Prof. Dr. Thomas Wicker
Department of Plant and Microbial Biology
University of Zürich
Zollikerstrasse 107
CH-8008 Zürich
wicker@botinst.uzh.ch

phone:
+41 (0)44 63 48252
fax:
+41 (0)44 63 48204
Research Interests
List of Publications

[ print version ]

Research Interests

Mechanisms of genome evolution

Plant genomes are very dynamic and evolve much more rapidly than animal genomes. We are investigating the molecular mechanisms that drive this rapid evolution. Plants show an enormous range in genome size. For example, the genome of the Lily Fritillaria assyriaca is more than 1,000 larger than the genome of Arabidopsis. Genomes are expanded by the amplification of transposable elements (TEs), small genetic units which can move around in the genome and make copies of themselves. The expansion of genomes is counteracted by deletion of DNA. We have identified several ways in which DNA can be removed from the genome. A central mechanism is the repair of double-strand breaks (DSBs) which can be highly inaccurate in plants, leading to extensive deletions and rearrangements. It turns out that the activity of TEs is a major cause of DSB and therefore a major driving force in the evolution of plant genomes.

Evolution of interaction

Using comparative genomics and transcriptomics approaches, we are studying the interactions of plants and microbes. This includes plant/pathogen interactions as well as symbioses. In recent years we were involved in sequencing and analysis of the genome of Blumeria graminis, the cause of the wheat powdery mildew disease. We are studying genetic diversity of the pathogen as well as the response of the plant to pathogen attach. Additionally, we are studying symbiotic systems such as lichens (a symbiosis of fungi and algae) and the symbiosis of Psychotria plants with Burkholderia.

Development of Bioinformatics methods

The ever-increasing capacity of sequencing technologies poses an enormous challenge to biologists, since much more data is being produced than can reasonably be analysed. An important focus of our work is therefore to develop bioinformatics tools that allow complex analyses on very large datasets. We have a large collection of tools for whole-genome TE analysis, comparative genomics and data visualization.


List of Publications

Abrouk M, Ahmed HI, Cubry P, Simonikova D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Cizkova J, Hribova E, Dolezel J, Arribat S, Berges H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG (2020) Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun. 11:4488.
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Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, Aquino C, Nishimura K, Kobayashi F, Murata K, Kuo T, Delorean E, Poland J, Haberer G, Spannagl M, Mayer KFX, Gutierrez-Gonzalez J, Muehlbauer GJ, Monat C, Himmelbach A, Padmarasu S, Mascher M, Walkowiak S, Nakazaki T, Ban T, Kawaura K, Tsuji H, Pozniak C, Stein N, Sese J, Nasuda S, Handa H (2020) De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium Resistance Genes in East Asian Genotypes. Plant Cell Physiol. 2020 Nov 27. pcaa152. doi: 10.1093/pcp/pcaa152
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Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M (2019) TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol. 20:284.
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Müller, M.C+., Praz, C.R+., Sotiropoulos, A.G., Menardo, F., Kunz, L., Schudel, S., Oberhänsli, S., Poretti, M., Wehrli, A., Bourras, S., Keller, B.* and Wicker, T.* (2019). A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew. New Phytologist, 221: 2176–2189.
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Poretti, M., Praz, C.R., Meile, L., Kälin, C., Schaefer, L.K., Schläfli, M., Widrig, V., Sanchez-Vallet, A., Wicker, T. and Bourras, S. (2019). Domestication of high-copy transposons underlays the wheat small RNA response to an obligate pathogen. Molecular biology and evolution.
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Ma, X., Keller, B., McDonald, B.A., Palma-Guerrero, J. and Wicker, T. 2018. Comparative transcriptomics reveals how wheat responds to infection by Zymoseptoria tritici. Molecular Plant Microbe Interactions, 31: 420-431.
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Stritt, C., Gordon, S. P., Wicker, T., Vogel, J. P., & Roulin, A. C. (2017). Recent activity in expanding populations and purifying selection have shaped transposable element landscapes across natural accessions of the Mediterranean grass Brachypodium distachyon. Genome biology and evolution, 10(1), 304-318.
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Baumgartner, Michael, et al. "Letting go: bacterial genome reduction solves the dilemma of adapting to predation mortality in a substrate-restricted environment." The ISME journal 11.10 (2017): 2258.
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Hyles, Jessica, et al. "Repeat-length variation in a wheat cellulose synthase-like gene is associated with altered tiller number and stem cell wall composition." Journal of experimental botany 68.7 (2017): 1519-1529.
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Luo, Ming-Cheng, et al. Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551.7681 (2017).
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Mascher, Martin, et al. "A chromosome conformation capture ordered sequence of the barley genome." Nature 544.7651 (2017): 427.
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Thind et al (2017) Rapid Identification of Rust Resistance Genes Through Cultivar-Specific De Novo Chromosome Assemblies. In : Periyannan S (ed) Methods in Molecular Biology 1659: 245-255. doi: 10.1007/978-1-4939-7249-4_21
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Thind, Anupriya Kaur, et al. "Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly." Nature biotechnology 35.8 (2017): 793.
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Wicker, Thomas, et al. The repetitive landscape of the 5100 Mbp barley genome. Mobile DNA 8.1 (2017): 22.
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Shi G, Zhang Z, Friesen TL, Bansal U, Cloutier S, Wicker T, Rasmussen JB and Faris JD. (2016) Marker development, saturation mapping, and high-resolution mapping of the Septoria nodorum blotch susceptibility gene Snn3-B1 in wheat. Mol Genet Genomics 291(1):107-19. doi: 10.1007/s00438-015-1091-x.

Amselem J, Vigouroux M, Oberhaensli S, Brown JKM, Bindschedler LV, Skamnioti P, Wicker T, Spanu PD, Quesneville H and Sacristan S. (2015) Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics> 16:917. doi: 10.1186/s12864-015-2185-x.
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Bourras S, McNally KE, Ben-David R, Parlange F, Roffler S, Praz CR, Oberhaensli S, Menardo F, Stirnweis D, Frenkel Z, Schaefer LK, Flückiger S, Treier G, Herren G, Korol AB, Wicker T and Keller B. (2015) Multiple avirulence loci and allele-specific effector recognition control the Pm3 race-specific resistance of wheat to powdery mildew. Plant Cell 27: 2991-3012. doi: 10.1105/tpc.15.00171
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Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. (2015) RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics. 16:538.
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Pourkheirandish M, Hensel G, Kilian B, Senthil N, Chen G, Sameri M, Azhaguvel P, Sakuma S, Dhanagond S, Sharma R, Mascher M, Himmelbach A, Gottwald S, Nair SK, Tagiri A, Yukuhiro F, Nagamura Y, Kanamori H, Matsumoto T, Willcox G, Middleton CP, Wicker T, Walther A, Waugh R, Fincher GB, Stein N, Kumlehn J, Sato K, Komatsuda T. (2015) Evolution of the Grain Dispersal System in Barley. Cell . 162:527-539.
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Roffler S and Wicker T. (2015) Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons. Mobile DNA. 6:8.
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Roffler S, Menardo F and Wicker T. (2015) The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants. Mobile DNA 6:23. doi: 10.1186/s13100-015-0054-4.
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Wicker T, Wing RA and Schubert I. (2015) Recurrent sequence exchange between homeologous grass chromosomes mimics recent duplication. Plant Jounal 84:747-759. doi: 10.1111/tpj.13040.
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Bansal, U., Bariana, H., Wong, D., Randhawa M., Wicker, T., Hayden M., Keller, B. (2014). Molecular mapping of an adult plant stem rust resistance gene Sr56 in winter cultivar Arina. Theor Appl Genet 127:1441–1448, doi: 10.1007/s00122-014-2311-1

The International Wheat Genome Sequencing Consortium (IWGSC). (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 6194 doi: 10.1126/science.1251788
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Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KF, Rounsley S, Wing RA. (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet. 46: 982-988.

Wicker, T., Oberhaensli, S., Parlange, F., Buchmann, J.P., Shatalina, M., Roffler, S., Ben-David, R., Dolezel, J., Simkova, H., Schulze-Lefert, P., Spanu, P.D., Bruggmann, R., Amselem, J., Quesneville, H., Ver Loren van Themaat, E., Paape, T., Shimizu, K.K. and Keller, B. (2013). The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature Genetics, 45: 1092 - 1096.
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Martis MM, Klemme S, Banaei-Moghaddam AM, Blattner FR, Macas J, Schmutzer T, Schloz U, Gundlach H, Wicker T, Simkova H, Novak P, Neumann P, Kubalakova M, Bauer E, Haseneyer G, Fuchs J, Dolezel J, Stein N, Mayer KF and Houben A. Selfish supernumerary chromosome reveals its origin as a mosaic of host genome and organellar sequences. (2012) PNAS 109(33):13343-6. doi: 10.1073/pnas.1204237109
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Buchmann JP, Matsumoto T, Stein N, Keller B, Wicker T (2012) Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity. Plant J. 488: 213-217.
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Kritsas K, Wuest SE, Hupalo D, Kern AD, Wicker T, Grossniklaus U. (2012) Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res. 22: 2455-2466.
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d'Hont A, Denoeud F, Aury JM, Baurens FC, Carreel F, Garsmeur O, Noel B, Bocs S, Droc G, Rouard M, et. al. (2012) The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature. 488: 213-217.

Oberhaensli S, Parlange F, Buchmann JP, Jenny FH, Abbott JC, Burgis TA, Spanu PD, Keller B, Wicker T (2011) Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity dates divergence and indicates host-pathogen co-evolution. Fungal Genet. Biol. 48: 327-334.
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Wicker T, Mayer KF, Gundlach H, Martis M, Steuernagel B, Scholz U, Simková H, Kubaláková M, Choulet F, Taudien S, Platzer M, Feuillet C, Fahima T, Budak H, Dolezel J, Keller B, Stein N (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat barley and their relatives. Plant Cell 23: 1706-1718.
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International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768.

Wicker T, Buchmann JP, Keller B. (2010) Patching gaps in plant genomes results in gene movement and erosion of colinearity. Genome Res. 20: 1229-1237.
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Loutre C, Wicker T, Travella S, Galli P, Scofield S, Fahima T, Feuillet C, Keller B, (2009) Two different CC-NBS-LRR genes are required for Lr10-mediated leaf rust resistance in tetraploid and hexaploid wheat. Plant J. 60: 1043-1054.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang, Y, Zhang, L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457: 551-556.

Wicker T, Krattinger, S, Lagudah, E.S, Komatsuda, T, Pourkheirandish, M, Matsumoto, T, Matsumoto, T, Cloutier, S, Reiser, L, Kanamori, H, Sato, K, Perovic, D, Stein N, Beat Keller B. (2009) Analysis of intraspecies diversity in wheat and barley genomes identifies breakpoints of ancient haplotypes and provides insight in the structure of diploid and hexaploid Triticeae gene pools. Plant Physiol. 149: 258-270.

Wicker T, Taudien S, Houben A, Keller B, Graner A, Platzer M, Stein N. (2009) A hole-genome snapshot of 454 sequences exposes the composition of the barley genome and provides evidence for parallel evolution of genome size in wheat and barley. Plant J. 59: 712-722.

Wicker T, Narechania, A, Sabot, F, Stein, J, Thi Ha Vu, G, Graner, A, Ware, D, Stein N. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9: 518.

Bossolini E, Wicker T, Knobel PA, Keller B. (2007) Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation. Plant J.49: 704-717. Erratum in: Plant J. 50:1129.

Wicker T, Keller B, (2007) Genome-wide comparative analysis of copia retrotransposons in Triticeae, rice, and Arabidopsis reveals conserved ancient evolutionary lineages and distinct dynamics of individual copia families. Genome Res. 17: 1072-1081.

Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante, M, Panaud O, Paux E, SanMiguel P, Schulman AH. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8: 973-982.

Wicker T, Yahiaoui N, Keller B, (2007) Illegitimate recombination is a major evolutionary mechanism for initiating size variation in plant resistance genes. Plant J. 51: 631-641.

Wicker T, Yahiaoui, N, Keller B, (2007) Contrasting rates of evolution in Pm3 loci from three wheat species and rice Genetics 177: 1207-1216.