Phylogenomic frameworks from deep archaeplastid evolution to embryophyte diversification

All photosynthesizing eukaryotes that are the major constituents of our biosphere can ultimately be traced back to the lineage of Archaeplastida. The Archaeplastida emerged in one of the great singularities that occurred during evolution, when the cyanobacterial progenitor of all plastids was engulfed by a heterotrophic protist. Not only did the immense diversity of primary plastid-housing red algae, green algae, plants, and more emerge from this unique event but so did, through secondary endosymbioses, other diverse major lineages like diatoms and kelps. Here, we focus on the primary plastid-bearing Archaeplastida. In the past years, major progress has been made in our understanding of the evolution of Archaeplastida, foremost expedited by phylodiverse genomic sequencing efforts that allow us to compute robust phylogenomics-based frameworks onto which, following a genotype-to-phenotype rationale, traits gleaned from the same genomic data can be placed. We discuss the emergence of body plans, tracing and understanding the modes of organelle evolution alongside the impact of endosymbiotic gene transfer, and general genome evolution. Finally, we outline how, reconciled, these reshaped our thinking about archaeplastid evolution and how it provides impetus for addressing the next outstanding challenges.