Regulatory impact of syntenic transitions in animal genomes

One of the most exciting genomic discoveries to date is that, despite living about 600 million years ago and having a relatively simple body plan, the last common ancestor of all multicellular animals (metazoans) had a complex genome sharing numerous genes with recent species such as humans. This important finding prompted the hypothesis that the evolutionary diversification of animal species depends not only on gene loss and the emergence of novel genes, but also on changes in how genes are arranged within the genome. Using current comparative genomics methods, we can detect conserved patterns of gene order (synteny) across all metazoan groups. Our goal is to determine whether these syntenies constitute actual functional units within animal genomes (i.e. co- or cross-regulated gene networks) and to assess their putative contribution to crucial evolutionary transitions within Metazoa. Specifically, we plan to address the origin of bilaterian symmetry (or bilaterian animals) from a non- bilaterian metazoan ancestor, because this transition involved addition of multiple novel syntenies. Thus, we will first develop an improved method of synteny detection that utilizes phylogenetic inference to identify ancient changes in gene order. Next, we will test if old and novel gene orders form functional genomic units and compare their specific biological roles, respectively by screening for co- /cross-regulatory gene interactions and by analyzing their downstream effects, i.e. on the establishment of (non-)bilaterian body axes. This approach will allow us to elucidate how re-organization of ancient genomes led to the emergence of new functional gene orders and, consequently, new biological characters. Taken together, this project will provide a first characterization of the contribution of both large-scale chromosomal rearrangements and smaller-scale local gene rearrangements to the evolution of novel gene regulatory landscapes as well as complex traits in metazoan animals.

The main goal of the project was to understand how animal genomes are organized and how different this organization can be between different clades. The project identified fundamental "building blocks" of animal genomes and how chromosomes of modern day animals are comprised of such blocks, many of which date back to the original of animals over 600 million years ago. Animal genomes can thus be represented as a combination of such ancient building blocks and the resulting chromosomes are a playground for the emergence of many novel local genomic features. The project developed novel bioinformatic approach to investigate these properties and their evolutionary history. Together, it helped us further decipher animal genomes, going beyond just genes and extending to how these genes are organized on chromosomes, and with this identify novel features that may have functional relevance.