Major transitions in evolution can be defined as those involving drastic habitat shifts or changes in organismal organization. These are special events in evolution where innovation and diversification rates accelerate, making them ideal systems to study the mechanisms that generate diversity. Genomic data, especially when combined with other data sources, offer an unprecedented opportunity to understand such events not only at the genomic but also at the phenotypic level. Often, this is done by studying species traits within a comparative framework, which uses phylogeny to discern convergence from common descent. Yet, the phylogeny underlying major evolutionary transitions is often blurred due precisely to the fast diversification we are interested in. In this talk, I will cover previous and current works on our attempt to clarify both the evolutionary relationships and genomic innovations in water-to-land transitions of vertebrates and plants and the origin of photosynthetic eukaryotes by symbiosis.