We study major transitions in metazoan evolution from the perspective of the underlying genomic changes. Over the past years, we have contributed to the broader sampling of metazoan genomes, revealing ancestral metazoan and bilaterian genomic architectures and their diversification patterns. While we can trace back many gene families to the ancient metazoan ancestor, we also find many of them linked at both micro- (local gene cluster) and macro-syntenic (chromosomal) levels. The functional significance of most of those linkages during development is unknown. Having a broad phylogenetic focus we aim to (1) characterize and expand our knowledge of conserved and novel gene linkages and their associated (non-coding) elements across metazoans, (2) study their evolutionary dynamics through comparative genomics and modeling approaches, and (3) establishing molecular tools for investigating their role during development and clade-specific innovation. Inspired by the analysis of the octopus genome, current research focuses on characterizing the genomes of other cephalopod species, in particular investigating the gene linkage and repetitive element dynamics and their role in the emergence of cephalopod novelties. We are also contributing to the functional study of gene linkages in an emerging cephalopod model system Euprymna scolopes (Hawaiian bobtail squid) and the cnidarian hydra (Hydra magnipapillata).