Letter | Published:

Whole-organism clone tracing using single-cell sequencing

Nature volume 556, pages 108112 (05 April 2018) | Download Citation


Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development1,2, monitoring the heritable expression of genetically encoded fluorescent proteins3 and, more recently, using next-generation sequencing technologies that exploit somatic mutations4, microsatellite instability5, transposon tagging6, viral barcoding7, CRISPR–Cas9 genome editing8,9,10,11,12,13 and Cre–loxP recombination14. Single-cell transcriptomics15 provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.

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This work was supported by a European Research Council Advanced grant (ERC-AdG 742225-IntScOmics), Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award (NWO-CW 714.016.001), and the Foundation for Fundamental Research on Matter, financially supported by NWO (FOM-14NOISE01). This work is part of the Oncode Institute which is partly financed by the Dutch Cancer Society. We thank M. Sen for help with sequencing, R. der Linden for cell sorting, and B. de Barbanson for help with programming, and all the other members of the A.v.O. laboratory for discussions and input. In addition, we thank B. Artegiani and J. Bakkers for discussions, P. Shang and N. Geijsen for sharing the Cas9–eScarlet fusion protein, the Hubrecht Sorting Facility, and the Utrecht Sequencing Facility, subsidized by the University Medical Center Utrecht, Hubrecht Institute and Utrecht University.

Author information

Author notes

    • Anna Alemany
    • , Maria Florescu
    • , Chloé S. Baron
    •  & Josi Peterson-Maduro

    These authors contributed equally to this work.


  1. Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands

    • Anna Alemany
    • , Maria Florescu
    • , Chloé S. Baron
    • , Josi Peterson-Maduro
    •  & Alexander van Oudenaarden


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A.v.O. conceived and designed the project. J.P.-M. developed the experimental protocol, with support from A.A., M.F. and C.S.B. C.S.B. performed WKM-related experiments; M.F. performed brain- and eye-related experiments; and C.S.B. and J.P.-M. performed fin-related experiments. A.A. developed the computational methods and modelling. A.A., C.S.B. and A.v.O. analysed WKM-related data; A.A. and M.F. analysed brain- and eye-related data; A.A., C.S.B. and J.P.-M. analysed fin-related data. All authors discussed and interpreted results, and wrote the manuscript. A.A., M.F., C.S.B. and J.P.-M. contributed equally to this work.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Alexander van Oudenaarden.

Reviewer Information Nature thanks L. Zon and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Supplementary information

PDF files

  1. 1.

    Life Sciences Reporting Summary

  2. 2.

    Supplementary Data 1

    This file summarizes the RaceID parameters used for transcriptome analysis.

  3. 3.

    Supplementary Data 3

    The reference manual for the scripts provided in Supplementary Data 2 to extract clones.

  4. 4.

    Supplementary Information

    This file contains Supplementary Sections 1-4.

Zip files

  1. 1.

    Supplementary Data 2

    This file contains a zipped file with scripts to extract extract scars and detect cones in single cells.

Excel files

  1. 1.

    Supplementary Table 1

    Cell specific barcodes used in transcriptome library preparation.

  2. 2.

    Supplementary Table 2

    Cell specific barcodes used in scar library preparation.

  3. 3.

    Supplementary Table 3

    Differently expressed genes detected in the different hematopoietic cell types.

  4. 4.

    Supplementary Table 4

    Differently expressed genes detected in the cell types detected in brain and eyes.

  5. 5.

    Supplementary Table 5

    Differently expressed genes detected in the cell types detected in the caudal fin.

  6. 6.

    Supplementary Table 6

    Differently expressed genes detected in subgroups of myeloid cells.

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