Mapping single-cell atlases throughout Metazoa unravels cell type evolution

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.