Single-Cell Genomic Sequencing of Three Peritrichs (Protista, Ciliophora) Reveals Less Biased Stop Codon Usage and More Prevalent Programmed Ribosomal Frameshifting Than in Other Ciliates

Bo Pan,Xiao Chen,Alan Warren,Zhuo Shen,Lifang Li,Chundi Wang,Chao Li,Borong Lu

doi:10.3389/fmars.2020.602323

Abstract

Peritrichs are one of the largest groups of ciliates with over 1,000 species described so far. However, their genomic features are largely unknown. By single-cell genomic sequencing, we acquired the genomic data of three sessilid peritrichs (Cothurnia ceramicola, Vaginicola sp., and Zoothamnium sp. 2). Using genomic data from another 53 ciliates including 14 peritrichs, we reconstructed their evolutionary relationships and confirmed genome skimming as an efficient approach for expanding sampling. In addition, we profiled the stop codon usage and programmed ribosomal frameshifting (PRF) events in peritrichs for the first time. Our analysis reveals no evidence of stop codon reassignment for peritrichs, but they have prevalent +1 or -1 PRF events. These genomic features are distinguishable from other ciliates, and our observations suggest a unique evolutionary strategy for peritrichs.

Highlights

Peritrich ciliates have ubiquitous distribution and occupy a broad array of freshwater, brackish water, marine, and terrestrial ecosystems (Lynn, 2008; Zhuang et al, 2016; Lu et al, 2019, 2020)
The large contig numbers (94,558 on average) and small N50 (1,539 on average) indicate that the genome assembly is not integral, probably due to the bias of whole-genome amplification, which is a necessary procedure during the library preparation in single-cell genomic sequencing (Lu et al, 2012)
After gene annotation and ortholog detection, the gene recovery rate (GRR), which is equivalent to the coverage of 157 common orthologous genes in each ciliate taxon (Gentekaki et al, 2014; Chen et al, 2018), is 50.3% for C. ceramicola, 32.5% for Vaginicola sp., and 51.0% for Zoothamnium sp. 2

Summary

Introduction

Peritrich ciliates have ubiquitous distribution and occupy a broad array of freshwater, brackish water, marine, and terrestrial ecosystems (Lynn, 2008; Zhuang et al, 2016; Lu et al, 2019, 2020). They are one of the largest groups within the phylum Ciliophora Doflein, 1901 with over 1,000 nominal species. Following the development of next-generation sequencing techniques, two studies using phylogenomic analysis of sequences from more than 100 genomic loci concluded that the orders Sessilida and Mobilida are sister groups, and the subclass Peritrichia is monophyletic (Gentekaki et al, 2017; Jiang et al, 2019). Genomic data are available for only about 2% of known peritrich species and are lacking for several families (Jiang et al, 2019), so it is probably too early to draw solid conclusions on high-level peritrich systematics based on phylogenomic analyses

Methods

Results

Conclusion