Genomics and bioinformatics in plants and fungi

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.

Recent Publications

  • 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
  • Advances in Wheat and Pathogen Genomics: Implications for Disease Control
    Keller, Beat; Wicker, Thomas; Krattinger, Simon G. Edited by: Leach JE; Lindow SE
    ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 56, 56 67-87; 10.1146/annurev-phyto-080516-035419 2018
  • Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome dynamics between two wheat cultivars
    Thind, AK; Wicker, T; Muller, T; Ackermann, PM; Steuernagel, B; Wulff, BBH; Spannagl, M; Twardziok, SO; Felder, M; Lux, T; Mayer, KFX; Keller, B; Krattinger, SG
    Group Author(s): Int Wheat Genome Sequencing
    GENOME BIOLOGY, 19 10.1186/s13059-018-1477-2 AUG 17 2018
  • Shifting the limits in wheat research and breeding using a fully annotated reference genome
    Appels, Rudi; Eversole, Kellye; Feuillet, Catherine; et al.
    Group Author(s): IWGSC; IWGSC RefSeq Principal; IWGSC Whole-Genome Assembly Prin; et al.
    SCIENCE 361(6403): 661-+   Article Number: eaar7191 10.1126/science.aar7191 AUG 17 2018
  • Comparative Transcriptomics Reveals How Wheat Responds to Infection by Zymoseptoria tritici
    Authors: Ma, X; Keller, B; McDonald, BA; Palma-Guerrero, J; Wicker, T
    MOLECULAR PLANT-MICROBE INTERACTIONS, 31 (4):420-431; https://doi.org/10.1094/MPMI-10-17-0245-R APR 2018
  • Impact of transposable elements on genome structure and evolution in bread wheat
    Wicker, Thomas; Gundlach, Heidrun; Spannagl, Manuel; et al.
    Group Author(s): Int Wheat Genome Sequencing
    GENOME BIOLOGY 19: 103  10.1186/s13059-018-1479-0  AUG 17 2018
  • Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza
    Stein, Joshua C.; Yu, Yeisoo; Copetti, Dario; et al.
    NATURE GENETICS   Volume: 50   Issue: 2   Pages: 285-+    https://doi.org/10.1038/s41588-018-0040-0 FEB 2018
  • Transcriptional profiling reveals no response of fungal pathogens to the durable, quantitative Lr34 disease resistance gene of wheat
    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; Chen, MS; Han, B; Henry, R; Hsing, YIC; Kurata, N; de Oliveira, AC; Panaud, O; Jackson, SA; Machado, CA; Sanderson, MJ; Long, MY; Ware, D; Wing, RA
    NATURE GENETICS   Volume: 50   Issue: 2   Pages: 285-+  10.1038/s41588-018-0040-0 FEB 2018
  • Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen 
    Praz, Coraline R.; Menardo, Fabrizio; Robinson, Mark D.; et al. 
    FRONTIERS IN PLANT SCIENCE, 9: JAN 30 2018 Document Type: Article (Details)
  • Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon 
    Stritt, Christoph; Gordon, Sean P.; Wicker, Thomas; et al. 
    GENOME BIOLOGY AND EVOLUTION, 10 (1): 304-318 10.1093/gbe/evx276 JAN 2018
Thomas Wicker Uni Zurich

PD Dr. Thomas Wicker
University of Zurich
Department of Plant and Microbial Biology
8008 Zurich

Tel: +41 44 63 48252

Research Topics

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

Interdisciplinarity

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