Placozoa cell atlas

The evolutionary assembly of major animal cell type programs occurred early in animal evolution. Studying non-bilaterian lineages like placozoans offers the opportunity to reconstruct this process. Placozoans are small disc-shaped animals that inhabit subtropical and tropical seas worldwide, feeding by extracellular digestion on microbial mats. Placozoans have no neurons, but their six described cell types show coordinated behaviours triggered by peptides secreted by specialized endocrine cells. To gain detailed insights into the diversity, regulation and evolution of placozoan cell type programs, here we measured 65,000 single-cell transcriptomes and genome-wide chromatin maps in four placozoan species. We found highly-conserved cell type gene expression programs across placozoans, including populations of meiotic, transdifferentiating and cycling cells. Our comparative atlas also reveals an unexpected diversity of peptidergic cell types in placozoans: fourteen compared with nine other somatic cell types. These cells express unique transcription factor, GPCR, and neuropeptide combinations, as well as a highly conserved set of neuronal genes, including a complete presynaptic scaffold and neuropeptide processing genes. Moreover, we identify peptidergic cell progenitors with hallmarks of cnidarian and bilaterian neurogenesis. In contrast, we show that these neuronal gene programs are absent from earlier-branching animal lineages like sponges and ctenophores. Altogether, our results suggest that key neuronal ontogenetic and effector gene modules evolved before the advent of cnidarian-bilaterian neurons, in the context of endocrine-secretory cells.

The app has two main components:

1) Cell atlases allows the exploration of the datasets in a species-focused manner and from different perspectives (single genes, groups of genes, cell type markers).

2) Species comparisons allows the comparison of cell type transcriptional similarities using different metrics, set of orthologs, and selection of variable markers. The interactive heatmaps allow the retrieval of shared gene lists between the selected pair of cell types.

Cell atlases

This section allows the exploration of the datasets in a species-focused manner and from different perspectives.

First, select your species of interest and click on Generate cell atlas.

Then you can explore four pages:

Overview – metacells and single-cells 2D projection, cell type labels, and metacell heatmap showing expression of highly variable genes. Here you can download the metacell regularized gene expression matrix and the raw single-cell UMI counts matrix.

Single gene query – select your gene of interest by geneID or launch a BLAST search with your protein of interest (you need to select the hit of interest, if any).

Multiple genes query – this allows the visualization of multiple genes at once. You can search genes by name or by Pfam domain (e.g. “Myosin_head/” will retrieve you all the genes with a myosin domain) and you can also upload a list of interest. We also provide predefined lists of genes for different families/sets of function (e.g. cell adhesion, GPCRs, transcription factors),

Cell type markers – first you need to select one or more metacells or a cell type of interest. Then, you need to select an expression threshold for marker selection. Optionally, you can request that the gene is expressed in all other metacells below a certain threshold (in each of them – absolute – or as a median value).
This generates a table of the top marker genes fulfilling the selected criteria. You can sort them using different metrics and also specifically select transcription factors. This table can be downloaded.

7. Species comparisons

This sections allows the systematic comparison of cell type transcriptomes across species and from two perspectives.

Pairwise comparison – select a pair of species and then click on Compare species. Then, you can select different parameters for the comparison and interactively explore the comparative heatmap to retrieve lists of genes shared between a pair of cell types.

Ortholog comparison – select a gene ID for any of the species and you can visualize the expression of the orthologs in all four placozoan species (if there are any).