Figures and data
Clytia single-cell dataset representations.
a,c) UMAPs colored by Leiden cell cluster, with schematic diagrams of Clytia medusa and planula (aboral end down) larva stage; b) self-similiarity of inferred Leiden cluster marker gene sets for medusa d) and planula single cell data sets (see methods). In the UMAPs Leiden cluster numbers are prefixed with ‘m’ for medusa’ and ‘p’ for planula and these are then prefixed with cell category abbreviations: cni, nematocytes; epi, epidermis; gas, gastrodermis; gla, gland; igc i-cells/germ cells; ner, neuron; nsc, neurosecretory; sec, secretory.
Significant numbers of shared marker genes between planula (x axis) and medusa (y axis) cell clusters.
The colour ramp scale represents −log10(P) values of Fisher’s exact test for enrichment of shared marker genes (see methods). The general class of each cell is given by the color annotation (consistent with Fig. 3) with abbreviations as for Fig. 1.
Examples of the distribution of major planula cell types.
a-l) marker gene ISH; m) summary diagram summarising cell type distributions; n) Dot plot of marker gene expression across clusters. Cell type classes are colour-coded across panels. Planulae are oriented with the oral pole at the top.
Ultrastructure of planula and medusa cells.
A) Diagram of the planula (aboral end down). B) Diagram of the medusa. C) Medusa manubrium. D) Medusa gonad. E) Section of umbrella and velum. F) Tentacle bulb and tentacle. a-w) TEM micrographs illustrating ultrastructural features of planula (a-j) and medusa (k-w) cell types, from sites indicated by boxes on the diagrams. Planulae micrographs were taken from longitudinal sections. Colour coding of broad cell categories as in Figures 2 and 3. a) Basal region of the epidermis and gastrodermis layers, separated by mesoglea (black arrowhead), taken from near the oral pole. Most cells are epitheliomuscular cells, whose basal muscle fibres mingle with neurites alongside the mesoglea. Large round inclusions (asterisk) are likely lipidic yolk inherited from the egg. b) Oral region of the epidermis, including a mature nematocyte. c) Epidermis region including part of a mucous cell. d) Basal region of the epidermis and gastrodermis taken from the trunk region, with a putative i-cell in the gastrodermis. e) Similar region including a nematoblast in the gastrodermis. f) Overview of the epidermis and gastrodermis separated by a layer of mesoglea (black arrowhead) taken at the aboral pole. Neurosecretory cells are embedded between the epidermal epitheliomuscular cells. Neurites from sensory and ganglionic cells intermingle with their basal muscle fibres. g) Neural plexus at the aboral pole. Neurons are embedded in the epidermis layer and are adjacent to the mesoglea. h) Overview of the oral gastrodermis. i) Neurosecretory cells containing small electron-dense granules in the aboral/lateral epidermis. The presence of the apical cilium suggests a potential sensory function. j) Neurosecretory cells within the aboral epidermis. k) Subumbrella section showing striated muscle layer and gastrodermal cells of the radial canal. l) Subumbrella section showing layered smooth and striated muscle cells, and the endodermal plate. m) Velum showing striated muscle cells separated by a layer of mesoglea (black arrowhead). n) Subumbrella region towards the manubrium, showing smooth muscles and flagella within the radial canal. o) Specialised neuro-epidermal cells forming a statocyst adjacent to neurites of the nerve ring. p) Exumbrella epidermis. q) Basal region of the manubrium. The epidermis and the gastrodermis are separated by a layer of mesoglea. The gastrodermis includes several types of gland cells shown in (r) and (s). t) Epidermis of the tentacle bulb overlying nematoblasts and i-cells. u) Early stage oocytes in the gonad, showing typical condensed, paired chromosomes (black arrowhead). v) Epidermis of the tentacle bulb, including an i-cell and three neurite bundles of the nerve rings. The epidermis and gastrodermis are separated by a layer of mesoglea (black arrowhead). w) Mature nematocyte in the tentacle epidermis. Abbreviations for all panels: epi, epidermis; gas, gastrodermis; can, gastrodermal canal; nem, nematoblast; mat nem, mature nematocyte; muc, mucous cell; nsc, neurosecretory cell; igc, i cell/oocyte; enpl, endodermal plate; vel sms, velum striated muscle; smms, subumbrellar smooth muscle; stsm, sub-umbrellar striated muscle; umb epi, exumbrellar epidermis; neu, neurons; stat, statocyst; jel, jelly; gc, gland cells. Scale Bars: 5μm
Ectoderm regionalisation along the oral-aboral axis predicts post-metamorphosis fates.
a) In situ hybridisation for genes expressed in different zones at three stages of planula development as indicated. b,c) Fate mapping of six ectodermal zones defined along the aboral-oral axis by photoconversion of Dendra2 protein expressed from mRNA injected before fertilisation. b) Bright field images of planulae before (top row) and during (middle row) metamorphosis, and in primary polyps (bottom row). The fluorescence signal overlaid in green in the planula images corresponds to endogenous GFP1 and non-converted Dendra2, and all magenta overlays to photoconverted Dendra2. Photoconverted gastroderm cells mainly become interspersed during this period and are not distinguished here. c) Cartoons showing the mapping of planula epidermis regions to structures of the primary polyp. Oral is at the top in all images. Scale bars 100μm.
Tree based on shared marker gene presence or absence under a Poisson model (see methods), for medusa (black) and planula (red) cell types.
Abbreviations: cni, nematocytes; epi, epidermis; gas, gastrodermis; gla, gland; igc i-cells/germ cells; ner, neuron; nsc, neurosecretory; pec, putative eicosanocyte; sec, secretory. The branch to gas-p3 is truncated.
Top 3 marker genes for each of the a) medusa and b) planula Leiden clusters.
c) selected planula cell type markers discussed in the text, by Leiden cluster. Suffix numbers in gene names are database accessions.
Gastroderm diversity in the two-day planula.
a) In situ hybridisation for genes expressed in the gastroderm in 2-day planulae as indicated. b) In situ hybridisation for PEC cell markers. c) Dot plot comparing marker expression between clusters. Oral is at the top in all planula images. Scale bars 100μm
Planula PEC cell overlap with bulk RNA-seq data from theca containing samples.
St bulk stolon; GO bulk gonozooid; PH bulk polyp head. Arrows point to PEC cell clusters.
