Genomics

Plant and fungal genomes are very dynamic and evolve much more rapidly than animal genomes. We are investigating the molecular mechanisms that drive this rapid evolution. Genomes are expanded by the amplification of transposable elements. The expansion of genomes is counteracted by deletion of DNA. We compare gene content, gene order and repeat content of different species. Comparative analysis is a powerful method to discover mechanisms that drive the evolution of genomes. We have so discovered mechanisms that cause gene duplications, gene movement and gene loss.

Using comparative genomics and transcriptomics, we also study interactions of plants and microbes. This includes plant/pathogen interactions as well as symbioses. We were involved in sequencing and analysis of the genome of wheat powdery mildew and the study of genetic diversity of the pathogen. Additionally, we study symbiotic systems such as lichens and the symbiosis of Psychotria plants with Burkholderia. An important focus of our work is the development of bioinformatics tools that allow complex analyses on large datasets for whole-genome analysis, comparative genomics and data visualization.

• Comparative Transcriptome Analysis of Wheat Lines in the Field Reveals Multiple Essential Biochemical Pathways Suppressed by Obligate Pathogens
  Poretti, Manuel; Sotiropoulos, Alexandros G.; Graf, Johannes; Jung, Esther; Bourras, Salim; Krattinger, Simon G.; Wicker, Thomas
  Frontiers In Plant Science 10.3389/fpls.2021.720462  SEP 29 2021
• A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen
  Oggenfuss, Ursula; Badet, Thomas; Wicker, Thomas; Hartmann, Fanny E.; Singh, Nikhil Kumar; Abraham, Leen; Karisto, Petteri; Vonlanthen, Tiziana; Mundt, Christopher; McDonald, Bruce A.; Croll, Daniel
  Elife 10.7554/eLife.69249 SEP 16 2021
• Long-read sequence assembly: a technical evaluation in barley
  Mascher, Martin; Wicker, Thomas; Jenkins, Jerry; Plott, Christopher; Lux, Thomas; et al.
  Plant Cell 10.1093/plcell/koab077  JUN 2021
• Alleles of a wall-associated kinase gene account for three of the major northern corn leaf blight resistance loci in maize
  Yang P; Scheuermann D; Kessel B; Koller T; Greenwood JR;  Hurni S; Herren G; Zhou SH; Marande, W; Wicker T; Krattinger SG; Ouzunova M; Keller, B
  Plant Journal  10.1111/tpj.15183  Published: APR 2021
• Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential
  Rabanus-Wallace, M. Timothy; Hackauf, Bernd; Mascher, Martin; Lux, Thomas; Wicker, Thomas; et al.
  Nature Genetics 10.1038/s41588-021-00807-0   Early Access: MAR 2021
• Wheat Pm4 resistance to powdery mildew is controlled by alternative splice variants encoding chimeric proteins
  Sanchez-Martin, Javier; Widrig, Victoria; Herren, Gerhard; Wicker, Thomas; Zbinden, Helen; Gronnier, Julien; Sporri, Laurin; Praz, Coraline R; Heuberger, Matthias; Kolodziej, Markus C.; Isaksson, Jonatan; Steuernagel, Burkhard; Karafiatova, Miroslava; Dolezel, Jaroslav; Zipfel, Cyril; Keller, Beat
  Nature Plants,  10.1038/s41477-021-00869-2 MAR 2021
• Defects in Cell Wall Differentiation of the Arabidopsis Mutant rol1-2 Is Dependent on Cyclin-Dependent Kinase CDK8
  Schumacher, Isabel; Ndinyanka Fabrice, Tohnyui; Abdou, Marie-Therese; Kuhn, Benjamin M.; Voxeur, Aline; Herger, Aline; Roffler, Stefan; Bigler, Laurent; Wicker, Thomas; Ringli, Christoph
  Cells  10.3390/cells10030685   Published: MAR 2021
• A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat
  Kolodziej, Markus C.; Singla, Jyoti; Sanchez-Martin, Javier; Zbinden, Helen; Simkova, Hana; Karafiatova, Miroslava; Dolezel, Jaroslav; Gronnier, Julien; Poretti, Manuel; Glauser, Gaetan; Zhu, Wangsheng; Koster, Philipp; Zipfel, Cyril; Wicker, Thomas; Krattinger, Simon; Keller, Beat
  Nature Communications,  DOI: 10.1038/s41467-020-20777-x FEB 11 2021
• De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes
  Shimizu, Kentaro K.; Copetti, Dario; Okada, Moeko; Wicker, Thomas; Tameshige, Toshiaki; et al.
  Plant And Cell Physiology, 10.1093/pcp/pcaa152, JAN 2021
• Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate
  Abrouk, Michael; Ahmed, Hanin Ibrahim; Cubry, Philippe; Simonikova, Denisa; Cauet, Stephane; et al.
  Nature Communications   DOI: 10.1038/s41467-020-18329-4  SEP 8 2020
• Multiple wheat genomes reveal global variation in modern breeding
  Walkowiak, Sean; Gao, Liangliang; Monat, Cecile; Haberer, Georg; Kassa, Mulualem T.; et al.
  Nature   DOI: 10.1038/s41586-020-2961-x  DEC 10 2020
• Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen
  Poretti, M; Praz, CR; Meile, L; Kalin, C; Schaefer, LK; Schlafli, M; Widrig, V; Sanchez-Vallet, A; Wicker, T; Bourras, S
  Molecular Biology And Evolution 37(3): 839-848  DOI: 10.1093/molbev/msz272 Published: MAR 2020
• Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat
  Schaefer, LK ; Parlange, F; Buchmann, G; Jung, E ; Wehrli, A ; Herren, G; Muller, MC; Stehlin, J ; Schmid, R; Wicker, T; Keller, B; Bourras, S
  Frontiers In Plant Science  DOI: 10.3389/fpls.2020.00253 Published: MAR 10 2020
• TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools
  Monat, Cecile; Padmarasu, Sudharsan; Lux, Thomas; Wicker, Thomas; Gundlach, Heidrun; et al.
  Genome Biology 20(1) Article Number: 284 DOI: 10.1186/s13059-019-1899-5 DEC 18 2019
• …

• Mechanisms of genome evolution
• Transposable elements
• Plant-microbe interactions

• Collaboration with research groups in microbiology
• Collaboration with members of the Dept of Systematic and Evolutionary Botany