Comparative single-cell transcriptional atlases ofBabesiaspecies reveal conserved and species-specific expression profiles

Abstract

ABSTRACTBabesiais a genus of Apicomplexan parasites that infect red blood cells in vertebrate hosts. Pathology occurs during rapid replication cycles in the asexual blood-stage of infection. Current knowledge ofBabesiareplication cycle progression and regulation is limited and relies mostly on comparative studies with related parasites. Due to limitations in synchronizingBabesiaparasites, fine-scale time-course transcriptomic resources are not readily available. Single-cell transcriptomics provides a powerful unbiased alternative for profiling asynchronous cell populations. Here, we applied single-cell RNA sequencing to threeBabesiaspecies (B. divergens, B. bovis, andB. bigemina). We used analytical approaches and algorithms to map the replication cycle and construct pseudo-synchronized time-course gene expression profiles. We identify clusters of co-expressed genes showingjust-in-timeexpression profiles, with gradually cascading peaks throughout asexual development. Moreover, clustering analysis of reconstructed gene curves reveals coordinated timing of peak expression in epigenetic markers and transcription factors. Using a regularized Gaussian Graphical Model, we reconstructed co-expression networks and identified conserved and species-specific nodes. Motif analysis of a co-expression interactome of AP2 transcription factors identified specific motifs previously reported to play a role in DNA replication inPlasmodiumspecies. Finally, we present an interactive web-application to visualize and interactively explore the datasets.