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A multicellular developmental program in a close animal relative

Nature volume 635, pages 382–389 (2024)Cite this article

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Abstract

All animals develop from a single-celled zygote into a complex multicellular organism through a series of precisely orchestrated processes1,2. Despite the remarkable conservation of early embryogenesis across animals, the evolutionary origins of how and when this process first emerged remain elusive. Here, by combining time-resolved imaging and transcriptomic profiling, we show that single cells of the ichthyosporean Chromosphaera perkinsii—a close relative that diverged from animals about 1 billion years ago3,4—undergo symmetry breaking and develop through cleavage divisions to produce a prolonged multicellular colony with distinct co-existing cell types. Our findings about the autonomous and palintomic developmental program of C. perkinsii hint that such multicellular development either is much older than previously thought or evolved convergently in ichthyosporeans.

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Fig. 1: C. perkinsii undergoes a series of cleavage divisions at constant volume.
Fig. 2: Transcriptional dynamics across the palintomic life cycle of C. perkinsii.
Fig. 3: Early developmental patterns in C. perkinsii.
Fig. 4: Cell differentiation in C. perkinsii’s colonies.

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Data availability

All data used for quantifications and Supplementary Videos 1–10 are available at Figshare (https://figshare.com/s/f20f6d471c719990471c)92. For all other raw images required, they are available on request due to their large data sizes. Raw RNA-seq data are publicly available on https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1091032.

Code availability

All the generated code for transcriptomic analysis is available at Zenodo (https://doi.org/10.5281/zenodo.13352464)93.

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Acknowledgements

We thank P. Gönczy, G. Dey, A. de Mendoza, C. Martín-Durán, H. Shah and A. Woglar for comments on the manuscript and general feedback; H. Suga for C. perkinsii cultures; and both the EPFL Bio Imaging and Optics Platform and the EPFL Gene Expression Core Facility for their support. We acknowledge funding from US National Science Foundation grant no. OIA-1826734 (J.B.), Swiss National Science Foundation Ambizione grant no. PZ00P3_185859 (O.D. and M.O.) and Swiss National Science Foundation Starting grant no. TMSGI3_218007 (O.D. and M.O.).

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Authors and Affiliations

  1. Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland

    Marine Olivetta, Chandni Bhickta & Omaya Dudin

  2. Department of Biochemistry, University of Geneva, Geneva, Switzerland

    Marine Olivetta & Omaya Dudin

  3. Bioimaging and Optics Core Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

    Nicolas Chiaruttini

  4. Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA

    John Burns

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  1. Marine Olivetta
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  2. Chandni Bhickta
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Contributions

Conceptualization: O.D. Methodology: M.O., C.B., N.C., J.B., O.D. Investigation: M.O., C.B., N.C., J.B. and O.D. Visualization: M.O., N.C., J.B. and O.D. Funding acquisition: J.B. and O.D. Project administration: O.D. Supervision: O.D. Writing—original draft: O.D. Writing—review and editing: M.O., N.C., J.B. and O.D.

Corresponding authors

Correspondence to John Burns or Omaya Dudin.

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Extended data figures and tables

Extended Data Fig. 1 Culture synchronization and growth dynamics of C. perkinsii.

(a) Schematic of the synchronization protocol of C. perkinsii. (b) Distribution of cells undergoing their first cleavage division or cell release throughout the life cycle at 23 °C, following either synchronization or not (n non-synchronized=129 cell/colony, n synchronized=233 cell/colony). Data are mean ± s.d. (c) The average time at which non-synchronized and synchronized cells undergo their 1st cleavage in a bulk culture (n non-synchronized=129 cell/colony, n synchronized=233 cell/colony). Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value. (d) Percentage of free-swimming flagellated cells over time (n 0 = 112 cells, n 24 = 84 cells, n 44 = 110 cells, n46 = 70 cells, n51 = 99 cells, n53 = 73 cells, n68 = 116 cells, n70 = 105 cells, n72 = 68 cells, n76 = 77 cells, n99 = 104 cells, n120 = 67 cells). Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value. (e) Cell diameter over time of 10 single cell traces aligned to time. Variability increases from 75 hr onwards due to asynchronous cell release. Data are mean ± s.d. (f) Cell diameter over time of fixed cells (n = 1571 cell/colony). The colours represent 3 independent replicates. (g) Distribution of number of nuclei per cell/colony across the life-cycle (n = 1571 cell/colony). The colours represent 3 independent replicates. Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value.

Extended Data Fig. 2 Transcriptional dynamics in C. perkinsii’s palintomic lifecycle and comparative analysis with S. arctica and early-branching animals.

(a) Multiple dimensional scaling (MDS) plot of RNAseq counts of 3 independent developmental time courses of C. perkinsii. “B” replicates were excluded from further analyses due to evidence of infection (Extended Data Table 1). (b) Expression profile distributions for the 5 distinct gene expression clusters for both replicates. Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value. (c) Heatmaps of gene expression dynamics between C. perkinsii and S. arctica highlight distinct transcriptional programs. (d) Statistical evaluation of gene expression correlation between C. perkinsii and S. arctica in select GO categories. (e) Correlation values comparing C. perkinsii to S. arctica expression patterns for genes important during coenocytic development of S. arctica35. (f) Network strategy used to decouple distinct expression patterns occurring within an orthogroup (methods). (g) Average correlation of OG expression values between early diverging animals and C. perkinsii. Orthogroups with an average correlation value greater than 0.5 (blue line) were subjected to GO enrichment analyses (Supplementary Tables 1, 2). (h) Average correlation of OG expression values between all animals and C. perkinsii. OGs with an average correlation value greater than 0.25 (blue line) were subjected to GO enrichment analyses (Supplementary Tables 1, 2). (i) Distribution of gene expression correlation values between C. perkinsii and each animal for non-developmental genes (Control Not DE) and differentially expressed gene clusters. The white dashed line indicates the median correlation value of the control distribution. (j) Average gene expression correlation among all animals plus C. perkinsii for a random sample of 34 OGs (black bars), developmental genes (pink line), and glycolysis genes (not developmentally regulated; blue line). (k) Pairwise correlation coefficient plots of gene clusters showing pairwise correlations among all animals and C. perkinsii. (l) Heatmap of gene expression for select OGs between C. perkinsii and developmental stages of early-branching animals spanning from zygote formation (Z) to the blastula stage (B). Credits: Silhouettes were obtained from PhyloPic (https://www.phylopic.org/). Schmidtea polychroa, created by by M. A. Grohme under a CC0 1.0 Universal Public Domain licence; Caenorhabditis elegans, created by B. Goldstein, vectorization by J. Warner under a CC0 1.0 Universal Public Domain licence; Isohypsibius dastychi, created by B. Lang under a CC0 1.0 Universal Public Domain licence; Sophophora melanogaster, created by A. Wilson under a CC0 1.0 Universal Public Domain licence; Strongylocentrotus purpuratus, created by C. Schomburg under a CC0 1.0 Universal Public Domain licence; Danio rerio, created by Ian Quigley under a CC BY 3.0 licence; Nematostella vectensis, created by J. Warner under a CC0 1.0 Universal Public Domain licence; Amphimedon queenslandica obtained under a CC0 1.0 Universal Public Domain licence; Mnemiopsis leidyi, created by J. R. Winnikoff under a CC0 1.0 Universal Public Domain licence; Creolimax, created by Y. Wong using scanning electron microscopy images by A. Sebé-Pedrós (public domain agreed by I. Ruiz-Trillo) under a licence free of copyright, CC PDM 1.0.

Extended Data Fig. 3 Symmetry breaking during early development of C. perkinsii.

(a) Cleavage division dynamics at constant volume over time, visualized using a plasma membrane (PM) marker FM4-64 (Supplementary Video 4). Scale bar, 10 µm. (b) PM-stained live late colonies exhibiting internal cavities (arrows). This result has been reproduced at least 2 independent times. Scale bar, 10 µm. (c) U-ExM stained cells for microtubules (green), and DNA (blue), highlighting nuclear migration to the cortex prior to 1st mitotic division. This result has been reproduced at least 3 independent times. Scale bar, 10 µm. (d) Actin (magenta) and DNA-stained (blue) colonies at various cell stages, accompanied by volumetric segmentation of cells, highlighting the asymmetry in volume following the first cleavage division. This result has been reproduced at least 3 independent times. Scale bar,10 µm. (e) U-ExM stained cell for pan-labelling with NHS-Ester (red), microtubules (green), and DNA (blue), illustrating the first mitotic division at the cortex. This result has been reproduced at least 3 independent times. Scale bar, 10 µm. (f) Actin (magenta) and DNA-stained (blue) colonies at distinct cell stages showing the asymmetrical cell division in volume and time between the Aa and Ab cells. This result has been reproduced at least 3 independent times. Scale bar, 10 µm. (g) U-ExM stained colonies for pan-labelling with NHS-Ester (red), microtubules (green), and DNA (blue), highlighting a three-cell stage. This result has been reproduced at least 3 independent times. Scale bar, 10 µm.

Extended Data Fig. 4 Distinct cell fates following the release of C. perkinsii’s colonies.

(a) Time-lapse images over 14 h of new born C. perkinsii cells post-release show a cell-size increase in proliferative/mitotic cells (black arrows) and no increase in flagellated cells (white arrows) (Supplementary Video 7). Scale bar: 10 µm. (b) A short-duration high-resolution time-lapse of new born C. perkinsii cells post-release (T = 104 h) shows a cell-size increase in proliferative/mitotic cells (black arrows) and no increase in flagellated cells (white arrows) (Supplementary Video 8). Bar, 10 µm. (c) Kymographs of both flagellated (F) and proliferative/mitotic (P/M) cells over 10 min show the increase in cell size for the P/M cell. Bar, 10 µm. (d) Cell area over time of single cell traces reveals the increase in size for the proliferative/mitotic (P/M) cells in contrast to the flagellated cells (F) (neach = 5 cells). (e) Growth ratio between t = 0 and t = 10 min for both proliferative/mitotic (P/M) and flagellated cells (F) (nF = 5, nP/M = 5 cells). Statistical analysis using a two-tailed Student’s t-test, **P = 0.001. Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value. (f) U-ExM stained cells for pan-labelling with NHS-Ester (red), microtubules (green), and DNA (blue), identifying proliferative/mitotic and flagellated cells, as well as cells undergoing mitosis. Scale bar: 10 µm. Zoomed-in insets represent Z-stacks of each cell. Scale bar: 1 µm. (g) Nuclear volume measured from U-ExM images for both proliferative/mitotic (P/M) and flagellated cells (F) (nF = 10, nP/M = 16 cells). Statistical analysis using a two-tailed Student’s t-test, **P = 0.00016. Box plots extend from the 25th to 75th percentile, including the median, and whiskers extend from the minimum to maximum value. (h) Image analysis workflow and quantifications showing the spatial clustering of flagellated cells within multicellular colonies (see methods). Two maximum projections per cell (upper and bottom halves) were split into four quarters (Q1, Q2, Q3, Q4). Flagellated cells were counted in each quarter, and the quarter with the highest number was aligned to Q1. Mean and standard deviation were calculated and represented (neach = 5 cells).

Extended Data Table 1 Enriched GO terms in differentially expressed genes in C. perkinsii replicate B compared to A and C replicates
Full size table
Extended Data Table 2 Developmental time points and time averaging windows for animal gene expression comparisons from the one or 2-cell stage through the blastula stage
Full size table

Supplementary information

Reporting Summary

Supplementary Video 1

Time-lapse of two synchronized cells of C. perkinsii obtained with epifluorescent microscopy. The time interval between frames is 1 h. The video is played at 7 fps. Both cells can be seen undergoing a full life cycle with the release of new-born cells. Scale bar, 15 µm.

Supplementary Video 2

Time-lapse of distinct cell types: amoeboflagellate (left) harbouring a flagellum and exhibiting cellular protrusions and a mitotic cell without a flagellum (right) undergoing seemingly cell division. The time interval between frames is 5 s. The video is played at 7 fps. Scale bar, 5 µm.

Supplementary Video 3

Flagellated cells freely moving around following cell release among other non-flagellated cells. The time interval between frames is 1 s. The video is played at 7 fps. Scale bar, 10 µm.

Supplementary Video 4

Time-lapse of a Plasma Membrane-stained (PM) C. perkinsii cell undergoing a series of cleavage divisions at constant volume and showcasing cortical rotations. The time interval between frames is 15 min. The video is played at 7 fps. Scale bar, 10 µm.

Supplementary Video 5

Z-stacks of PM-stained live colonies at distinct cell stages, highlighting the patterned cleavage divisions, tetrahedral four-cell stage and formation of spatially organized multicellular colonies. Scale bar, 10 µm.

Supplementary Video 6

Z-stacks of two U-ExM stained colonies for pan-labelling with NHS-Ester (red), microtubules (green) and DNA (blue) at the three-cell stage. Scale bar, 10 µm.

Supplementary Video 7

Time-lapse video of new-born C. perkinsii cells post-release obtained with epifluorescent microscopy. The time interval between frames is 1 h. The video is played at 7 fps. We can observe the proliferating/mitotic cells rapidly increasing their cell size, whereas flagellated cells do not, following release. Scale bar, 10 µm.

Supplementary Video 8

Time-lapse video of new-born C. perkinsii cells post-release obtained with epifluorescent microscopy with a time interval of 1 s. The video is played at 7 fps. Proliferative/mitotic cells rapidly increase in size, whereas flagellated cells do not. Scale bar, 10 µm.

Supplementary Video 9

Three-dimensional visualization of U-ExM stained late colonies for pan-labelling with NHS-Ester (grey), microtubules (red) and DNA (cyan), highlighting the co-existence and clustering of flagellated and non-flagellated cells in the multicellular colony. The bar is uncorrected for an expansion factor of 4.2×.

Supplementary Video 10

Thhree-dimensional visualization of U-ExM stained late colonies for pan-labelling with NHS-Ester (grey), microtubules (red) and DNA (cyan), highlighting the co-existence and clustering of flagellated and non-flagellated cells in the multicellular colony. The bar is uncorrected for an expansion factor of 4.2×.

Supplementary Table 1

Gene ontology term enrichment for the five different gene expression clusters throughout the life cycle of C. perkinsii.

Supplementary Table 2

C. perkinsii genes associated with enriched gene ontology terms (one-sided Fisher’s exact test, topGO weight algorithm) for the five different gene expression clusters plus enriched gene ontology terms (one-sided Fisher’s exact test, topGO weight algorithm) of highly correlated genes among early-diverging animals (distribution of correlations shown in Extended Data Fig. 2g) and all animals (distribution of correlations shown in Extended Data Fig. 2h).

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Olivetta, M., Bhickta, C., Chiaruttini, N. et al. A multicellular developmental program in a close animal relative. Nature 635, 382–389 (2024). https://doi.org/10.1038/s41586-024-08115-3

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