC7603 but lacking in FGSC7600, was not present in the progeny post generation five. Inheritance of complete chromosomes without crossover was frequently observed. A deletion of approximately 140 kilobases, containing 54 predicted genes on chromosome 4, occurred in generation 4 and was retained in generation 5 indicating that these genes are dispensable for growth and both asexual and sexual reproduction. The final MAT1-2 strain TMRU10/35 is about 93% identical to FGSC7600. TMRU10/35 is available from the Fungal Genetics Stock Center as FGSC27326 and from the ARS Culture Collection as NRRL64809. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

Author

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

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

Author

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

Published
2014

25. FUSARIUM-ID v.3.0: An Updated, Downloadable Resource for Fusarium Species Identification

Author

Torres-Cruz, Terry J., primary, Whitaker, Briana K., additional, Proctor, Robert H., additional, Broders, Kirk, additional, Laraba, Imane, additional, Kim, Hye-Seon, additional, Brown, Daren W., additional, O’Donnell, Kerry, additional, Estrada-Rodríguez, Tania L., additional, Lee, Yong-Hwan, additional, Cheong, Kyeongchae, additional, Wallace, Emma C., additional, McGee, Chyanna T., additional, Kang, Seogchan, additional, and Geiser, David M., additional

Published
2022
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26. DNA Sequence-Based Identification ofFusarium: A Work in Progress

Author

O’Donnell, Kerry, primary, Whitaker, Briana K., additional, Laraba, Imane, additional, Proctor, Robert H., additional, Brown, Daren W., additional, Broders, Kirk, additional, Kim, Hye-Seon, additional, McCormick, Susan P., additional, Busman, Mark, additional, Aoki, Takayuki, additional, Torres-Cruz, Terry J., additional, and Geiser, David M., additional

Published
2022
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31. Additional file 9 of Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

Author

Hye-Seon Kim, Lohmar, Jessica M., Busman, Mark, Brown, Daren W., Naumann, Todd A., Divon, Hege H., Lysøe, Erik, Uhlig, Silvio, and Proctor, Robert H.

Abstract

Additional file 9. Proposed sphingofungin C biosynthetic pathway inferred by comparison of the chemical structure of sphingofungin C and the content of enzyme-encoding genes in the putative sphingofungin biosynthetic gene cluster. Proposed functions of genes in the putative sphingofungin biosynthetic gene cluster based on sequence homology to genes of known function (Additional file 9 Table 1). Arrangement of genes in the putative sphingofungin biosynthetic gene cluster. Arrows represent genes and point in the direction of transcription. The designations for the 13 genes in the cluster are Afu3g14670 – Afu3g14770, Afu3g14790 and Afug14800. However, only the last three digits of these designations are shown above the genes in the figure. Genes encoding the PKS, AT and SDR enzymes are indicated (Additional file 9 Figure 1). Proposed sphingofungin C biosynthetic pathway (Additional file 9 Figure 2).

Published
2020
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32. Additional file 5 of Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

Author

Hye-Seon Kim, Lohmar, Jessica M., Busman, Mark, Brown, Daren W., Naumann, Todd A., Divon, Hege H., Lysøe, Erik, Uhlig, Silvio, and Proctor, Robert H.

Abstract

Additional file 5. Phylogenetic tree from NOTUNG reconciliation analysis inferred horizontal transfer events for each SAM cluster, SAM1 (Additional file 5 Figure 1), SAM2 (Additional file 5 Figure 2), SAM3 (Additional file 5 Figure 3), SAM4 (Additional file 5 Figure 4), and SAM5 (Additional file 5 Figure 5). In the NOTUNG analysis, the species tree was inferred from concatenated alignments of the coding region sequences of 13 housekeeping genes from 96 representative Fusarium strains (Additional file 5 Figure 6).

Published
2020
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33. Additional file 8 of Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

Author

Hye-Seon Kim, Lohmar, Jessica M., Busman, Mark, Brown, Daren W., Naumann, Todd A., Divon, Hege H., Lysøe, Erik, Uhlig, Silvio, and Proctor, Robert H.

Abstract

Additional file 8. Deletion analysis of the SAM5 PKS gene, AOD1, in F. babinda NRRL 25539 and F. tricinctum strain NRRL 25481.

Published
2020
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35. Additional file 2 of Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

Author

Hye-Seon Kim, Lohmar, Jessica M., Busman, Mark, Brown, Daren W., Naumann, Todd A., Divon, Hege H., Uhlig, Silvio, and Proctor, Robert H.

Abstract

Additional file 2. Organization of the genes and flanking genes in putative SAM clusters: SAM2 (Additional file 2 Figure 1), SAM3 (Additional file 2 Figure 2), SAM5 (Additional file 2 Figure 3) and FUM (Additional file 2 Figure 4) from two representative Fusarium strains (red-outlined box) in phylogenetic tree inferred by maximum likelihood analysis of nucleotide sequences of PKS gene coding regions with 1000 bootstrap. Colored arrows represent genes and flanking genes of each SAM clusters. The direction of the arrows indicates direction of gene transcriptions. Yellow arrows indicate PKS, SDR and AT genes; and colors indicate genes predicted to have other functions based on sequence homology. The prefixes for locus tag number of gene or flanking gene designations corresponding to each SAM clusters are listed in Additional file 3.

Published
2020
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36. Additional file 1 of Identification and distribution of gene clusters required for synthesis of sphingolipid metabolism inhibitors in diverse species of the filamentous fungus Fusarium

Author

Hye-Seon Kim, Lohmar, Jessica M., Busman, Mark, Brown, Daren W., Naumann, Todd A., Divon, Hege H., Lysøe, Erik, Uhlig, Silvio, and Proctor, Robert H.

Abstract

Additional file 1. Phylogenies inferred by maximum likelihood analysis of alignment of predicted amino acid sequences of SAM polyketide synthase (PKS, Additional file 1 Figure 1), aminotransferase (AT, Additional file 1 Figure 2) and short-chain dehydrogenase reductase (SDR, Additional file 1 Figure 3) genes from Fusarium species and other ascomycetous fungi. The six phylogenetically distinct clades are color-coded according to genes in SAM cluster and labeled with known fumonisin and novel SAM1-SAM5 to the right of the tree. The prefix for protein designations for PKS, AT and SDR gene homologs from other ascomycetous fungi corresponding to NCBI GenBank accession are listed in Additional file 6 and the locus tag numbers for Fusarium genes are listed in Additional file 3.

Published
2020
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42. Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

Author

Ma, Li-Jun, van der Does, Charlotte H., 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, Carmen M., Sain, Divya, Sakthikumar, Sharadha, Sykes, Sean, Schwartz, David C., Turgeon, Gillian B., Wapinski, Ilan, Yoder, Olen, Young, Sarah, Zeng, Qiandong, Zhou, Shiguo, Galagan, James, Cuomo, Christina A., Kistler, Corby H., and Rep, Martijn

Published
2010
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45. Supplemental Material for Rhoades et al., 2019

Author

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

Subjects
FOS: Biological sciences, Genetics
Abstract

Supplementary Information

Published
2019
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48. 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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