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bioRxiv · 10.64898/2026.07.30.741939

Reconstructing whole-organism cell phylogenies with resolved ancestral transcriptional states

He, X.·Liu, Z.·Deng, S.·Zeng, H.·Zhang, M.·Liu, B.·Xiang, H.·Chen, Z.·Zhang, A.·Shendure, J.
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Abstract

Combining cell lineage tracing with single-cell RNA sequencing can reconstruct a phylogenetic tree to integrate single-cell transcriptomic atlas. However, the internal nodes of this tree - representing ancestral cells - remain transcriptionally silent, preventing along-lineage longitudinal tracing of cell state dynamics. Here, we overcome this by reconstructing high-resolution zygote-to-larva developmental cell phylogenies for 15 zebrafish larvae, with directly measured transcriptomes of the terminal nodes (i.e., sampled cells). Leveraging a set of lineage-committed upregulated genes (LUGs), we developed LUG-encoded ancestral projection (LEAP), a novel phylogeny-based computational framework, and successfully imputed the transcriptional states of internal nodes of the phylogenies. This enabled, for the first time in a non-nematode organism, lineage-informed longitudinal analysis of cell state dynamics throughout development. Our analysis revealed a major, previously unappreciated wave of fate specializations associated with hatching, distinct from the well-characterized events of gastrulation. Furthermore, we uncovered abundant incipient cell states that are already fate-determined but exhibit minimal transcriptional differentiation, revealing a hidden layer of developmental fate specializations. In sum, by resolving ancestral transcriptional states of a reconstructed cell phylogeny, this work paves the way for constructing lineage-resolved cell atlases in complex organisms to characterize comprehensive cell state dynamics.

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He, X., Liu, Z., Deng, S., Zeng, H., Zhang, M., Liu, B., Xiang, H., Chen, Z., Zhang, A., Shendure, J.. 2026-07-31. Reconstructing whole-organism cell phylogenies with resolved ancestral transcriptional states. https://doi.org/10.64898/2026.07.30.741939

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