Progress 10/22/14 to 09/30/19
Outputs
Target Audience:Target Audience:The target audience reached in this reporting period includes foresters, plant pathologists, evolutionary biologists, mycologists, biochemists.? Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Three graduate students and two undergraduate students were trained in mycology and comparative genomics. How have the results been disseminated to communities of interest?One genome report was published. Three papers on the genomics of plant-fungal interactions were published. A review perspective on the evolution of fungal genomes was published. Six presentations on fungal interactions and genomics were given. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
In this project a number of molecular and computational approaches were taken toward understanding the ways in which fungi are adapted to plant defenses. A major contribution was to identify through comparative genomics dozens of potential defensive "gene clusters", which are multiple genes that can enable the whole process of degrading a given plant chemical defense. We cloned several of the genes in one type of cluster (for stilbene degradation) and were able to show how different fungal speciescan exchange genes through horizontal gene transfer to reconfigure these gene clusters so theyperform new functions. Genetic exchange between fungal species is shown to potentially be more important than simple DNA mutations, suggesting that fungi can adapt much like bacteria to a changing environment. These results thus form the basis of future work to develop novel fungicides that exploit the defenses of fungi, and at the same time provide new genetic resources for biological processing of plant biomass. For example, gene clusters capable of breaking down complex plant defenses may be useful for biomass conversion by enabling the predigestion of enzyme inhibitors that reduce the efficiency of e.g. bioethanol production from lignocellulosic materials.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Boyce, G. R., Gluck-Thaler, E., Slot, J. C., Stajich, J. E., Davis, W. J., James, T. Y., ... & Macias, A. M. (2019). Psychoactive plant-and mushroom-associated alkaloids from two behavior modifying cicada pathogens. Fungal Ecology, 41, 147-164.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Farinas, C., Gluck-Thaler, E., Slot, J. C., & Hand, F. P. (2019). Whole-Genome Sequence of the Phlox Powdery Mildew Pathogen Golovinomyces magnicellulatus Strain FPH2017-1. Microbiology resource announcements, 8(36), e00852-19.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Gluck?Thaler, E., Vijayakumar, V., & Slot, J. C. (2018). Fungal adaptation to plant defences through convergent assembly of metabolic modules. Molecular ecology, 27(24), 5120-5136.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Blei, F., Fricke, J., Wick, J., Slot, J. C., & Hoffmeister, D. (2018). Iterative l?Tryptophan Methylation in Psilocybe Evolved by Subdomain Duplication. ChemBioChem, 19(20), 2160-2166.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Scott K, Gluck-Thaler E, Farinas C, Valero-David G, Konkel Z, Chaverri P, Slot J. (2019).Identification and comparison of gene clusters in a diverse collection of Trichoderma species. 2019 Annual Meeting of the Mycological Society of America.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Valero-David G, Konkel Z, Bushley K, Slot J. (2019). Are Cordyceps secondary metabolite gene clusters involved in insect behavior manipulation? 2019 Annual Meeting of the Mycological Society of America.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Konkel Z, de Castro-Moretti F, Smith B, Cocuron J, Kowtha A, Alonso A, Slot J. (2019). Psilocybin production by termite egg-mimicking symbiont, Fibularhizoctonia sp. 2019 Annual Meeting of the Mycological Society of America.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Slot, J. C., & Gluck-Thaler, E. (2019). Metabolic gene clusters, fungal diversity, and the generation of accessory functions. Current opinion in genetics & development, 58, 17-24.
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum
- Type:
Journal Articles
Status:
Published
Year Published:
2019
Citation:
Armaleo, D., M�ller, O., Lutzoni, F., Andr�sson, �. S., Blanc, G., Bode, H. B., ... & Joneson, S. (2019). The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata. BMC genomics, 20(1), 605.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Escudero E, Granados M, Alvarado E, Slot J, Alonso A, Chaverri P. (2019). Endophytic Trichoderma with fungicide tolerance. 2019 Annual Meeting of the Mycological Society of America.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Gonzalez H, Alonso A, Staniczenko P, Slot J, Chaverri P. (2019). Unraveling the endophytic diversity associated with Rubiaceae tropical plants and the ecological factors driving community assemblage. 2019 Annual Meeting of the Mycological Society of America.
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Progress 10/01/17 to 09/30/18
Outputs
Target Audience:The target audience reached in this reporting period includes foresters, plant pathologists, evolutionary biologists, mycologists, biochemists. Changes/Problems:Our mycovirus approach is being re-evaluated because researchers at other institutions identified a mycovirus as being widespread in Pseudogymnoascus destructans that might be associated with virulence. Our mycovirus and comparative genomics descriptive work will be completed, but efforts to construct infected strains have been halted. What opportunities for training and professional development has the project provided?Three graduate students and one undergraduatewere trained on the functional and comparative genomics. How have the results been disseminated to communities of interest?Basic research has been disseminated in professional conferences and institutional symposia: International Mycological Congress (1abstract),Oregon State University, Center for Genome Research and Biocomputing Seminar Series,Jena School for Microbial Communication Colloquium,Ohio State, Center for Applied Plant Sciences Seminar Series. What do you plan to do during the next reporting period to accomplish the goals?We will continue to heterologously express genes from stilbene degradation clusters and analyze their functions by UPLCMass Spectrometry. We will adopt the CRISPR technology for Magnaporthe gene knockouts. We will continue to use comparative genomics to identify virulence/ecology associated genes in plant associated fungi.
Impacts
What was accomplished under these goals?
Two new publications report results of experiments on the fungal metabolism of plant metabolites (e.g. stilbenes), and progress has been made in identifying viruses interacting with the genus of fungi that contains the White-nose syndrome pathogen (Pseudogymnoascus). In Gluck-Thaler and Slot (The ISME Journal, 2018), we reported the discovery of over 1000 putative fungal gene clusters associated with degrading plant defense compounds. These will be important for future work to characterize the genetics and evolution of fungal resistance to plant defenses by pathogenic and decay fungi. In Gluck-Thaler et al. (Molecular Ecology, 2018) we reported on the diversity of alternative mechanisms of fungi for the degradation of stilbenes and the differential capacity of stilbene degradation enzymes to act on alternative plant defense compounds. The products of this work may be useful in the growth of solid state biomass fermentation for biofuel production by providing new knowledge of detoxification processes that may be employed. Two new viruses identified in Pseudogymnoascus species, however, reduced the likelihood that control of the White-nose pathogen by fungal-viruses will be effective. These viruses are actually associated with increased virulence in plant pathogenic fungi, and recently a related virus has been reported among all epidemic isolates of the White-nose pathogen; however it is still not known whether the virus contributes to virulence of this pathogen. Our work is not yet published on those results.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Sipos, G., Prasanna, A. N., Walter, M. C., OConnor, E., B�lint, B., Krizs�n, K., ... & Riley, R. (2017). Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria. Nature ecology & evolution, 1(12), 1931.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Reynolds, H. T., Slot, J. C., Divon, H. H., Lys�e, E., Proctor, R. H., & Brown, D. W. (2017). Differential retention of gene functions in a secondary metabolite cluster. Molecular biology and evolution, 34(8), 2002-2015.
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Slot, J. C. (2017). Fungal gene cluster diversity and evolution. In Advances in genetics (Vol. 100, pp. 141-178). Academic Press.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2018
Citation:
Gluck-Thaler, E., Bushley, K., Haridas, S., Grigoriev, I, Crous, P., Spatafora, J., Slot, J.C. (2018). Exploring the diversity of secondary metabolite clusters in Dothideomycete fungi. 11th International Mycological Congress, San Juan, Puerto Rico.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2018
Citation:
Castro-Moretti, F.R; Gonzalez, H.C; Slot, J.C; Chaverri, P; Alonso, A.P. Phenolic compounds shape fungal endophyte diversity in Rubiaceae leaves. 14th Annual Conference of the Metabolomics Society, Seattle, WA (June 2018).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2018
Citation:
Gluck-Thaler, E.*; Vijayakumar V.; Slot J.C. (2018). The evolution of diversity and function in fungal catabolic gene clusters. GRC Cellular and Molecular Fungal Biology, Holderness, NH, USA.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Gluck-Thaler, E., & Slot, J. C. (2018). Specialized plant biochemistry drives gene clustering in fungi. The ISME journal, 1.
- Type:
Journal Articles
Status:
Published
Year Published:
2018
Citation:
Gluck?Thaler, E., Vijayakumar, V., & Slot, J. C. (2018). Fungal adaptation to plant defenses through convergent assembly of metabolic modules. Molecular ecology.
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Progress 10/01/16 to 09/30/17
Outputs
Target Audience:The target audience reached in this reporting period includes foresters, plant pathologists,evolutionary biologists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?One graduate student and four undergraduates were trained in comparative and functional genomics methods. One postdoc was trained in comparative genomics andbioinformatics. Another postdoc has been trained in lab-based molecular genetics of the mechanisms of plant-fungal interactions. The graduate student and postdocs were involved in manuscript preparation and submission, and the postdocs were involved in grant proposal preparation. Undergraduates presented work at university symposia and graduate student and postdocs presented work at international meetings. How have the results been disseminated to communities of interest?Basic research has been disseminated in professional conferences: 29th Fungal Genetics Conference (2 abstracts), Mycological Society of America (2 abstracts). What do you plan to do during the next reporting period to accomplish the goals?We will continue to heterologously express genes from stilbene degradation clusters and analyze their functions by UPLC-Mass Spectrometry. We will attempt to isolate viruses identified by high throughput sequencing.
Impacts
What was accomplished under these goals?
Generate mutants of Magnaporthe oryzae stilbene degradation clusters for functional analysis. Nothing to report on these activities this period. Analyze metabolism of a range of stilbenes among diverse wild type fungi and laboratory constructs through metabolic profiling and transcriptome analysis. We completed characterization of five heterologously expressedstilbene cleavage enzymes over a broader panel of stilbenes and related compounds, and analyzed the evolution of three different types of gene clusters related to stilbene degradation across fungal lineages. This work is being prepared for publication. The complete cluster for stilbene degradation in Magnaporthe oryzaehas been heterologously expressed and two enzyme functions have been confirmed. Isolate and evaluate the genetic diversity of dsRNA mycoviruses in the genus Pseudogymnoascus. We screened 60 RNAseq libraries for dsRNA mycoviruses and identified 3 viruses. We will continue work to isolate these viruses from fungal strains. Generate mycovirus-infected Pd strains and assess transmissibility. Nothing to report on these activities this period. Identify emergent virulence factors through comparative genomics. We have identified approximately 1000 gene clusters involved in resistance to plant defense compounds, predominantly in the Dothideomycetes, the main lineage of plant pathogens. Characterize the effects of mycoviruses on Pd physiology and geneexpression. Nothing to report on these activities this period.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Riley, R., Haridas, S., Wolfe, K. H., Lopes, M. R., Hittinger, C. T., G�ker, M., ... & Aerts, A. L. (2016). Comparative genomics of biotechnologically important yeasts. Proceedings of the National Academy of Sciences, 201603941.
- Type:
Journal Articles
Status:
Published
Year Published:
2017
Citation:
Reynolds, H. T., Slot, J. C., Divon, H. H., Lys�e, E., Proctor, R. H., & Brown, D. W. (2017). Differential retention of gene functions in a secondary metabolite cluster. Molecular Biology and Evolution, msx145.
- Type:
Book Chapters
Status:
Published
Year Published:
2017
Citation:
Nagy, L. G., Toth, R., Kiss, E., Slot, J., Gacser, A., & Kovacs, G. M. (2017). Six Key Traits of Fungi: Their Evolutionary Origins and Genetic Bases. Microbiology spectrum, 5(4).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Slot J. (2017). Horizontal gene transfer: resolving functional diversity in fungal communities. 29th Fungal Genetics Conference.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Gluck-Thaler E., Vijayakumar V, Slot J. (2017). Fungal gene clusters adapted to plant secondary metabolites. 29th Fungal Genetics Conference.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Gluck-Thaler E., Vijayakumar V, Slot J. (2017). Fungal gene clusters adapted to degrade plant secondary metabolites. Mycological Society of America 2017.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Wang Y, Slot J, Pringle A. (2017). Contribution of multiple horizontal gene transfer to ectomycorrhizal niche transition in Amanita. Mycological Society of America 2017.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2017
Citation:
Vijayakumar V, Gluck-Thaler E, Slot J. (2017). The functional diversity of stilbene catabolism clusters in fungi. Mycological Society of America 2017.
- Type:
Journal Articles
Status:
Under Review
Year Published:
2017
Citation:
Gluck-Thaler E, Slot J. (2017). Specialized plant biochemistry drives gene clustering in fungi.
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Progress 10/01/15 to 09/30/16
Outputs
Target Audience:The target audience reached in this reporting period includes wildlife managers, plant pathologists, and evolutionary biologists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Two graduate students and two undergraduates were trained in comparative genomics methods. Two additional undergraduates were trained in lab-based molecular genetics. One postdoc was trained in comparative genomics and bioinformatics, and is now starting a new lab as university faculty. Another postdoc has been trained in lab-based molecular genetics of the mechanisms of plant-fungal interactions. How have the results been disseminated to communities of interest?Basic research has been disseminated in professional conferences: American Phytopathological Society (1 abstract), Mycological Society of America (2 abstracts), Gordon Research Conferences Cellular & Molecular Fungal Biology (1 abstract), as well as conference calls with stake-holders in the White-Nose Syndrome Disease Management Working Group (USFWS). What do you plan to do during the next reporting period to accomplish the goals?Generate mutants of Magnaporthe oryzae stilbene degradation clusters for functional analysis. We will continue to generate mutants of stilbene cluster genes in M. oryzae. We also plan to generate mutants of Diplodia sapinea, a pine pathogen with a different complement of stilbene degradation genes. We will then test the differential virulence of these mutants on their respective hosts (rice and austrian pine) in collaboration with two other labs in the Department of Plant Pathology. Analyze metabolism of a range of stilbenes among diverse wild type fungi and laboratory constructs through metabolic profiling and transcriptome analysis. We plan to continue developing heterologous expression vectors for a comparative stilbene degradation gene cluster set to test hypotheses of specialization of function. We intend to characterize the function of each enzyme in the cluster, and of the associated solute transporter. We will then test for differential co-evolution of genes and genetic modules within gene clusters in in vitro assays of substrate degradation. Isolate and evaluate the genetic diversity of dsRNA mycoviruses in the genus Pseudogymnoascus. We plan to continue using bioinformatics to screen RNA libraries for dsRNA viruses, and phylogenetics to characterize the observed diversity of these viruses. Depending on available staff, we will next build plasmid vectors of dsRNA viruses for storage and downstream analysis. Generate mycovirus-infected Pd strains and assess transmissibility. We do not anticipate progressing on this goal in the next year given previous findings and staffing constraints. Identify emergent virulence factors through comparative genomics. Using new funding obtained from the National Science Foundation, we plan to begin sequencing 50 fungal endophyte genomes isolated from coffee leaves and those of relatives. These genomes will be profiled using the recently developed gene cluster identification pipeline, for gene clusters associated with plant metabolites that are simultaneously profiled by mass spectrometry. Characterize the effects of mycoviruses on Pd physiology and gene expression. We do not anticipate progressing on this goal in the next year given previous findings and staffing constraints.
Impacts
What was accomplished under these goals?
Generate mutants of Magnaporthe oryzae stilbene degradation clusters for functional analysis. Mutation protocols were developed to target specific genes in stilbene degradation clusters. Several mutant fungal lines have been generated for one gene in the M. oryzae stilbene degradation cluster. Mutants have been confirmed by DNA and RNA screening. Additional mutations are subject of ongoing lab work. Analyze metabolism of a range of stilbenes among diverse wild type fungi and laboratory constructs through metabolic profiling and transcriptome analysis. Metabolism of one stilbene was performed using UPLC and LC-MS metabolomic profiling. Metabolomics revealed stilbene modification was more complex than originally hypothesized, so a new approach was developed for characterizing the functions of genes in stilbene degradation clusters. Five stilbene degradation genes have been cloned and their products produced heterologously for in vitro characterization of functions. Four stilbene dioxygenases from differently composed clusters have been expressed in E. coli and their activity on a panel of stilbenes profiled. Additional genes in the M. oryzae cluster are in various stages of heterologous expression and will be characterized in the coming year. Isolate and evaluate the genetic diversity of dsRNA mycoviruses in the genus Pseudogymnoascus. Approximately 50 dsRNA isolations have been performed from multiple species of Pseudogymnoascus, including P. destructans from multiple locations in Europe and North America. Sequencing of these isolates was performed using two separate Illumina MiSeq runs. The first set of extractions were analyzed and yielded two RNA viruses, which have been phylogenetically characterized as potential virulence-affecting lineages. The second set of RNA sequences await screening. Generate mycovirus-infected Pd strains and assess transmissibility. There is nothing to report. Identify emergent virulence factors through comparative genomics. Four comparative genomics searches for virulence factors were performed over the reporting period. A database of Pseudogymnoascus genomes was assembled from existing and newly generated whole genome sequences. First, the emergence of novel nitrate metabolism was characterized in P. destructans, by first performing the largest phylogenomic analysis of the genus to date, and then characterizing duplication of function in nitrate assimilation through phylogenetic analysis and physiological assays. A bioinformatic pipeline was then developed to identify lineage-specific gene duplications. This pipeline recovers the only known virulence factor in P. destructans along with several candidate emergent virulence genes. An additional pipeline was developed to identify gene clusters associated with enzymes of interest in the degradation of plant defense compounds. Approximately 900 metabolic gene clusters thought to be involved in fungal colonization of plant hosts were identified across 481 fungal genomes. Four genomes of Botrytis cinerea were also sequenced and analyzed. A gene cluster putatively involved in production of plant hormones was identified by comparing differently isolated strains. Characterize the effects of mycoviruses on Pd physiology and gene expression. There is nothing to report.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2016
Citation:
Reynolds, Hannah T., Hazel A. Barton, and Jason C. Slot. "Phylogenomic analysis supports a recent change in nitrate assimilation in the White-nose Syndrome pathogen, Pseudogymnoascus destructans." Fungal Ecology 23 (2016): 20-29.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2016
Citation:
Slot J, Gluck-Thaler, E. 2016. Specialized catabolism clusters in fungi. Cellular and Molecular Fungal Biology, Gordon Research Conferences, Holderness, NH.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2016
Citation:
Vijayakuma, V. Cottrell, B., Slot J., Reynolds, H., Hand F., Valero, G., Tomaschuk, C. 2016 Functional genomic analysis of Botrytis cinerea isolates from Ohio. American Phytopathological Society.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2016
Citation:
Gluck-Thaler, E. 2016. Clustering of catabolic genes in fungi is an adaptation to specialized plant biochemistry. Mycological Society of America.
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Progress 10/22/14 to 09/30/15
Outputs
Target Audience:Target audience includes plant breeders, wildlife management and ecologists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?1 undergraduate summer internship How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?We plan to continue searching for mycoviruses and to generate infected fungal strains. We plan to continue characterizing the function of stilbene cleavage enzymes.
Impacts
What was accomplished under these goals?
Generate mutants of Magnaporthe oryzae stilbene degradation clustersfor functional analysis. nothing to report. Analyze metabolism of a range of stilbenes among diverse wild type fungi and laboratory constructs through metabolic profiling and transcriptome analysis: Accomplishment-Three stilbene cleavage genes were cloned and expressed in heterologous systems. Enzyme function was verified by UPLC. Isolate and evaluate the genetic diversity of dsRNA mycoviruses in the genus Pseudogymnoascus: Accomplishments- 1. Four genomes and ten transcriptomes of Pseudogymnoascus were sequenced. 2. Two RNA viruses were identified Generate mycovirus-infected Pd strains and assess transmissibility:? nothing to report Identify emergent virulence factors through comparative genomics. nothing to report Characterize the effects of mycoviruses on Pd physiology and gene expression. nothing to report
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Gluck-Thaler, Emile, and Jason C Slot. 2015. Dimensions of Horizontal Gene Transfer in Eukaryotic Microbial Pathogens.. PLoS Pathogens 11 (10): e1005156. doi:10.1371/journal.ppat.1005156.
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