Genomics and bioinformatics in plants and fungi
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.
- Domestication of High-Copy Transposons Underlays the Wheat Small RNA Response to an Obligate Pathogen
Poretti, Manuel; Praz, Coraline Rosalie; Meile, Lukas; Kalin, Carol; Schaefer, Luisa Katharina; Schlafli, Michael; Widrig, Victoria; Sanchez-Vallet, Andrea; Wicker, Thomas; Bourras, Salim
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, Luisa Katharina; Parlange, Francis; Buchmann, Gabriele; Jung, Esther; Wehrli, Andreas; et al.
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
- Updated Genome Assembly and Annotation for Metrosideros polymorpha, an Emerging Model Tree Species of Ecological Divergence
Izuno, Ayako; Wicker, Thomas; Hatakeyama, Masaomi; Copetti, Dario; Shimizu, Kentaro K.
G3-genes Genomes Genetics, DOI: 10.1534/g3.119.400643
- Mutations in the Arabidopsis ROL17/isopropylmalate synthase 1 locus alter amino acid content, modify the TOR network, and suppress the root hair cell development mutant lrx1
Schaufelberger, M; Galbier, F; Herger, A; Francisco, RD; Roffler, S; Clement, G; Diet, A; Hortensteiner, S; Wicker, T; Ringli, C
JOURNAL OF EXPERIMENTAL BOTANY, 70 (8):2313-2323; SI 10.1093/jxb/ery463 APR 1 2019
- The highly divergent Jekyll genes, required for sexual reproduction, are lineage specific for the related grass tribes Triticeae and Bromeae
Radchuk, V; Sharma, R; Potokina, E; Radchuk, R; Weier, D; Munz, E; Schreiber, M; Mascher, M; Stein, N; Wicker, T; Kilian, B; Borisjuk, L
PLANT JOURNAL, 98 (6):961-974; 10.1111/tpj.14363 JUN 2019
- The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat
Bourras, S; Kunz, L; Xue, MF; Praz, CR; Muller, MC; Kalin, C; Schlafli, M; Ackermann, P; Fluckiger, S; Parlange, F; Menardo, F; Schaefer, LK; Ben-David, R; Roffler, S; Oberhaensli, S; Widrig, V; Lindner, S; Isaksson, J; Wicker, T; Yu, DZ; Keller, B
NATURE COMMUNICATIONS, 10 10.1038/s41467-019-10274-1 MAY 23 2019
- A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew
Muller, MC; Praz, CR; Sotiropoulos, AG; Menardo, F; Kunz, L; Schudel, S; Oberhansli, S; Poretti, M; Wehrli, A; Bourras, S; Keller, B; Wicker, T
NEW PHYTOLOGIST, 221 (4):2176-2189; 10.1111/nph.15529 MAR 2019
- The evolution of functional complexity within the β-amylase gene family in land plants
Thalmann, M; Coiro, M; Meier, T; Wicker, T; Zeeman, SC; Santelia, D
BMC EVOLUTIONARY BIOLOGY, 19 10.1186/s12862-019-1395-2 FEB 28 2019
- Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza (vol 50, pg 285, 2018)
Stein, JC; Yu, Y; Copetti, D; Zwickl, DJ; Zhang, L; Zhang, CJ; Chougule, K; Gao, DY; Iwata, A; Goicoechea, JL; Wei, SR; Wang, J; Liao, Y; Wang, MH; Jacquemin, J; Becker, C; Kudrna, D; Zhang, JW; Londono, CEM; Song, X; Lee, S; Sanchez, P; Zuccolo, A; Ammiraju, JSS; Talag, J; Danowitz, A; Rivera, LF; Gschwend, AR; Noutsos, C; Wu, CC; Kao, SM; Zeng, JW; Wei, FJ; Zhao, Q; Feng, Q; El Baidouri, M; Carpentier, MC; Lasserre, E; Cooke, R; Farias, DD; da Maia, LC; dos Santos, RS; Nyberg, KG; McNally, KL; Mauleon, R; Alexandrov, N; Schmutz, J; Flowers, D; Fan, CZ; Weigel, D; Jena, KK; Wicker, T; …
NATURE GENETICS, 50 (11):1618-1618; 10.1038/s41588-018-0261-2 NOV 2018
- Shifting the limits in wheat research and breeding using a fully annotated reference genome
Appels, R; Eversole, K; Feuillet, C; Keller, B; … Wicker, T; …; Uauy, C
SCIENCE, 361 (6403):661-+; 10.1126/science.aar7191 AUG 17 2018
- 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