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

Protists are vastly diverse, forming over 20 supergroups of the eukaryotic diversity and fulfilling plentiful functions. Rhizaria is a widespread and highly abundant clade 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 limited genomic and transcriptomic data and methodological challenges associated with cross-species comparative transcriptome analyses. In this study, we assembled 15 transcriptomes of the bacterivorous Rhogostoma and their eukaryvorous relatives. By combining phylogenomic analyses and comparative analyses of population-level transcriptomes, we established an evolutionary framework to which we relate orthogroup similarity, orthogroup expression patterns, and functional annotations. The morphologically highly similar Rhogostoma strains formed two distinct phylogenetic clusters differing in orthogroups and orthogroup expression patterns related to cell adhesion and biofilm formation. Furthermore, we observed considerable intra-genus variation in amino acid and lipid metabolism in Rhogostoma, as well as lower completeness of these pathways compared to their eukaryvorous relatives. We hypothesize that the thecofilosean ancestor underwent a reduction in metabolic versatility, explained by increased specialization and reduced food spectra, which provided the foundation for subsequent metabolic radiation within Rhogostoma. Overall, our findings indicate that even closely related and morphologically similar species in Rhizaria may differ distinctly in their functional repertoire.