Comparative genomic analysis of Fusarium candidate virulence genes and plant detoxification genes
Final Report Abstract
A successful collaboration on both, the fungal pathogen and plant host side between BOKU researchers and bioinformatics experts from Munich has been established throughout the funding periods. One focus of project part F3705 (with the start of phase 3 renamed: LAP3714) on the pathogen side was on de-novo and iterative improvement of the structural annotation of Fusarium genomes with emphasis on secondary metabolite gene clusters. A comparative custom search for these local gene clusters resulted in extended lists of known and potential new SM gene clusters with implications on the evolution of these important features. Integration of different gene call sets assisted by multiple RNA-seq based transcript data resulted in overhauled gene call sets. The closely related genome of F. asiaticum was also further investigated which helped in comparative annotation and structural improvements of the genome assembly of F. graminearum. Besides, the more distant F. fujikuroi species group (FFC) was also thoroughly investigated and numerous genomes annotated. The genomic data sets were used extensively to map and quantify expression data (RNA-seq) and to correlate regulated gene sets to functional annotation, local gene clusters etc. The public FGDB/Pedant interface was further developed to hold genomic data on multiple Fusarium species in a consistent framework allowing comparative approaches and visualization of omics data. The focus on the host-plant side shifted during the project runtime from using the model system Brachypodium distachyon towards using the cereal crop-plant genomic backbones, bread wheat and barley, that have recently become available. Exploiting these resources allowed addressing the effects of F. graminearum infection with an unprecedented precision. To this end gene expression data generated by RNA-seq was mapped against current, state-of-the art genome assemblies and annotations and the underlying molecular mechanisms and network based expression adaptations were studied. Most notably among these now available genome drafts is the 17Gb hexaploid bread wheat genome, which has been deciphered with the contribution of the applicant. By combining the genomic gene expression data with bioinformatics, biostatistics, and network-based data analyses methods groups of genes that react in a pathogen-responsive or QTL-specific manner were extracted. In addition to the core work packages essential ad-hoc support to project partners was provided on numerous specific topics helping to interpret wet lab data.
Publications
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2013. Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites. PLoS Pathog. 9, e1003475
Wiemann, P., Sieber, C.M.K., von Bargen, K.W., Studt, L., Niehaus, E.-M., Espino, J.J., Huß, K., Michielse, C.B., Albermann, S., Wagner, D., Bergner, S.V., Connolly, L.R., Fischer, A., Reuter, G., Kleigrewe, K., Bald, T., Wingfield, B.D., Ophir, R., Freeman, S., Hippler, M., Smith, K.M., Brown, D.W., Proctor, R.H., Münsterkötter, M., Freitag, M., Humpf, H.-U., Güldener, U., Tudzynski, B.
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2014. The Fusarium graminearum Genome Reveals More Secondary Metabolite Gene Clusters and Hints of Horizontal Gene Transfer. PLoS ONE 9, e110311
Sieber, C.M.K., Lee, W., Wong, P., Münsterkötter, M., Mewes, H.-W., Schmeitzl, C., Varga, E., Berthiller, F., Adam, G., Güldener, U.
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chromoWIZ: a web tool to query and visualize chromosome-anchored genes from cereal and model genomes. BMC Plant Biol. 2014 Dec 10;14:348
Nussbaumer T, Kugler KG, Schweiger W, Bader KC, Gundlach H, Spannagl M, Poursarebani N, Pfeifer M, Mayer KF
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2015. Fusarium Mycotoxins and Their Role in Plant–Pathogen Interactions, in: Zeilinger, S., Martín, J.-F., García-Estrada, C. (Eds.), Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Volume 2, Fungal Biology. Springer New York, pp. 199–233
Adam, G., Wiesenberger, G., Güldener, U.
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Joint Transcriptomic and Metabolomic Analyses Reveal Changes in the Primary Metabolism and Imbalances in the Subgenome Orchestration in the Bread Wheat Molecular Response to Fusarium graminearum. G3 (Bethesda). 2015 Oct 4;5(12):2579-92
Nussbaumer T, Warth B, Sharma S, Ametz C, Bueschl C, Parich A, Pfeifer M, Siegwart G, Steiner B, Lemmens M, Schuhmacher R, Buerstmayr H, Mayer KF, Kugler KG, Schweiger W
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2016. Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. Genome Biol Evol 8, 3574–3599
Niehaus, E.-M., Münsterkötter, M., Proctor, R.H., Brown, D.W., Sharon, A., Idan, Y., Oren-Young, L., Sieber, C.M., Novák, O., Pěnčík, A., Tarkowská, D., Hromadová, K., Freeman, S., Maymon, M., Elazar, M., Youssef, S.A., El-Shabrawy, E.S.M., Shalaby, A.B.A., Houterman, P., Brock, N.L., Burkhardt, I., Tsavkelova, E.A., Dickschat, J.S., Galuszka, P., Güldener, U., Tudzynski, B.
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2016. Comparison of Fusarium graminearum Transcriptomes on Living or Dead Wheat Differentiates Substrate-Responsive and Defense-Responsive Genes. Fusarium graminearum 1113
Boedi, S., Berger, H., Sieber, C., Münsterkötter, M., Maloku, I., Warth, B., Sulyok, M., Lemmens, M., Schuhmacher, R., Güldener, U., Strauss, J.
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Ribosome quality control is a central protection mechanism for yeast exposed to deoxynivalenol and trichothecin. BMC Genomics. 2016 Jun 1;17:417
Kugler KG, Jandric Z, Beyer R, Klopf E, Glaser W, Lemmens M, Shams M, Mayer K, Adam G, Schüller C
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2017. Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles. PLoS Pathog. 13, e1006670
Niehaus, E.-M., Kim, H.-K., Münsterkötter, M., Janevska, S., Arndt, B., Kalinina, S.A., Houterman, P.M., Ahn, I.-P., Alberti, I., Tonti, S., Kim, D.-W., Sieber, C.M.K., Humpf, H.-U., Yun, S.-H., Güldener, U., Tudzynski, B.
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Time-course expression QTL-atlas of the global transcriptional response of wheat to Fusarium graminearum. Plant Biotechnol J. 2017 Nov;15(11):1453-1464
Samad-Zamini M, Schweiger W, Nussbaumer T, Mayer KFX, Buerstmayr H
