Diplonemids are among the most abundant and species-rich protists in the oceans. Marine heterotrophic flagellates, including diplonemids, have been suggested to play important roles in global biogeochemical cycles. Diplonemids are also the sister taxon of kinetoplastids, home to trypanosomatid parasites of global health importance, and thus are informative about the evolution of kinetoplastid biology. However, the genomic and cellular complement that underpins diplonemids' highly successful lifestyle is underexplored. At the same time, our framework describing cellular processes may not be as broadly applicable as presumed, as it is largely derived from animal and fungal model organisms, a small subset of extant eukaryotic diversity. In addition to uniquely evolved machinery in animals and fungi, there exist components with sporadic (i.e., "patchy") distributions across other eukaryotes. A most intriguing subset are components ("jötnarlogs") stochastically present in a wide range of eukaryotes but lost in animal and/or fungal models. Such components are considered exotic curiosities but may be relevant to inferences about the complexity of the last eukaryotic common ancestor (LECA) and frameworks of modern cell biology. Here, we use comparative genomics and phylogenetics to comprehensively assess the membrane-trafficking system of diplonemids. They possess several proteins thought of as kinetoplastid specific, as well as an extensive set of patchy proteins, including jötnarlogs. Diplonemids apparently function with endomembrane machinery distinct from existing cell biological models but comparable with other free-living heterotrophic protists, highlighting the importance of including such exotic components when considering different models of ancient eukaryotic genomic complexity and the cell biology of non-opisthokont organisms.

Division of Infectious Diseases Department of Medicine and Department of Biological Sciences University of Alberta 1 124 Clinical Sciences Building 11350 83 Avenue Edmonton AB T6G 2G3 Canada; Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 1160 31 České Budějovice 370 05 Czech Republic; Life Science Research Centre Department of Biology and Ecology Faculty of Science University of Ostrava Chittussiho 10 Ostrava 710 00 Czech Republic; Department of Parasitology Faculty of Science Charles University BIOCEV Průmyslová 595 Vestec 252 50 Czech Republic

Division of Infectious Diseases Department of Medicine and Department of Biological Sciences University of Alberta 1 124 Clinical Sciences Building 11350 83 Avenue Edmonton AB T6G 2G3 Canada; Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 1160 31 České Budějovice University College London Gower Street London WC1E 6BT UK

Institute of Parasitology Biology Centre Czech Academy of Sciences Branišovská 1160 31 České Budějovice 370 05 Czech Republic; Faculty of Science University of South Bohemia Branišovská 1645 31a České Budějovice 370 05 Czech Republic

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