The Rapidly Evolving Pan Genome of the Globally Distributed Coccolithophore Emiliania huxleyi

Coccolithophores are a critical functional group of marine phytoplankton. Through their ability to both calcify and photosynthetically fix carbon, this group of small calcite-covered microalgae exerts profound control over global climate by mediating the exchange of CO2 between the atmosphere and the ocean and has done so for hundreds of thousands of years. The haptophyte Emiliania huxleyi is the dominant coccolithophorid forming mesoscale blooms across diverse regimes in the contemporary oceans, often in regions inhospitable to other phytoplankton. We report the sequencing of 168 Mb draft genome sequence of E. huxleyi strain 1516, the first coccolithophore and the first of the haptophyte phylum, filling a major gap in the eukaryotic tree of life. Analysis of this novel organism identified genes related to key steps in the biomineralization of calcite. Resequencing genomes of 13 additional E. huxleyi isolates collected from disparate biogeographical locations, identified the presence of a diverse pan-genome, the first reported for a microbial eukaryote. Remarkably, the distribution of gene sets, including those related to harvesting light, acquiring nutrients and the metabolism of trace metals is highly variable between strains. This finding suggests that the composition of the genome could explain the extraordinary phenotypic diversity that has long been recognized in E. huxleyi, and is likely the mechanism that allows it to bloom in diverse regions of the global ocean.