165: Protist Genomics: Key to Understanding Eukaryotic Evolution

️ Episode 165: Protist Genomics: Key to Understanding Eukaryotic Evolution In this episode of PaperCast Base by Base, we explore how accelerating protist genomics—spanning single-cell approaches, metagenomics, and long-read assemblies—unlocks deep insights into eukaryotic evolution, symbiosis, organelle origins, ecosystem dynamics, and the methodological shifts needed to go beyond plant/animal-centric standards. Study Highlights:This review argues that protists encompass most eukaryotic diversity yet remain severely underrepresented in genome databases, creating blind spots in phylogenomics and models of eukaryotic evolution. It synthesizes emerging wet-lab and computational strategies—such as FACS-enabled single-cell sequencing, nuclei extraction for high-molecular-weight DNA, and long-read plus Hi-C scaffolding—to recover genomes from uncultured and symbiotic taxa. The authors emphasize tailored decontamination and annotation pipelines, taxon-specific BUSCO core sets, and the value of releasing intermediate-quality assemblies to bootstrap reference databases. The article connects genomic advances to big-picture questions including endosymbiosis, repeated origins of multicellularity, terrestrialization, and the roles of protists in biogeochemical cycles and community networks. Conclusion:Centering protist diversity in genome initiatives, and embracing fit-for-purpose standards and pipelines, will rapidly expand high-quality resources and transform our understanding of eukaryotic cell evolution and ecosystem function. Reference:Schoenle A, Francis O, Archibald JM, Burki F, de Vries J, Dumack K, Eme L, Florent I, Hehenberger E, Hoffmeyer TT, Irisarri I, Lara E, Leger MM, Lukeš J, Massana R, Mathur V, Nitsche F, Strassert JFH, Worden AZ, Yurchenko V, del Campo J, Waldvogel A-M. Protist genomics: key to understanding eukaryotic evolution. Trends in Genetics. 2025. https://doi.org/10.1016/j.tig.2025.05.004 License:This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/ Support:If you'd like to support Base by Base, you can make a one-time or monthly donation here: https://basebybase.castos.com/

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