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A large-scale bioinformatics approach to study the role of transposable elements in plant genome evolution and the interaction of the host genome with its mobile DNA fraction

English title A large-scale bioinformatics approach to study the role of transposable elements in plant genome evolution and the interaction of the host genome with its mobile DNA fraction
Applicant Wicker Thomas
Number 122242
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Genetics
Start/End 01.10.2008 - 31.12.2011
Approved amount 185'225.00
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Keywords (6)

bioinformatics; transposable element; genome-wide survey; illegitimate recombination; genome evolution; software development

Lay Summary (English)

Lead
Lay summary
BackgroundTransposable elements (TEs) are ubiquitous components of all genomes. Their variety and abundance, especially in large plant genomes, pose one of the greatest challenges for plant genomics both in a technical and an intellectual sense. TEs are usually seen as “junk” or “selfish” DNA which replicate and move within the environment of their “host” genome. TEs and their host genomes interact in many of ways: TE amplification increases genome size while the host genome has mechanism to remove repetitive DNA. However, emerging data challenges the view of TEs as purely selfish by describing TEs as sources of genetic variation, vehicles of gene movement or providers of novel coding or regulatory sequences. Such research has been patchy and mostly restricted to one specific TE type in a single species or genomic region. With this proposed project, we would like to address the fundamental biological question as to the contribution of TEs to plant genome evolution.Specific aimsThrough systematic bioinformatics analysis of TE in entire plant genomes and comparison of TEs from different species, we would like to study the role of TEs for genome evolution. In particular, we would like to search for patterns that indicate whether they are purely “selfish” or whether they might have an underlying beneficial role for genome evolution. Expected value of the proposed projectOur large-scale approach will provide an improved understanding of the biological role of TEs in plant genome evolution. We expect to be able to identify patterns of diversifying or purifying selection which can then give hints of whether certain TE families have a positive effect on genome evolution or whether they have to be seen as purely selfish. We should also be able to elucidate to what degree purely random genetic drift drives the evolution of TEs and their “host” genome. We anticipate that our results will be the basis for further bioinformatics and wet lab studies on the biological function of TEs and their interaction with their host genomes. Establishment and maintenance of a comprehensive and consistent database for repetitive DNA will strengthen the role of our lab as important hub for exchange of information and expertise on repetitive DNA. This is a position of high strategic value considering the growing speed at which genomic sequences will be produced in the future. Additionally, we hope to contribute to an improvement and growth Bioinformatics research in Zurich.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts.
Buchmann Jan, Löytynoja Ari, Wicker Thomas, Schulman Alan (2014), Analysis of CACTA transposases reveals intron loss as major factor influencing their exon/intron structure in monocotyledonous and eudicotyledonous hosts., in Mobile DNA, 5, 24.
Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution.
Oberhaensli Simone, Parlange Francis, Buchmann Jan P, Jenny Fabian H, Abbott James C, Burgis Timothy A, Spanu Pietro D, Keller Beat, Wicker Thomas (2011), Comparative sequence analysis of wheat and barley powdery mildew fungi reveals gene colinearity, dates divergence and indicates host-pathogen co-evolution., in Fungal Genet Biol, 48(3), 327-334.
Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley.
Vu Giang T H, Wicker Thomas, Buchmann Jan P, Chandler Peter M, Matsumoto Takashi, Graner Andreas, Stein Nils (2010), Fine mapping and syntenic integration of the semi-dwarfing gene sdw3 of barley., in Funct. Integr. Genomics, 10, 509-521.
Genome sequencing and analysis of the model grass \textit{Brachypodium distachyon}.
The International Brachypodium Initiative (2010), Genome sequencing and analysis of the model grass \textit{Brachypodium distachyon}., in Nature, 463(7282), 763-768.
Patching gaps in plant genomes results in gene movement and erosion of colinearity.
Wicker Thomas, Buchmann Jan P, Keller Beat (2010), Patching gaps in plant genomes results in gene movement and erosion of colinearity., in Genome Res., 20, 1229-1237.
Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity
Buchmann Jan P, Matsumoto Takashi, Stein Nils, Keller Beat, Wicker Thomas, Interspecies sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity, in The Plant Journal.

Collaboration

Group / person Country
Types of collaboration
National Institute of Agrobiological Sciences Japan (Asia)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
IPK Gatersleben Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Helmholtz-Zentrum München Germany (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
University of Helsinki Finland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Communication with the public

Communication Title Media Place Year
Media relations: print media, online media Weizen-Gene 20 Minuten German-speaking Switzerland 2010

Awards

Title Year
Poster Prize 2008

Associated projects

Number Title Start Funding scheme
138504 A bioinformatics study to unravel molecular mechanisms that drive genome evolution 01.01.2012 Project funding (Div. I-III)

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