Cryptomonads: A Model Organism Sheds Light on the Evolutionary History of Genome Reorganization in Secondary Endosymbioses

The cryptomonads are ubiquitous in the earth's hydrosphere. Most members of this unicellular group are photosynthetic and retain red alga-derived plastids. The significant feature of cryptomonads from an evolutionary and biological point of view is that they contain the residual nucleus of a eukaryotic endosymbiont, the so-called nucleomorph, which is direct evidence of eukaryote–eukaryote endosymbiosis. Besides cryptomonads, this unusual organelle has been found only in chlorarachniophytes so far. In the first half of this chapter, we briefly describe cryptomonad morphology, classification, and phylogeny. The evolutionary history of auto- or heterotrophic lifestyle transitions in cryptomonads is discussed. In the latter part, we focus on the recent outcomes of comparative genomics and review perspectives on the genome reorganization process that occurs during the integration of two eukaryotes into one organism.