Impact of secondary endosymbiosis on eukaryotic genome evolution

The process of endosymbiosis has been a monumental force in the origin and diversification of eukaryotic (nucleus-containing) organisms. 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 non-photosynthetic host. Secondary endosymbiosis has given rise to some of the most abundant and ecologically significant aquatic photosynthesizers on the planet, including heterokonts (e.g., diatoms and giant kelp) and the 'red tide'-causing dinoflagellates. We are leading a DOE Joint Genome Institute (JGI)-funded effort to sequence the nuclear genomes of two secondary plastid-containing algae of pivotal evolutionary and cell biological significance, the cryptomonad Guillardia theta and the chlorarachniophyte Bigelowiella natans. Together, these organisms are unique in that they still possess the nucleus (nucleomorph) and cytoplasm of their algal endosymbionts in a highly reduced and simplified form. The limited coding capacity of the cryptomonad and chlorarachniophyte nucleomorphs indicates that the nuclear genomes of these organisms have been repositories for thousands of endosymbiont-derived genes throughout their evolutionary history. The goal of this project is to (i) spearhead community efforts to 'annotate' the Guillardia and Bigelowiella genome sequences (ii) establish the bioinformatic resources with which to store, manage and analyze our whole genome datasets, and (iii) perform a variety of genomic analyses related to the DOE-JGI project's main goals. Comparing and contrasting the Guillardia and Bigelowiella genome sequences will provide an unprecedented window into the process of secondary endosymbiosis and the integration of their respective hosts and endosymbionts at the genetic, biochemical and cellular level.