Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics
Abstract
Mapping the planarian transcriptome: A cell type's transcriptome defines the active genes that control its biology. Two groups used single-cell RNA sequencing to define the transcriptomes for essentially all cell types of a complete animal, the regenerative planarian Schmidtea mediterranea.Because pluripotent stem cells constantly differentiate to rejuvenate any part of the body of this species, all developmental lineages are active in adult animals. Fincher et al.determined the transcriptomes for most, if not all, planarian cell types, including some that were previously unknown. They also identified transition states and genes governing positional information. Plass et al.used single-cell transcriptomics and computational algorithms to reconstruct a lineage tree capturing the developmental progressions from stem to differentiated cells. They could then predict gene programs that are specifically turned on and off along the tree, and they used this approach to study how the cell types behaved during regeneration. These whole-animal transcriptome “atlases” are a powerful way to study metazoan biology. Science, this issue p.eaaq1736, p.eaaq1723
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The validation cohort consisted of 141,267 single cells spanning 266 phenotypes, nine biological systems, five species, and nine scRNA-seq platforms.
“These datasets represent diverse developmental and differentiation processes and consist of 141,267 single cells spanning 266 phenotypes, nine biological systems, five species [including two whole organisms (29, 30)], and nine scRNA-seq platforms”
From Single-cell transcriptional diversity is a hallmark of developmental potential (2020) · cites this paper as [29]
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- Authors
- Plass, M., Solana, J., Wolf, F. A., Ayoub, S., Misios, A., Glažar, P., Obermayer, B., Theis, F. J., Kocks, C., & Rajewsky, N.
- Affiliations
- Max Delbrück Center (DE)
- Helmholtz Munich (DE)
- Corresponding author
- Rajewsky, Nikolaus
- ORCID
- Venue
- Science
- Published
- 2018-05-25
- Volume
- 360
- Issue
- 6391
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2801443765
- Cited by
- 474
- References
- 79
- Citations by year
- 2026: 23 · 2025: 50 · 2024: 41 · 2023: 58 · 2022: 66 · 2021: 72 · 2020: 58 · 2019: 69 · 2018: 34 · 2017: 1 · 2013: 2
- FWCI
- 20.98
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (submittedVersion)
- Site cant be reached (submittedVersion)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
- Funders
- Deutsches Zentrum für Herz-Kreislaufforschung (DZHK BER 1.2 VD)
- Deutsche Forschungsgemeinschaft (DFG RA 838/5-1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Planarian Biology and Electrostimulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- Schmidtea mediterranea, Tricladida, cell type atlas, cell lineage trees, single-cell transcriptomics, pluripotent stem cells, regeneration, positional information
- MeSH terms
- Animals, Atlases as Topic, Cell Differentiation, Cells, Planarians, Regeneration, Cell Lineage, Gene Expression Profiling, Pluripotent Stem Cells, Single-Cell Analysis, Transcriptome
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