Phylogenetic relationship analyses of complicated class Spirotrichea based on transcriptomes from three diverse microbial eukaryotes: Uroleptopsis citrina, Euplotes vannus and Protocruzia tuzeti.

Ciliates are one of the eukaryotic unicellular organisms which are thought to be the oldest life forms, and widely geographically distributed. For a variety of reasons, some groups of ciliates have attracted more attention than others, such as the class Spirotrichea and related species with its complicated evolutionary relationships. In this study, we obtained the transcriptome data of three typical ciliates, Uroleptopsis citrina, Euplotes vannus, Protocruzia tuzeti using high throughput sequencing. The genetic relationships were revealed by phylogenomic analysis of 109 genes comprising of 34,882 amino acid residues, and analyses based on SSU rDNA of 55 species, as well as the comparison of gene content among spirotricheans and related species. Our phylogenomic analyses show the Spirotrichea is monophyletic when Protocruzia is excluded, in which four subclasses: Oligotrichia, Choreotrichia, Hypotrichia and Euplotia also formed momophyletic groups respectively. The Hypotrichia was placed as a sister branch to the assemblage, in which two oligotrichs clustered with two choreotrichs. In addition to this, the Protocruziidia was placed in an independent lineage status out of the Spirotrichea. Together with its high binding-related gene content compared to other species and the significant variation in morphological characters, these findings support the removal of Protocruzia from the class Spirotrichea.