Project

Back to overview

A bioinformatics study to unravel molecular mechanisms that drive genome evolution

English title A bioinformatics study to unravel molecular mechanisms that drive genome evolution
Applicant Wicker Thomas
Number 138504
Funding scheme Project funding
Research institution Institut für Pflanzen- und Mikrobiologie Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Molecular Biology
Start/End 01.01.2012 - 31.12.2015
Approved amount 258'438.00
Show all

Keywords (4)

Genome evolution; Transposable element; Double-strand break repair; Genome colinearity

Lay Summary (English)

Lead
Lay summary

Genomes evolve through mutations, deletions and duplications of sequences. Several molecular mechanisms that drive these re-arrangements have been unraveled in recent years, but many questions are still not answered. Transposable elements (TEs) are mobile genetic units which can move around in the genome and/or make copies of themselves. Some TE are extremely successful colonisers which can reach thousands of copies in a genome. When the excise from or insert into the genome they can create double-strand breaks in the DNA that have to be repaired by the cell. This repair process is often not perfect and can lead to the loss or the duplication of DNA fragments. Recent results indicate that TEs are a major source of genetic variability and therefore probably one of the main driving force of genome evolution.

By comparing the complete genome sequences of three rice genomes we will study how often these TEs move and replicate in the genome. This will allows us to trace how much of their activity leads to DNA damage and what kind of rearrangements follow during the DNA repair process. Especially, we will investigate the frequency with which gene sequences are duplicated and moved across the genome in this process. Performing the same type of analysis also in animal (e.g. Drosophila) and fungal (e.g. yeast) genomes will reveal if the same mechanisms are at work in all eukaryotic genomes.

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses
Wicker Thomas, et al., Roffler Stefan (2016), DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses, in Nat Commun, 7(12790), 1-9.
Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles.
Parlange Francis, Roffler Stefan, Menardo Fabrizio, Ben-David Roi, Bourras Salim, McNally Kaitlin E, Oberhaensli Simone, Stirnweis Daniel, Buchmann Gabriele, Wicker Thomas, Keller Beat (2015), Genetic and molecular characterization of a locus involved in avirulence of Blumeria graminis f. sp. tritici on wheat Pm3 resistance alleles., in Fungal genetics and biology : FG & B, 82, 181-92.
Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons.
Roffler Stefan, Wicker Thomas (2015), Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons., in Mobile DNA, 6, 8-8.
Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species.
Menardo Fabrizio, Praz Coraline R, Wyder Stefan, Ben-David Roi, Bourras Salim, Matsumae Hiromi, McNally Kaitlin E, Parlange Francis, Riba Andrea, Roffler Stefan, Schaefer Luisa K, Shimizu Kentaro K, Valenti Luca, Zbinden Helen, Wicker Thomas, Keller Beat (2015), Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species., in Nature genetics, 48(2), 201-5.
Multiple Avirulence Loci and Allele-Specific Effector Recognition Control the Pm3 Race-Specific Resistance of Wheat to Powdery Mildew.
Bourras Salim, McNally Kaitlin Elyse, Ben-David Roi, Parlange Francis, Roffler Stefan, Praz Coraline Rosalie, Oberhaensli Simone, Menardo Fabrizio, Stirnweis Daniel, Frenkel Zeev, Schaefer Luisa Katharina, Flückiger Simon, Treier Georges, Herren Gerhard, Korol Abraham B, Wicker Thomas, Keller Beat (2015), Multiple Avirulence Loci and Allele-Specific Effector Recognition Control the Pm3 Race-Specific Resistance of Wheat to Powdery Mildew., in The Plant cell, 27(10), 2991-3012.
The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants
Stafan Roffler, Fabrizio Menardo, Thomas Wicker (2015), The making of a genomic parasite - the Mothra family sheds light on the evolution of Helitrons in plants, in Mobile DNA, 6, 23.
Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe.
Middleton Christopher (2013), Sequencing of Chloroplast Genomes from Wheat, Barley, Rye and Their Relatives Provides a Detailed Insight into the Evolution of the Triticeae Tribe., in PlosOne, 9, e85761.
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph.
Wicker Thomas, Oberhaensli Simone, Parlange Francis, Buchmann Jan P, Shatalina Margarita, Roffler Stefan, Ben-David Roi, Doležel Jaroslav, Šimková Hana, Schulze-Lefert Paul, Spanu Pietro D, Bruggmann Rémy, Amselem Joelle, Quesneville Hadi, Ver Loren van Themaat Emiel, Paape Timothy, Shimizu Kentaro K, Keller Beat (2013), The wheat powdery mildew genome shows the unique evolution of an obligate biotroph., in Nature genetics, 45(9), 1092-6.

Collaboration

Group / person Country
Types of collaboration
Arizona Genomics Institute (AGI) United States of America (North America)
- in-depth/constructive exchanges on approaches, methods or results
- Publication
Beat Keller, Universität Zürich Switzerland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
Plant and Animal Genome XXIV Conference Talk given at a conference DNA Transposons Specifically Accelerate the Evolution of Genes in Grasses 09.01.2016 San Diego, United States of America Wicker Thomas;
Plant and Animal Genome XXIV Conference Talk given at a conference How do gene content and gene order change over time? – Answers from Comparison of Closely Related Grasses 09.01.2016 San Diego, United States of America Wicker Thomas;
Plant and Animal Genome XXIII Conference Talk given at a conference Genome-Wide Analysis of Transposon Insertion and Excision Patterns in the Two Rice Species O. sativa and O. glaberrima 10.01.2015 San Diego, United States of America Wicker Thomas; Roffler Stefan;


Associated projects

Number Title Start Funding scheme
122242 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 01.10.2008 Project funding
163325 A study on the origin of plant-specific genes 01.07.2016 Project funding

Abstract

Background:Genomes evolve through mutations, deletions and duplications of sequences. Several molecular mechanisms that drive these re-arrangements have been unraveled in recent years, but many questions are still not answered. For instance, it is only in part understood how (and how frequently) genes and other genomic sequences are moved across the genome during evolution, leading to the erosion of sequence colinearity between species. Additionally, the impact of transposable elements (TEs) on genome evolution is still obscure, although TEs contribute most of the genomic sequences in many species. Working hypothesis:When TEs insert into or excise (in the case of DNA transposons) from the genome, they introduce double-strand breaks (DSBs). We propose that the repair of these DSBs is the major source of genomic re-arrangements. Depending on which DSB repair pathway is employed, it can lead to extensive deletions or duplications of genomic sequences. Since TEs and DSB repair mechanisms are ubiquitous in all eukaryotes, the same types of genomic rearrangements should be observable in all eukaryotic genomes. Specific claim:The excision of class 2 (DNA) transposons is the most frequent cause for genomic re-arrangements. Repair of the DSB can lead to deletions that range from a few bp to several kb. Alternatively, a copy of a foreign DNA fragment is inserted as “filler” at the site of the breakpoint. Such fillers can be dozens of kb is size. This process can lead to the duplication of genes, thereby driving the slow erosion of sequence colinearity between species. Experimental design:By comparing several closely related rice species, we want to track transposon activity (insertions and excisions) at a genome-wide level. This will provide data on the frequency of TE insertions and excisions and allows to calculate an activity index for different TE superfamilies and families. Detailed analysis of TE insertion and excision sites will provide information on how often genomic sequences are deleted or duplicated as a result of TE activity. Especially, we will investigate the frequency with which gene sequences are duplicated and moved across the genome in this process. Performing the same type of analysis also in animal (e.g. Drosophila) and fungal (e.g. yeast) genomes will reveal if the same mechanisms are at work in all eukaryotic genomes. The proposed analyses will require the compilation of a comprehensive high-quality TE database from all the species investigated. This database can then also be used for a broad phylogenetic study on the evolutionary origin and early evolution of TE populations in eukaryotes. Expected value of the proposed project:Understanding the mechanisms by which genomes evolve is at the very basis of our understanding of evolution. We address two major questions, namely how often do TEs move around in the genome and how does their activity influence the structure of the genome. Additionally, with our analysis we want to cross the (mainly historical) division of plant, animal and fungal genomics. The proposed research is timely because now, a very large number of genome sequences have become or will become publicly available. Analyzing this vast amount of data will be the primary challenge in biology in the coming years. Important biological discoveries will come from large-scale comparative analyses such as the one proposed. Additionally, an important methodological outcome of the proposed project will be the development of bioinformatics tools and algorithms that allow the efficient processing of very large amount of genomic sequence data.
-