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
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2) Functional annotation transfer
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3) Phylostratigraphy and evolution of gene interaction networks.
Phylogenetic profiles of proteins sharing the same function allow reconstructing when in evolutionary history individual gene interaction networks emerged, and help assessing their fate in individual phylogenetic lineages. This provides valuable insights into the direction of organismal evolution. Partial or complete losses of evolutionary old pathways indicate reductive evolution often associated with the change of an ancestral phenotype. For example, Microsporidia, obligate intracellular parasites closely related to fungi, lack more than half of the otherwise highly conserved eukaryotic ribosome biogenesis factors. Whether this reduction coincides with an - among eukaryotes - unique way of ribosome biogenesis facilitated by their endoparasitic lifestyle, or whether they recruit host proteins to rescue the conventional pathway remains unclear. Evolutionary young functional modules confined to few and closely related organisms living under similar environmental conditions represent the other extreme. They can pinpoint recent innovations facilitating the adaptation of species to their particular ecological niches. Part of this work with a particular focus on the evolution of calcium and stress signaling in plants is funded by the FP7-PEOPLE-2013-ITN CALIPSO (http://itn-calipso.univie.ac.at/).
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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