Exploring Nuclear Duality in Foraminifera: Insights from Single-cell ‘Omics and Fluorescence Microscopy

Foraminifera are unicellular eukaryotes known to display unusual genome dynamics reflected in their nuclear architecture, including rare heterokaryosis (distinction of two nuclei types within the cell; Grell, 1954, 1979). We compare our cultured rotaliids to previously documented heterokaryotic Rotaliella species to assess potential heterokaryosis. Using the modern technologies of fluorescence microscopy, transcriptomics, and phylogenetic analysis, we assessed the rotaliids nuclear organization and phylogenomic placement with foraminifera. Fluorescence imaging revealed the rotaliids to be multinucleate and broadly exhibited features consistent with heterokaryotic architecture previously described in the species of R. heterocaryotica and R. elatiana. SSU rDNA-inferred and species trees (concatenated from 300 protein-coding genes) revealed the rotaliids to be in a well-supported Rotaliella clade. Our findings support the identification of our rotaliid samples as Rotaliella, suggesting potential heterokaryosis, which is prevalent in this genus. Our phylogenies differed at the super familial level, forcing us to consider their limitations. Ultimately, future transcriptome sequencing will be crucial in resolving such conflicts. Collectively, the molecular and microscopic evidence in this study advances our understanding of nuclear diversity and evolution in foraminifera and in eukaryotes in general.