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.
- 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
- 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
- The repetitive landscape of the 5100 Mbp barley genome
By: Wicker, Thomas; Schulman, Alan H.; Tanskanen, Jaakko; et al.
MOBILE DNA Volume: 8 Article Number: 22 Published: DEC 20 2017
- Genome sequence of the progenitor of the wheat D genome Aegilops tauschii
By: Luo, Ming-Cheng; Gu, Yong Q.; Puiu, Daniela; et al.
NATURE Volume: 551 Issue: 7681 Pages: 498-+ Published: NOV 23 2017
- 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