Abstract
Ciliated protists (ciliates) are widely used for investigating evolution, mostly due to their successful radiation after their early evolutionary branching. In this study, we employed high-throughput sequencing technology to reveal the phylogenetic position of Synhymenia, as well as two classes Nassophorea and Phyllopharyngea, which have been a long-standing puzzle in the field of ciliate systematics and evolution. We obtained genomic and transcriptomic data from single cells of one synhymenian (Chilodontopsis depressa) and six other species of phyllopharyngeans (Chilodochona sp., Dysteria derouxi, Hartmannula sinica, Trithigmostoma cucullulus, Trochilia petrani, and Trochilia sp.). Phylogenomic analysis based on 157 orthologous genes comprising 173,835 amino acid residues revealed the affiliation of C. depressa within the class Phyllopharyngea, and the monophyly of Nassophorea, which strongly support the assignment of Synhymenia as a subclass within the class Phyllopharyngea. Comparative genomic analyses further revealed that C. depressa shares more orthologous genes with the class Nassophorea than with Phyllopharyngea, and the stop codon usage in C. depressa resembles that of Phyllopharyngea. Functional enrichment analysis demonstrated that biological pathways in C. depressa are more similar to Phyllopharyngea than Nassophorea. These results suggest that genomic and transcriptomic data can be used to provide insights into the evolutionary relationships within the “Nassophorea–Synhymenia–Phyllopharyngea” assemblage.
Highlights
Members of the order Synhymeniida are characterized by a cytopharyngeal basket of well-developed nematodesmata bound proximally by the presence of a band of somatic dikinetid cilia (Kivimaki et al, 2009; Figure 1)
Cells were washed in phosphate-buffered saline (PBS) buffer, and genomic DNA extracted from a single cell was amplified using a Single Cell WGA Kit (Yikon, YK001A) based on MALBAC technology (Lu et al, 2012)
The results showed that the stop codon usage of C. depressa was closer to Chilodonella uncinata and D. derouxi than to Nassophorea species
Summary
Members of the order Synhymeniida are characterized by a cytopharyngeal basket of well-developed nematodesmata bound proximally by the presence of a band of somatic dikinetid cilia (Kivimaki et al, 2009; Figure 1). Synhymeniida was assigned to the class Nassophorea because it possesses a cytopharyngeal basket (nasse), a character shared by the typical nassophorean groups (nassulids and microthoracids) (Small and Lynn, 1985; Lynn and Small, 2002; Lynn, 2008; Table 1). Phylogenetic studies based mainly on the small subunit ribosomal DNA (SSU rDNA) gene and other related genes (e.g., LSU rDNA, ITS, alpha-tubulin), as well as a comparison of ultrastructural synapomorphies and autapomorphies, suggested that the subclass Synhymenia should be moved from the class Nassophorea to Phyllopharyngea (Gong et al, 2009; Zhang et al, 2014; Gao et al, 2016; Table 1). Based on a study of the ultrastructure of the typical synhymenian species Zosterodasys agamalievi Kivimaki et al (1997) concluded that the synhymenians cannot be assigned to either Phyllopharyngea or Nassophorea, because they have a combination of characters that precludes their inclusion in either. For example, have yet to be reported (Lynn and Small, 2002)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
