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527 results on '"Hammond-Kosack, Kim"'

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

Author

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

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

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

Published
2021

5. Author Reply to Peer Reviews of Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

Author

Hill, Rowena, primary, Grey, Michelle, additional, Olivera Fedi, Mariano, additional, Smith, Daniel P, additional, Canning, Gail, additional, Ward, Sabrina J, additional, Irish, Naomi, additional, Smith, Jade, additional, McMillan, Vanessa, additional, Hammond, Jess, additional, Osborne, Sarah-Jane, additional, Chancellor, Tania, additional, Swarbreck, David, additional, Hall, Neil, additional, Palma-Guerrero, Javier, additional, Hammond-Kosack, Kim E, additional, and McMullan, Mark, additional

Published
2024
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6. The trichothecene mycotoxin deoxynivalenol facilitates cell‐to‐cell invasion during wheat‐tissue colonization by Fusarium graminearum.

Author

Armer, Victoria J., Urban, Martin, Ashfield, Tom, Deeks, Michael J., and Hammond‐Kosack, Kim E.

Subjects
DEOXYNIVALENOL, PLANT cell walls, FUSARIUM, CELL analysis, PLASMODESMATA
Abstract

Fusarium head blight disease on small‐grain cereals is primarily caused by the ascomycete fungal pathogen Fusarium graminearum. Infection of floral spike tissues is characterized by the biosynthesis and secretion of potent trichothecene mycotoxins, of which deoxynivalenol (DON) is widely reported due to its negative impacts on grain quality and consumer safety. The TRI5 gene encodes an essential enzyme in the DON biosynthesis pathway and the single gene deletion mutant, ΔTri5, is widely reported to restrict disease progression to the inoculated spikelet. In this study, we present novel bioimaging evidence revealing that DON facilitates the traversal of the cell wall through plasmodesmata, a process essential for successful colonization of host tissue. Chemical complementation of ΔTri5 did not restore macro‐ or microscopic phenotypes, indicating that DON secretion is tightly regulated both spatially and temporally. A comparative qualitative and quantitative morphological cellular analysis revealed infections had no impact on plant cell wall thickness. Immunolabelling of callose at plasmodesmata during infection indicates that DON can increase deposits when applied exogenously but is reduced when F. graminearum hyphae are present. This study highlights the complexity of the interconnected roles of mycotoxin production, cell wall architecture and plasmodesmata in this highly specialized interaction. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

Author

Hill, Rowena, primary, Grey, Michelle, additional, Fedi, Mariano Olivera, additional, Smith, Daniel, additional, Ward, Sabrina J., additional, Canning, Gail, additional, Irish, Naomi, additional, Smith, Jade, additional, McMillan, Vanessa E., additional, Hammond, Jess, additional, Osborne, Sarah-Jane, additional, Chancellor, Tania, additional, Swarbreck, David, additional, Hall, Neil, additional, Palma-Guerrero, Javier, additional, Hammond-Kosack, Kim E., additional, and McMullan, Mark, additional

Published
2024
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11. Exploring the family feud: a fungal endophyte induces local cell wall-mediated resistance in wheat roots against the closely related "take-all" pathogen

Author

Chancellor, Tania, primary, Smith, Daniel P, additional, Chen, Wanxin, additional, Clark, Suzanne J, additional, Venter, Eudri, additional, Halsey, Kirstie, additional, McMillan, Vanessa, additional, Canning, Gail, additional, Hammond-Kosack, Kim E., additional, and Palma-Guerrero, Javier, additional

Published
2023
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17. Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

Author

Goodwin, Stephen B, M'barek, Sarrah Ben, Dhillon, Braham, Wittenberg, Alexander HJ, Crane, Charles F, Hane, James K, Foster, Andrew J, Van der Lee, Theo AJ, Grimwood, Jane, Aerts, Andrea, Antoniw, John, Bailey, Andy, Bluhm, Burt, Bowler, Judith, Bristow, Jim, van der Burgt, Ate, Canto-Canché, Blondy, Churchill, Alice CL, Conde-Ferràez, Laura, Cools, Hans J, Coutinho, Pedro M, Csukai, Michael, Dehal, Paramvir, De Wit, Pierre, Donzelli, Bruno, van de Geest, Henri C, van Ham, Roeland CHJ, Hammond-Kosack, Kim E, Henrissat, Bernard, Kilian, Andrzej, Kobayashi, Adilson K, Koopmann, Edda, Kourmpetis, Yiannis, Kuzniar, Arnold, Lindquist, Erika, Lombard, Vincent, Maliepaard, Chris, Martins, Natalia, Mehrabi, Rahim, Nap, Jan PH, Ponomarenko, Alisa, Rudd, Jason J, Salamov, Asaf, Schmutz, Jeremy, Schouten, Henk J, Shapiro, Harris, Stergiopoulos, Ioannis, Torriani, Stefano FF, Tu, Hank, de Vries, Ronald P, Waalwijk, Cees, Ware, Sarah B, Wiebenga, Ad, Zwiers, Lute-Harm, Oliver, Richard P, Grigoriev, Igor V, and Kema, Gert HJ

Subjects
Chromosomes, Fungal, Ascomycota, Triticum, Plant Diseases, Gene Rearrangement, Synteny, Genome, Fungal, Genetics, Infectious Diseases, Biotechnology, 2.2 Factors relating to the physical environment, Infection, Developmental Biology
Abstract

The plant-pathogenic fungus Mycosphaerella graminicola (asexual stage: Septoria tritici) causes septoria tritici blotch, a disease that greatly reduces the yield and quality of wheat. This disease is economically important in most wheat-growing areas worldwide and threatens global food production. Control of the disease has been hampered by a limited understanding of the genetic and biochemical bases of pathogenicity, including mechanisms of infection and of resistance in the host. Unlike most other plant pathogens, M. graminicola has a long latent period during which it evades host defenses. Although this type of stealth pathogenicity occurs commonly in Mycosphaerella and other Dothideomycetes, the largest class of plant-pathogenic fungi, its genetic basis is not known. To address this problem, the genome of M. graminicola was sequenced completely. The finished genome contains 21 chromosomes, eight of which could be lost with no visible effect on the fungus and thus are dispensable. This eight-chromosome dispensome is dynamic in field and progeny isolates, is different from the core genome in gene and repeat content, and appears to have originated by ancient horizontal transfer from an unknown donor. Synteny plots of the M. graminicola chromosomes versus those of the only other sequenced Dothideomycete, Stagonospora nodorum, revealed conservation of gene content but not order or orientation, suggesting a high rate of intra-chromosomal rearrangement in one or both species. This observed "mesosynteny" is very different from synteny seen between other organisms. A surprising feature of the M. graminicola genome compared to other sequenced plant pathogens was that it contained very few genes for enzymes that break down plant cell walls, which was more similar to endophytes than to pathogens. The stealth pathogenesis of M. graminicola probably involves degradation of proteins rather than carbohydrates to evade host defenses during the biotrophic stage of infection and may have evolved from endophytic ancestors.

Published
2011

31. Transcriptome and Metabolite Profiling of the Infection Cycle of Zymoseptoria tritici on Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

Author

Rudd, Jason J., Kanyuka, Kostya, Hassani-Pak, Keywan, Derbyshire, Mark, Andongabo, Ambrose, Devonshire, Jean, Lysenko, Artem, Saqi, Mansoor, Desai, Nalini M., Powers, Stephen J., Hooper, Juliet, Ambroso, Linda, Bharti, Arvind, Farmer, Andrew, Hammond-Kosack, Kim E., Dietrich, Robert A., and Courbot, Mikael

Published
2015

32. PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions

Author

Urban, Martin, Cuzick, Alayne, Seager, James, Wood, Valerie, Rutherford, Kim, Venkatesh, Shilpa Yagwakote, Sahu, Jashobanta, Iyer, S Vijaylakshmi, Khamari, Lokanath, De Silva, Nishadi, Martinez, Manuel Carbajo, Pedro, Helder, Yates, Andrew D, Hammond-Kosack, Kim E, Urban, Martin [0000-0003-2440-4352], Cuzick, Alayne [0000-0001-8941-3984], Seager, James [0000-0001-7487-610X], Wood, Valerie [0000-0001-6330-7526], Rutherford, Kim [0000-0001-6277-726X], De Silva, Nishadi [0000-0003-4802-2375], Pedro, Helder [0000-0001-7582-1565], Yates, Andrew D [0000-0002-8886-4772], Hammond-Kosack, Kim E [0000-0002-9699-485X], and Apollo - University of Cambridge Repository

Subjects
Internet, Insecta, Bacteria, Databases, Factual, Nematoda, Virulence, Fungi, Plants, Diplomonadida, User-Computer Interface, Phenotype, Host-Pathogen Interactions, Animals, Apicomplexa, Phylogeny
Abstract

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

Published
2022
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33. Detection of Multi-clustered Genes and Community Structure for the Plant Pathogenic Fungus Fusarium graminearum

Author

Bennett, Laura, Lysenko, Artem, Papageorgiou, Lazaros G., Urban, Martin, Hammond-Kosack, Kim, Rawlings, Chris, Saqi, Mansoor, Tsoka, Sophia, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Gilbert, David, editor, and Heiner, Monika, editor

Published
2012
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41. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

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

Published
2007
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43. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Author

Yates, Andrew D, primary, Allen, James, additional, Amode, Ridwan M, additional, Azov, Andrey G, additional, Barba, Matthieu, additional, Becerra, Andrés, additional, Bhai, Jyothish, additional, Campbell, Lahcen I, additional, Carbajo Martinez, Manuel, additional, Chakiachvili, Marc, additional, Chougule, Kapeel, additional, Christensen, Mikkel, additional, Contreras-Moreira, Bruno, additional, Cuzick, Alayne, additional, Da Rin Fioretto, Luca, additional, Davis, Paul, additional, De Silva, Nishadi H, additional, Diamantakis, Stavros, additional, Dyer, Sarah, additional, Elser, Justin, additional, Filippi, Carla V, additional, Gall, Astrid, additional, Grigoriadis, Dionysios, additional, Guijarro-Clarke, Cristina, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Howe, Kevin L, additional, Jaiswal, Pankaj, additional, Kaikala, Vinay, additional, Kumar, Vivek, additional, Kumari, Sunita, additional, Langridge, Nick, additional, Le, Tuan, additional, Luypaert, Manuel, additional, Maslen, Gareth L, additional, Maurel, Thomas, additional, Moore, Benjamin, additional, Muffato, Matthieu, additional, Mushtaq, Aleena, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Parker, Anne, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Quinton-Tulloch, Mark, additional, Rodgers, Faye, additional, Rosello, Marc, additional, Ruffier, Magali, additional, Seager, James, additional, Sitnik, Vasily, additional, Szpak, Michal, additional, Tate, John, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Ware, Doreen, additional, Wei, Sharon, additional, Williams, Gary, additional, Winterbottom, Andrea, additional, Zarowiecki, Magdalena, additional, Finn, Robert D, additional, and Flicek, Paul, additional

Published
2021
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44. PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions

Author

Urban, Martin, primary, Cuzick, Alayne, additional, Seager, James, additional, Wood, Valerie, additional, Rutherford, Kim, additional, Venkatesh, Shilpa Yagwakote, additional, Sahu, Jashobanta, additional, Iyer, S Vijaylakshmi, additional, Khamari, Lokanath, additional, De Silva, Nishadi, additional, Martinez, Manuel Carbajo, additional, Pedro, Helder, additional, Yates, Andrew D, additional, and Hammond-Kosack, Kim E, additional

Published
2021
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