Loss of key endosymbiont genes may facilitate early host control of the chromatophore in .

The primary plastid endosymbiosis (∼124 Mya) that occurred in the heterotrophic amoeba lineage, , is at an earlier stage of evolution than in Archaeplastida, and provides an excellent model for studying organelle integration. Using genomic data from photosynthetic , we identified a plausible mechanism for the evolution of host control of endosymbiont (termed the chromatophore) biosynthetic pathways and functions. Specifically, random gene loss from the chromatophore and compensation by nuclear-encoded gene copies enables host control of key pathways through a minimal number of evolutionary innovations. These gene losses impact critical enzymatic steps in nucleotide biosynthesis and the more peripheral components of multi-protein DNA replication complexes. Gene retention in the chromatophore likely reflects the need to maintain a specific stoichiometric balance of the encoded products (e.g., involved in DNA replication) rather than redox state, as in the highly reduced plastid genomes of algae and plants.