Our view on organismal evolution is intimately connected to our understanding of how genomes and the encoded information change over time, and how this translates to the phenotypic and functional characteristics of contemporary species. The sequencing of entire genomes and transcriptomes from species covering all major groups in the tree of life has lifted the data basis for evolutionary research with a functional perspective to an unprecedented level. In its combination, this data facilitates access to the full repertoire of information stored in a species’ genome and allows unraveling individual cellular programs translating genetic information into a diverse set of functions. However, the effort connected to the experimental functional characterization of even considerably few proteins in the lab is still enormous. It is for this reason that exhaustive functional studies are limited to few and well established model organisms, many of which are of economical or medical relevance. More often only individual pathways are studied in niche model organisms featuring a particular trait of interest. However, for the vast majority of species only a draft genome assembly or transcript data is available without further experimental support. In these instances the in silico prediction of genes together with a subsequent tentative transfer of functional annotation from corresponding sequences in experimentally characterized model organisms provides the only source of functional information. Integrating all available information into a comprehensive picture of organismal and functional evolution is the common denominator of the individual projects in our group.
More specifically, we concentrate on the following main topics: Expand all...
1) Deep phylogenies and phylogenetic profiling
We use phylogenomics approaches considering hundreds of genes across a similar number of species to reconstruct comprehensive phylogenies up to the kingdom level. We attempt to assess the credibility of the reconstructed trees by using – whenever possible – multiple and non-overlapping data sets to support individual splits. The resulting trees provide the scaffold for subsequently mapping information about the presence and absence of genes in large numbers of species considering both sequence homology and functional domain architecture. With the help of these phylogenetic profiles we can start tracing entire protein interaction networks together with the associated function across species and provide insights into their evolutionary history.
2) Functional annotation transfer
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3) Phylostratigraphy and evolution of gene interaction networks.
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4) Source of genetic and functional innovation
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5) Development of software and workflows for biological sequence analysis
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