Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

Abstract

The emergence and diversification of cell types is a leading factor in animal evolution. So far, systematic characterization of the gene regulatory programs associated with cell type specificity was limited to few cell types and few species. Here, we perform whole-organism single-cell transcriptomics to map adult and larval cell types in the cnidarian Nematostella vectensis, a non-bilaterian animal with complex tissue-level body-plan organization. We uncover eight broad cell classes in Nematostella, including neurons, cnidocytes, and digestive cells. Each class comprises different subtypes defined by the expression of multiple specific markers. In particular, we characterize a surprisingly diverse repertoire of neurons, which comparative analysis suggests are the result of lineage-specific diversification. By integrating transcription factor expression, chromatin profiling, and sequence motif analysis, we identify the regulatory codes that underlie Nematostella cell-specific expression. Our study reveals cnidarian cell type complexity and provides insights into the evolution of animal cell-specific genomic regulation.

Transcriptional remodelling upon light removal in a model cnidarian: Losses and gains in gene expression

“…Nematostella , like other cnidarians, has a complex but diffuse nervous system without a centralized concentration of neurons (Marlow, Srivastava, Matus, Rokhsar, & Martindale, ), which presumably arose in a later common ancestor (Arendt, Tosches, & Marlow, ). Recent work (Sebé‐Pedrós et al, ) has revealed the complex transcriptional differences of the more than eight broad cells types of Nematostella . Moving forward, these cell‐type‐specific analyses of oscillating gene expression will be useful to identify what cells in heterogeneous cell populations may be driving the circadian phenotypes of cnidarians.…”

“…Nematostella, like other cnidarians, has a complex but diffuse nervous system without a centralized concentration of neurons (Marlow, Srivastava, Matus, Rokhsar, & Martindale, 2009), which presumably arose in a later common ancestor (Arendt, Tosches, & Marlow, 2015). Recent work (Sebé-Pedrós et al, 2018) has revealed the complex transcriptional differences of the more than eight broad cells types of Nematostella.…”

Population Specific Adaptations in Venom Production to Abiotic Stressors in a Widely Distributed Cnidarian

“…For each population (for each nCounter batch separately), every stress condition was compared to the control and p-values (Student's T-test) and fold changes were calculated. The raw reads were mapped to Nematostella gene models [35] by Star aligner [36]. Differential expression analysis was performed by EdgeR Bioconductor package [37].…”

“…Using information derived from the previously predicted and annotated gene models [35] we evaluated whether differentially expressed transcripts may have carried both functional information based on TMM normalized fold change values as well as LogCPM values. TMM normalization aides when scaling for variation in library size as well as transcript diversity being sampled [40].…”

The draft genome of Actinia tenebrosa reveals insights into toxin evolution

“…Recent studies have revealed a high frequency of cnidarian-specific genes is enriched within the cnidocyte (Sebé-Pedrós et al, 2018;Sunagar et al, 2018). Many of these cnidarian-specific genes expressed in the cnidocytes encode for toxin peptides Sebé-Pedrós et al, 2018).…”