Endosymbiosis has been a driving force in the evolution of eukaryotic cells. Subsequent to the evolution of ‘primary’ plastids (chloroplasts) from endosymbiotic cyanobacteria, photosynthesis has spread across the eukaryotic tree by ‘secondary endosymbiosis’, a process in which a primary plastid-bearing alga is assimilated by a non-photosynthetic eukaryote. Cryptophytes and chlorarachniophytes are unique among secondary plastid-containing algae in that the nuclei of their endosymbionts persist in a highly reduced and simplified form—the ‘nucleomorph’. Despite striking similarities in the size and structure of their genomes, the cryptophyte and chlorarachniophyte nucleomorphs are the product of independent endosymbiotic events involving different endosymbionts (red and green algae, respectively) and unrelated eukaryotic hosts. In this presentation I will discuss analysis of the recently sequenced nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, highlighting the unexpectedly complex ways in which their respective hosts and endosymbionts have melded at the genetic, biochemical and cellular level. In light of such data, challenges relating to our ability to accurately infer the evolutionary history of photosynthetic eukaryotes are also considered.
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