Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics

Free-living core dinoflagellates are commonly infected by members of two parasitic clades that are themselves closely related to dinoflagellates, the marine alveolates and perkinsids. These parasites are abundant and ecologically important, but most species have been difficult to observe directly or cultivate, so our knowledge of them is usually restricted to environmental 18S rRNA gene sequences, and genome-scale molecular data are not available for most species. Here, we report numerous syndinian parasites and one parasite that is sister to all known perkinsids from isolated single cells of diverse, free-living dinoflagellates. Of the 14 infected host cells collected, only five were noticeably infected via light microscopy at the time of collection. Single-cell transcriptome sequencing yielded relatively high transcriptomic coverage for parasites as well as their hosts. Host and parasite homologs were distinguished phylogenetically allowing us to infer a robust phylogenomic tree based on 198 genes. The tree showed one parasite belongs to an undescribed lineage that is sister to perkinsids, whereas the remainder are members of the syndinian clade. Close relatives of all these parasites have been observed in 18S rRNA gene surveys, but until now none had been linked to a specific host. These findings illustrate the efficacy of single-cell isolation and transcriptome sequencing as a strategy for gaining deeper insights into the evolutionary history and host relationships of hidden single-celled parasites.