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bioRxiv · 10.1101/2025.10.20.683504

Physiological diversity and adaptation of Rhizaria revealed by phylogenomics and comparative transcriptomics

Freudenthal, J.·Bonkowski, M.·Engelmann, N.-J. M.·Schlegel, M.·Dumack, K.
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Abstract

Protists are vastly diverse, forming over 20 supergroups of the eukaryotic diversity and fulfilling plentiful functions. Rhizaria is a widespread and highly abundant supergroup comprising important parasites and a huge diversity of free-living heterotrophic predators. Despite the diversity and biogeochemical importance of Rhizaria, our understanding of their physiology and metabolic capabilities remains limited, mainly due to a general lack of data and bioinformatic tools for cross-species comparisons of physiological traits. In this study, we assembled a total of 15 transcriptomes of the parasite-related bacterivorous Rhogostoma and their eukaryvorous relatives. By phylogenomic analyses and whole transcriptome comparison, we established an evolutionary framework to which we relate physiological traits. The morphologically highly similar Rhogostoma strains branch in two distinct clusters differing in orthogroups and gene expression patterns related to cell adhesion and biofilm formation. Furthermore, we reveal considerable intra-genus variation in amino acid and lipid metabolism, which might be explained by an ancient streamlining through gradual specialization to parasitism, bearing the potential for subsequent metabolic radiation. We conclude that even closely related and morphologically similar species in Rhizaria may differ distinctly in their functional repertoire. With the here established and showcased analyses, we create a basis for future characterization of the physiological traits of microeukaryotes.

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Freudenthal, J., Bonkowski, M., Engelmann, N.-J. M., Schlegel, M., Dumack, K.. 2025-10-22. Physiological diversity and adaptation of Rhizaria revealed by phylogenomics and comparative transcriptomics. https://doi.org/10.1101/2025.10.20.683504

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