If you are someone who is interested in the evolution, ecology or genomics of basal land plants and willing to use a rigorous statistical framework, population genetics, phylogenetics, modeling, sequence analysis (next-gen and genome data) or some combination of these to pursue hypothesis driven research you are at the right place. Basically, we encourage students to develop and bring in their own research ideas but joining to a running project is also possible. Please drop Peter a mail if you are interested to join us.
Putative Projects (as of 2015 Sept.)
1. Master project in evolutionary genomics (genome assembly)
This master project involves the sequencing, annotation and improvement of the Hornwort genome to begin to understand the evolution of developmental mechanisms in land plants.Keywords: Genome assembly, bioinformatics, evolution, DNA, genome annotation, evo-devo
Bryophytes are the extant representatives of the first plants that colonized the land about 480 million years ago. Morphological and functional complexity of land plants has rapidly increased after colonization from the relatively simple bryophytes to the highly complex vascular plants. Bryophytes are key to understand the evolutionary trajectories of developmental mechanisms during the land plant tree of life. Although, model systems are available for the lineages of mosses and the liverworts but investigation on the biology of hornworts was until now hindered by the lack of a proper model system and available genomic data. In order to study these questions we recently established a tractable hornwort model species, Anthoceros agrestis, and currently sequencing the genome of this species. We also developing efficient strategies to genetically transform this species. Master projects in this topic would involve bioinformatics analysis of the hornwort genome (assembly improvement, DNA extraction, genome annotation and phylogenomic analysis) and the testing of transformation methods previously established for mosses and liverworts.
Master projects in this topic would involve bioinformatic analysis of the hornwort genome (assembly improvement, DNA extraction, genome annotation and phylogenomic analysis) and the testing of transformation methods previously established for mosses and liverworts.
2. Ploidy imposed constraints on developmental processes
Autopolyploids are derived by the multiplication of the very same chromosomal set which only weakly affects gene regulation in most but not all organisms studied. This study addresses the question why does autoploidy has strong effects in some but weak effects in other groups of organisms. The effects of ploidy on gene regulation are of interest in plants because ploidy change has been known to have significantly contributed to the macro- and microevolution of extant species. Gene regulatory changes induced by ploidy are of also primary interest in animal systems owing to their central role in diseases development and progression.
Ploidy change can happen in two fundamentally different ways which differ in their molecular and phenotypic effects. Aneuploidy refers to the chromosomal situation where there are extra or missing segments of the genome. In contrast, polyploidy refers to the situation where there are multiple copies of the genome present beyond the normal diploid. It has been early observed that aneuploidy usually produces greater phenotypic effects than polyploidy. This observation is explained by the dosage balance hypothesis which predicts that aneuploidy strongly alters stoichiometry of subunits of regulatory complexes which changes the function as a whole and lead to strong phenotypic effects. In contrast, multiplication of the very same genome in autopolyploids will leave stoichiometry of
subunits intact and thus have minor phenotypic consequences. Much of the current work has focused on the effect of ploidy on gene regulation in aneuploids/allopolyploids and very little is known on autoploidy induced gene expression.
This project proposes to perform a study on the effect of autoploidy on gene regulation in the moss model system to gain insights into the molecular mechanisms of ploidy induced gene regulation. This will be done by the combination of high-throughput gene expression and methylation profiling. Follow up work with the toolbox of reverse genetic is also planned.
3. Polyploid speciation, meiosis and gene expression
Allopolyploids contain two sets of homeolog chromosomes (sub genomes) of two species. Often gene expression of the homeolog gene copies is biased towards one of the parental species, that is, one sub genome is dominant over the other. Nevertheless, the ultimate molecular mechanism responsible for the dominance of one genome over the other remains poorly understood. Furthermore, the association of sub genome dominance and the phenotype of the newly formed allopolyploid is vague. This study uses a complex of species consisting of two haploid progenitors, and their allopolyploid derivative. Although the two haploid progenitors are morphologically distinct the allopolyploid has the morphology of one of its progenitor. We use the system of these three species to investigate two major evolutionary questions: 1.) Which sub genome dominates in the allopolyploid and what is the plasticity of this dominance over developmental stages. 2.) What is the association of sub genome dominance and morphology and whether this can explain the strong morphological bias of the allopolyploid towards one of the progenitor species. In order to answer these questions we use a combination of large-scale sequencing, gene expression profiling and ecological experiments.
4. Sex chromosome evolution in haploid dioecy
Evolution of sex chromosomes is well-studied in organisms in which sex is expressed in the diploid phase. In such organisms the lack of recombination and the asymmetry in haploidy are assumed to lead to the progressive decay of the Y chromosome. In organisms in which sex is expressed in the haploid phase both U and V chromosomes are equally devoid of recombination and show no asymmetry in recombination suppression. This provides a unique opportunity to tease apart the effect of this two factors on the evolutionary trajectory of sex chromosomes. We are using a combination of classical genetic and comparative genomic approaches to test hypotheses concerning sex chromosome evolution in haploid dioecy using liverworts as a suitable model system (Marchantia polymorpha, Preissia quadrata and many more).
5. Evolutionary genomics of fungal hyperparasites
Understanding the biology of fungal parasites is of tremendous importance both for theoretical and practical reasons. From a theoretical point of it is of interest to understand how evolutionary trajectories of the parasite and host genomes is affected by their evolutionary arms race. From a practical point of view this information can guide the engineering of resistant strains. One special form of parasitism is hyper parasitism when a parasite has its own parasite. Ampelomyces spp. are intracellular mycoparasites of powdery mildew which are themselves important plant pathogens. While much is known on how host-parasite interactions shape evolutionary genomics of the two partners almost nothing is known in this respect on fungal hyper parasites. To begin to understand the evolutionary genomics of host parasite interaction we initiated sequencing of multiple Ampelomyces strains and we use this genomic data to understand how hyperparasitism shapes genome evolution of this special group of fungal parasites. This project is appropriate for students who want to gain experience in evolutionary theory, evolutionary genetics and bioinformatics.
NO DATA COLLECTION STEP IS NEEDED!
Ecology and population genetics
Testing the inverse isolation hypothesis: modeling island colonization using Approximate Bayesian Computation
Testing Darwin`s wind dispersal hypothesis: comparison of dispersal costs in spore- and seed-dispersed plants
Combining palynological and genetic data: GIS modeling of post-glacial recolonization of Europe
Local adaptation in haploid organisms: latitudinal and altitudinal clines
The genetic memory hypothesis of spore banks: are bryophyte spore banks a reservoir of genetic diversity?
Gene expression evolution
Comparative analysis of gene expression data across land plants (next-gen data sets)
Genome assembly and comparative analysis using next gen. sequencing data
Comparative genome assembly and analysis
This master project involves the sequencing, annotation and improvement of the Hornwort genome to begin to understand the evolution of developmental mechanisms in land plants.Keywords: Genome assembly, bioinformatics, evolution, DNA, genome annotation, evo-devo
Bryophytes are the extant representatives of the first plants that colonized the land about 480 million years ago. Morphological and functional complexity of land plants has rapidly increased after colonization from the relatively simple bryophytes to the highly complex vascular plants. Bryophytes are key to understand the evolutionary trajectories of developmental mechanisms during the land plant tree of life. Although, model systems are available for the lineages of mosses and the liverworts but investigation on the biology of hornworts was until now hindered by the lack of a proper model system and available genomic data. In order to study these questions we recently established a tractable hornwort model species, Anthoceros agrestis, and currently sequencing the genome of this species. We also developing efficient strategies to genetically transform this species. Master projects in this topic would involve bioinformatics analysis of the hornwort genome (assembly improvement, DNA extraction, genome annotation and phylogenomic analysis) and the testing of transformation methods previously established for mosses and liverworts.
Master projects in this topic would involve bioinformatic analysis of the hornwort genome (assembly improvement, DNA extraction, genome annotation and phylogenomic analysis) and the testing of transformation methods previously established for mosses and liverworts.
2. Ploidy imposed constraints on developmental processes
Autopolyploids are derived by the multiplication of the very same chromosomal set which only weakly affects gene regulation in most but not all organisms studied. This study addresses the question why does autoploidy has strong effects in some but weak effects in other groups of organisms. The effects of ploidy on gene regulation are of interest in plants because ploidy change has been known to have significantly contributed to the macro- and microevolution of extant species. Gene regulatory changes induced by ploidy are of also primary interest in animal systems owing to their central role in diseases development and progression.
Ploidy change can happen in two fundamentally different ways which differ in their molecular and phenotypic effects. Aneuploidy refers to the chromosomal situation where there are extra or missing segments of the genome. In contrast, polyploidy refers to the situation where there are multiple copies of the genome present beyond the normal diploid. It has been early observed that aneuploidy usually produces greater phenotypic effects than polyploidy. This observation is explained by the dosage balance hypothesis which predicts that aneuploidy strongly alters stoichiometry of subunits of regulatory complexes which changes the function as a whole and lead to strong phenotypic effects. In contrast, multiplication of the very same genome in autopolyploids will leave stoichiometry of
subunits intact and thus have minor phenotypic consequences. Much of the current work has focused on the effect of ploidy on gene regulation in aneuploids/allopolyploids and very little is known on autoploidy induced gene expression.
This project proposes to perform a study on the effect of autoploidy on gene regulation in the moss model system to gain insights into the molecular mechanisms of ploidy induced gene regulation. This will be done by the combination of high-throughput gene expression and methylation profiling. Follow up work with the toolbox of reverse genetic is also planned.
3. Polyploid speciation, meiosis and gene expression
Allopolyploids contain two sets of homeolog chromosomes (sub genomes) of two species. Often gene expression of the homeolog gene copies is biased towards one of the parental species, that is, one sub genome is dominant over the other. Nevertheless, the ultimate molecular mechanism responsible for the dominance of one genome over the other remains poorly understood. Furthermore, the association of sub genome dominance and the phenotype of the newly formed allopolyploid is vague. This study uses a complex of species consisting of two haploid progenitors, and their allopolyploid derivative. Although the two haploid progenitors are morphologically distinct the allopolyploid has the morphology of one of its progenitor. We use the system of these three species to investigate two major evolutionary questions: 1.) Which sub genome dominates in the allopolyploid and what is the plasticity of this dominance over developmental stages. 2.) What is the association of sub genome dominance and morphology and whether this can explain the strong morphological bias of the allopolyploid towards one of the progenitor species. In order to answer these questions we use a combination of large-scale sequencing, gene expression profiling and ecological experiments.
4. Sex chromosome evolution in haploid dioecy
Evolution of sex chromosomes is well-studied in organisms in which sex is expressed in the diploid phase. In such organisms the lack of recombination and the asymmetry in haploidy are assumed to lead to the progressive decay of the Y chromosome. In organisms in which sex is expressed in the haploid phase both U and V chromosomes are equally devoid of recombination and show no asymmetry in recombination suppression. This provides a unique opportunity to tease apart the effect of this two factors on the evolutionary trajectory of sex chromosomes. We are using a combination of classical genetic and comparative genomic approaches to test hypotheses concerning sex chromosome evolution in haploid dioecy using liverworts as a suitable model system (Marchantia polymorpha, Preissia quadrata and many more).
5. Evolutionary genomics of fungal hyperparasites
Understanding the biology of fungal parasites is of tremendous importance both for theoretical and practical reasons. From a theoretical point of it is of interest to understand how evolutionary trajectories of the parasite and host genomes is affected by their evolutionary arms race. From a practical point of view this information can guide the engineering of resistant strains. One special form of parasitism is hyper parasitism when a parasite has its own parasite. Ampelomyces spp. are intracellular mycoparasites of powdery mildew which are themselves important plant pathogens. While much is known on how host-parasite interactions shape evolutionary genomics of the two partners almost nothing is known in this respect on fungal hyper parasites. To begin to understand the evolutionary genomics of host parasite interaction we initiated sequencing of multiple Ampelomyces strains and we use this genomic data to understand how hyperparasitism shapes genome evolution of this special group of fungal parasites. This project is appropriate for students who want to gain experience in evolutionary theory, evolutionary genetics and bioinformatics.
NO DATA COLLECTION STEP IS NEEDED!
Ecology and population genetics
Testing the inverse isolation hypothesis: modeling island colonization using Approximate Bayesian Computation
Testing Darwin`s wind dispersal hypothesis: comparison of dispersal costs in spore- and seed-dispersed plants
Combining palynological and genetic data: GIS modeling of post-glacial recolonization of Europe
Local adaptation in haploid organisms: latitudinal and altitudinal clines
The genetic memory hypothesis of spore banks: are bryophyte spore banks a reservoir of genetic diversity?
Gene expression evolution
Comparative analysis of gene expression data across land plants (next-gen data sets)
Genome assembly and comparative analysis using next gen. sequencing data
Comparative genome assembly and analysis