Mapping single-cell atlases throughout Metazoa unravels cell type evolution.
Mapping single-cell atlases throughout Metazoa unravels cell type evolution.
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作者：
Tarashansky AJ;Musser JM;Khariton M;Li P;Arendt D;Quake SR;Wang B
比较来自不同生物的单细胞转录组图谱可以阐明细胞多样性的起源，并有助于注释新的细胞图谱。然而，远亲之间的比较受到复杂的基因历史和表达程序多样性的阻碍。之前，我们引入了自组装流形（SAM）算法来从单细胞数据稳健地重建流形（Tarashansky等人，2019年）。在这里，我们建立在SAM映射跨物种的细胞图谱流形。这种新方法，SAMap，确定同源细胞类型与跨门内遥远的物种共享的表达程序，即使在复杂的例子中，同源组织出现从不同的胚层。SAMap还发现许多基因与其旁系同源物的表达比其直系同源物的表达更相似，这表明旁系替代在进化中可能比以前认识到的更常见。最后，比较动物门的物种，从海绵到老鼠，揭示了古老的收缩细胞和干细胞家族，它们可能在动物进化的早期就出现了。
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 sponge to mouse, reveals ancient contractile and stem cell families, which may have arisen early in animal evolution.