Mapping single-cell atlases throughout Metazoa unravels cell type evolution
- Stanford University, United States
- European Molecular Biology Laboratory, Germany
Abstract
Comparing single-cell transcriptomic atlases from diverse organisms can elucidate the origins of cellular diversity and assist the annotation of new cell atlases. Yet, comparison between distant relatives is hindered by complex gene histories and diversifications in expression programs. Previously, we introduced the self-assembling manifold (SAM) algorithm to robustly reconstruct manifolds from single-cell data (Tarashansky et al., 2019). Here, we build on SAM to map cell atlas manifolds across species. This new method, SAMap, identifies homologous cell types with shared expression programs across distant species within phyla, even in complex examples where homologous tissues emerge from distinct germ layers. SAMap also finds many genes with more similar expression to their paralogs than their orthologs, suggesting paralog substitution may be more common in evolution than previously appreciated. Lastly, comparing species across animal phyla, spanning mouse to sponge, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.
Data availability
All data analyzed during this study are available through various sources as listed in Supplementary File 1.
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Whole-body single-cell RNA sequencing reveals components of elementary neural circuits in a spongeNCBI Gene Expression Omnibus, GSE134912.
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Stem cell differentiation trajectories in Hydra resolved at single cell resolutionNCBI Gene Expression Omnibus, GSE121617.
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Cell type transcriptome atlas for the planarian Schmidtea mediterraneaNCBI Gene Expression Omnibus, GSE111764.
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Single-cell analysis reveals regulation of germline stem cell fate in the human parasite Schistosoma mansoniNCBI Gene Expression Omnibus, GSE147355.
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The dynamics of gene expression in vertebrate embryogenesis at single cell resolutionNCBI Gene Expression Omnibus, GSE113074.
Article and author information
Author details
Funding
Arnold and Mabel Beckman Foundation (Beckman Young Investigator Award)
- Bo Wang
National Institutes of Health (1R35GM138061)
- Bo Wang
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Alex K Shalek, Broad Institute of MIT and Harvard, United States
Ethics
Animal experimentation: All experiments with and care of mice are performed in accordance with protocols approved by the Institutional Animal Care and Use Committees (IACUC) of Stanford University (protocol approval number 30366).
Version history
- Received: January 26, 2021
- Accepted: April 30, 2021
- Accepted Manuscript published: May 4, 2021 (version 1)
- Version of Record published: May 21, 2021 (version 2)
Copyright
© 2021, Tarashansky et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Mapping single-cell atlases throughout Metazoa unravels cell type evolution
eLife 10:e66747.
https://doi.org/10.7554/eLife.66747
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