Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years. [Display omitted] •Nearly 300 billion metagenomic reads were co-assembled from plankton in the oceans•Hundreds of eukaryotic environmental genomes were characterized and curated•These genomes better represent eukaryotic plankton compared to cultivation•These genomes reveal a functional convergence of distantly related eukaryotes Delmont et al. use nearly 300 billion metagenomic reads to characterize the genomic content of some of the most abundant and widespread eukaryotic populations in the sunlit ocean. This large genomic resource covers taxa underrepresented in our culture portfolio and exposes a functional convergence of distantly related eukaryotic plankton lineages.