Single-Cell Transcriptomes and Phylogenomic Analysis of Uncultivated Oxymonads

The oxymonads are anaerobic protist symbionts of animals with spectacular morphological complexity and variability, but because only a handful of species have been cultured, very little data are available for the group. This includes molecular data, with only a couple of species having sequenced genomes or transcriptomes. Oxymonads are divided into five families in a classification that has remained more or less unchanged for 35 years, but the relationships of these families are unknown due to a lack of molecular data from three of them. Here, we used single cell transcriptomics on six species from five genera (Oxymonas, Streblomastix, Pyrsonympha, Saccinobaculus, and Laeohelix) to carry out the first phylogenomic analysis of oxymonads that includes all five families. We find a major division between Polymastigidae and Streblomastigidae on one side, and Saccinobaculidae, Oxymonadidae, and Pyrsonymphidae on the other, with Oxymonadidae and Pyrsonymphidae branching as sisters in the latter clade. The phylogenomic tree largely confirms the SSU rRNA tree but provides stronger support at all nodes and suggests a different root. This tree represents a strong starting point to reconstruct the evolution of oxymonads many unusual morphological and molecular characters and to test whether new lineages might represent new families.