Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.

Centre de Recherches Interdisciplinaires Paris France

CNRS IBPS Laboratoire de Biologie Computationnelle et Quantitative UMR 7238 Sorbonne Université Paris France

CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution FR2022 Tara Oceans GOSEE Paris France

Faculty of Mathematics and Physics Charles University Prague Czechia

Faculty of Science Charles University BIOCEV Vestec Czechia

Institut de Biologie de l'École Normale Supérieure École Normale Supérieure CNRS INSERM Université PSL Paris France

Institute Jacques Monod Paris France

Tsinghua UC Berkeley Shenzhen Institute Shenzhen China

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