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Gastrulation

Gastrulation

Gastrulation establishes the three primary tissues of an embryo: the ectoderm, mesoderm, and endoderm. This developmental process relies on a series of intricate cellular movements, which in humans transforms a flat, “bilaminar disc” composed of two cell sheets into a three-tiered structure. In the resulting embryo, the endoderm serves as the bottom layer, and stacked directly above it is the intermediate mesoderm, and then the uppermost ectoderm. Respectively, these tissue strata...

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Related Experiment Video

Updated: Nov 7, 2025

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

Published on: April 30, 2019

Mapping single-cell atlases throughout Metazoa unravels cell type evolution.

Alexander J Tarashansky¹, Jacob M Musser², Margarita Khariton¹

¹Department of Bioengineering, Stanford University, Stanford, United States.

|May 4, 2021

Summary

We developed SAMap, a new method to compare cell atlases across species, identifying homologous cell types and revealing ancient cell families. This advances our understanding of cellular diversity origins and evolution.

Keywords:

cell type evolution computational biology contractile cells evolutionary biology gene expression program gene orthology mouse planarian single-cell atlas stem cells systems biology xenopus zebrafish

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Last Updated: Nov 7, 2025

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Area of Science:

Evolutionary biology
Comparative genomics
Single-cell transcriptomics

Background:

Comparing single-cell transcriptomic atlases across species is crucial for understanding cellular diversity origins.
Gene histories and expression program diversification complicate cross-species comparisons.

Purpose of the Study:

To develop a method for mapping cell atlas manifolds across species.
To identify homologous cell types and shared expression programs in distant species.
To investigate gene evolution, including orthologs and paralogs, across animal phyla.

Main Methods:

Building upon the self-assembling manifold (SAM) algorithm.
Developing SAMap for cross-species cell atlas manifold mapping.
Applying SAMap to compare diverse animal species from sponge to mouse.

Main Results:

SAMap successfully identifies homologous cell types across distant species, even with distinct germ layer origins.
The study found evidence suggesting paralog substitution is a more common evolutionary mechanism than previously thought.
Ancient contractile and stem cell families were identified, potentially originating early in animal evolution.

Conclusions:

SAMap is a powerful tool for cross-species cell atlas comparison and annotation.
Gene duplication and divergence (paralogs) play a significant role in evolutionary innovation.
Comparative single-cell transcriptomics reveals deep evolutionary histories of fundamental cell types.