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3. 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

7. Membrane Proteins in Plant Viruses

Author

Adams, Michael J., Antoniw, John F., Atassi, M. Zouhair, editor, Berliner, Lawrence J., editor, Chang, Rowen Jui-Yoa, editor, Jörnvall, Hans, editor, Kenyon, George L., editor, Wittman-Liebold, Brigitte, editor, and Fischer, Wolfgang B., editor

Published
2005
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9. 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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17. 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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23. OmniMapFree: A unified tool to visualise and explore sequenced genomes

Author

Antoniw John, Beacham Andrew M, Baldwin Thomas K, Urban Martin, Rudd Jason J, and Hammond-Kosack Kim E

Subjects
Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract • Background Acquiring and exploring whole genome sequence information for a species under investigation is now a routine experimental approach. On most genome browsers, typically, only the DNA sequence, EST support, motif search results, and GO annotations are displayed. However, for many species, a growing volume of additional experimental information is available but this is rarely searchable within the landscape of the entire genome. • Results We have developed a generic software which permits users to view a single genome in entirety either within its chromosome or supercontig context within a single window. This software permits the genome to be displayed at any scales and with any features. Different data types and data sets are displayed onto the genome, which have been acquired from other types of studies including classical genetics, forward and reverse genetics, transcriptomics, proteomics and improved annotation from alternative sources. In each display, different types of information can be overlapped, then retrieved in the desired combinations and scales and used in follow up analyses. The displays generated are of publication quality. • Conclusions OmniMapFree provides a unified, versatile and easy-to-use software tool for studying a single genome in association with all the other datasets and data types available for the organism.

Published
2011
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31. Ascorbic Acid Deficiency Activates Cell Death and Disease Resistance Responses in Arabidopsis1

Author

Pavet, Valeria, Olmos, Enrique, Kiddle, Guy, Mowla, Shaheen, Kumar, Sanjay, Antoniw, John, Alvarez, María E., and Foyer, Christine H.

Subjects
Cell Nucleus, Cell Death, Glutathione Disulfide, Arabidopsis Proteins, fungi, Arabidopsis, Pseudomonas syringae, Ascorbic Acid, Glutathione, Antioxidants, Plant Leaves, Cysteine Endopeptidases, Protein Transport, Phenotype, Gene Expression Regulation, Plant, Genes, Bacterial, Mutation, Oxidation-Reduction, Research Article, Cell Size, Plant Diseases
Abstract

Programmed cell death, developmental senescence, and responses to pathogens are linked through complex genetic controls that are influenced by redox regulation. Here we show that the Arabidopsis (Arabidopsis thaliana) low vitamin C mutants, vtc1 and vtc2, which have between 10% and 25% of wild-type ascorbic acid, exhibit microlesions, express pathogenesis-related (PR) proteins, and have enhanced basal resistance against infections caused by Pseudomonas syringae. The mutants have a delayed senescence phenotype with smaller leaf cells than the wild type at maturity. The vtc leaves have more glutathione than the wild type, with higher ratios of reduced glutathione to glutathione disulfide. Expression of green fluorescence protein (GFP) fused to the nonexpressor of PR protein 1 (GFP-NPR1) was used to detect the presence of NPR1 in the nuclei of transformed plants. Fluorescence was observed in the nuclei of 6- to 8-week-old GFP-NPR1 vtc1 plants, but not in the nuclei of transformed GFP-NPR1 wild-type plants at any developmental stage. The absence of senescence-associated gene 12 (SAG12) mRNA at the time when constitutive cell death and basal resistance were detected confirms that elaboration of innate immune responses in vtc plants does not result from activation of early senescence. Moreover, H2O2-sensitive genes are not induced at the time of systemic acquired resistance execution. These results demonstrate that ascorbic acid abundance modifies the threshold for activation of plant innate defense responses via redox mechanisms that are independent of the natural senescence program.

Published
2005

39. Weak expression of the pathogenesis related PR-b1 gene and localization of related protein during symbiotic endomycorrhizal interactions in tobacco roots

Author

Gianinazzi-Pearson, Vivienne, Tahiri-Alaoui, Abdessamad, Antoniw, John Fitzgerald, Gianinazzi, Silvio, and Dumas-Gaudot, Eliane

Subjects
G. mosseae, Endomycorrhiza symbiosis, Tobacco, RNA, PR-b₁ protein, C.elegans, Immunolocalization
Abstract

The production of pathogenesis related PR-b₁ protein has been compared in tobacco roots infected by the pathogenic fungus Chalara elegans and during symbiotic interactions with the vesicular arbuscular endomycorrhizal fungus Glomus mosseae. PR-b₁ protein could be detected by Western blotting of soluble protein extracts from pathogen-infected roots but not of endomycorrhizal tobacco roots. However, Northern analysis of total RNA extracts from endomycorrhizal roots revealed a single hybridization signal which was extremely weak when compared to that of C. elegans-infected tobacco roots. Indirect immunogold labelling showed that PR-b₁ antigen was very localized in endomycorrhizal roots and limited to host material in the interfacial matrix surrounding living intracellular fungal haustoria (arbuscules) in parenchyma cortical cells. Results are discussed in relation to PR-b₁ protein synthesis in pathogen interactions and host control in the endomycorrhizal symbiosis.

Published
1992

48. Membrane Proteins in Plant Viruses.

Author

Atassi, M. Zouhair, Berliner, Lawrence J., Chang, Rowen Jui-Yoa, Jörnvall, Hans, Kenyon, George L., Wittman-Liebold, Brigitte, Fischer, Wolfgang B., Adams, Michael J., and Antoniw, John F.

Abstract

It is clear that MPs play an essential role in the pathogenesis and movement within the plant of many plant viruses. However, studies of the structure and function of such proteins are still in their infancy. Substantial progress may be expected in the next few years, particularly in the area of cell-to-cell movement where viruses are proving useful tools to study the basic processes of macromolecular trafficking between adjacent plant cells. [ABSTRACT FROM AUTHOR]

Published
2005
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49. Alphacryptovirus.

Author

Antoniw, John F.

Subjects
*VIRUSES, *MORPHOLOGY, *REPRODUCTION, *PROTEINS, *SPECIES
Abstract

This chapter offers information on alphacryptovirus. It covers a wide range of different aspects of alphacryptovirus, including history, virion morphology, electron microscopic image, genome properties, and replication strategy. The properties of individual transcripts and proteins, biological properties in vitro and in vivo are given, as well as specific information about individual virus species.

Published
2002

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