The process of endosymbiosis, where one organism lives inside another, has been a monumental force in the origin and diversification of eukaryotic life. The primary endosymbiotic origin of plastids (chloroplasts) occurred more than a billion years ago and spawned three lineages--the green algae (and their land plant relatives), red algae, and glaucophytes--whose energy-generating capabilities paved the way for a transformation of the biosphere. The photosynthetic organelles of red and green algae have spread to unrelated eukaryotes by secondary endosymbiosis--the engulfment and retention of an algal cell inside a nonphotosynthetic host. Secondary endosymbiosis has given rise to some of the most abundant and ecologically significant aquatic photosynthesizers on the planet, including the heterokonts (e.g., diatoms and giant kelp), haptophytes (e.g., Emiliania), and the 'red tide'- causing dinoflagellate algae, as well as a variety of eukaryotic microbes of critical importance to human health (e.g., the malaria parasite Plasmodium).
To better understand the process of secondary endosymbiosis and its impact on the molecular and cell biology of secondary plastid-containing algae, the nuclear genome of the cryptophyte alga Guillardia theta was sequenced. Together with chlorarachniophytes, the cryptophytes are unusual in that they still possess the nucleus (nucleomorph) and cytoplasm of their algal endosymbionts in a highly reduced and simplified form. The chlorarachniophytes and cryptophytes are the product of independent secondary endosymbiotic events involving different endosymbionts (green and red algae, respectively) and unrelated eukaryotic host cells. The limited coding capacity of the nucleomorphs and plastids of both lineages indicates that their respective nuclear genomes have been repositories for thousands of endosymbiont-derived genes throughout their evolutionary history. Together with the nuclear genome of the chlorarachniophyte Bigelowiella natans, which has also been sequenced, the G. theta genome provides an important window into the process of host-endosymbiont integration at the genetic, biochemical, and cellular levels.