Elucidating changes in gene expression driving nuclear dynamics across a foraminiferal life cycle with Pheno2Seq

In many microeukaryotes, conserved morphology masks transitions between haploid and diploid phases of the life cycle, making it difficult to link gene expression to development. Hence, insights on such transitions come largely from model lineages of animals, plants and fungi. To address this gap, we developed a method, Pheno2Seq, that enables visualization of fluorescently-stained individuals followed by identification of candidate genes through single-cell transcriptome analyses. We applied this method in Allogromia laticollaris, a foraminifera with a complex life cycle that alternates between haploid and diploid phases and includes endoreplication to ~11,000N. As this taxon lacks a reference genome, we used a conservative phylogenomic approach to identify gene families present across diverse foraminifera. We identified >800 differentially expressed genes underlying life cycle transitions along with a similar number of constitutively-expressed genes. During Zerfall, a phase of extreme endoreplication, the transcriptome is largely silenced with the exception of gene families involved in genome processes and stability. Intriguingly, these gene families include chromatin modifiers, spliceosomal components and histone paralogs, some of which are known to contribute to cell type differentiation in multicellular eukaryotes. We also find numerous genes involved in DNA repair (e.g. DNA damage response and R-loop regulating genes). We speculate that these genes are part of an ancient eukaryotic toolkit, likely present in the last eukaryotic common ancestor (LECA) and that regulates genomes during life cycle transitions. Our method, Pheno2Seq, can be adapted to diverse lineages to enable the study of life cycle regulation in microeukaryotes that lack morphologically distinguishable life cycle stages.