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The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution

Nature volume 645, pages 877–885 (2025)Cite this article

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Abstract

Cell types are fundamental functional units that can be traced across the tree of life. Rapid advances in single-cell technologies, coupled with the phylogenetic expansion in genome sequencing, present opportunities for the molecular characterization of cells across a broad range of organisms. Despite these developments, our understanding of eukaryotic cell diversity remains limited and we are far from decoding this diversity from genome sequences. Here we introduce the Biodiversity Cell Atlas initiative, which aims to create comprehensive single-cell molecular atlases across the eukaryotic tree of life. This community effort will be phylogenetically informed, rely on high-quality genomes and use shared standards to facilitate comparisons across species. The Biodiversity Cell Atlas aspires to deepen our understanding of the evolution and diversity of life at the cellular level, encompassing gene regulatory programs, differentiation trajectories, cell-type-specific molecular profiles and inter-organismal interactions.

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Fig. 1: The BCA aims at molecularly characterizing cell types across the eukaryotic tree of life.
Fig. 2: BCA anticipated impacts.
Fig. 3: Phylogenetic state-of-the-art of single-cell atlases across eukaryotes.

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Acknowledgements

We thank J. C. Carvalho for her expert work on the scientific illustrations and figure design. The BCA phase 0 is supported by the Gordon and Betty Moore Foundation (Grant GBMF12189). We also acknowledge financial support from the Wellcome Trust for the inaugural BCA meeting.

Author information

Author notes

  1. A full list of members and their affiliations appears in the Supplementary Information

Authors and Affiliations

  1. Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain

    Arnau Sebé-Pedrós, Mafalda Dias, Anamaria Elek, Jonathan Frazer, Xavier Grau-Bové, Roderic Guigó, Manuel Irimia & Sebastián R. Najle

  2. Tree of Life, Wellcome Sanger Institute, Cambridge, UK

    Arnau Sebé-Pedrós, Mara K. N. Lawniczak & Mark Blaxter

  3. Universitat Pompeu Fabra, Barcelona, Spain

    Arnau Sebé-Pedrós, Mafalda Dias, Jonathan Frazer, Roderic Guigó & Manuel Irimia

  4. ICREA, Barcelona, Spain

    Arnau Sebé-Pedrós, Toni Gabaldón & Manuel Irimia

  5. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel

    Amos Tanay

  6. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel

    Amos Tanay

  7. Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

    Detlev Arendt

  8. Laboratory of Computational Biology, VIB Center for AI and Computational Biology, Leuven, Belgium

    Stein Aerts

  9. VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium

    Stein Aerts

  10. Department of Human Genetics, KU Leuven, Leuven, Belgium

    Stein Aerts

  11. Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada

    John Archibald

  12. Stazione Zoologica Anton Dohrn, Napoli, Italy

    Maria Ina Arnone

  13. Department of Embryology, Carnegie Science, Baltimore, MD, USA

    Phillip Cleves

  14. Department of Biology, Johns Hopkins University, Baltimore, MD, USA

    Phillip Cleves

  15. Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany

    Susana M. Coelho

  16. Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA

    Casey Dunn

  17. Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, Barcelona, Spain

    Toni Gabaldón

  18. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain

    Toni Gabaldón

  19. Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Jesse Gillis

  20. Department of Physiology, University of Toronto, Toronto, Ontario, Canada

    Jesse Gillis

  21. Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY, USA

    Oliver Hobert

  22. Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo-UPM, Madrid, Spain

    Jaime Huerta-Cepas

  23. Department of Systems Biology, Harvard Medical School, Boston, MA, USA

    Allon Klein

  24. Global Futures Laboratory, Arizona State University, Tempe, AZ, USA

    Harris Lewin

  25. Department of Evolution and Ecology, University of California, Davis, CA, USA

    Harris Lewin

  26. Department of Biology, Stanford University, Stanford, CA, USA

    Christopher J. Lowe

  27. Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA

    Heather Marlow

  28. Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA

    Jacob M. Musser

  29. Systems Biology Institute, Yale University, New Haven, CT, USA

    Jacob M. Musser

  30. HUN-REN Biological Research Centre Szeged, Szeged, Hungary

    László G. Nagy

  31. Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA

    Lior Pachter

  32. Department of Computer Science, California Institute of Technology, Pasadena, CA, USA

    Lior Pachter

  33. The Rockefeller University, New York, NY, USA

    Sadye Paez

  34. Earlham Institute, Norwich Research Park, Norwich, UK

    Irene Papatheodorou

  35. Medical School, University of East Anglia, Norwich Research Park, Norwich, UK

    Irene Papatheodorou

  36. Genomics Department, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

    Michael J. Passalacqua

  37. Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany

    Nikolaus Rajewsky

  38. Charité—Universitätsmedizin, Berlin, Germany

    Nikolaus Rajewsky

  39. German Center for Cardiovascular Research (DZHK), Berlin, Germany

    Nikolaus Rajewsky

  40. NeuroCluster of Excellence, Berlin, Germany

    Nikolaus Rajewsky

  41. Plant Resilience Institute, Michigan State University, East Lansing, MI, USA

    Seung Y. Rhee

  42. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA

    Seung Y. Rhee

  43. Department of Plant Biology, Michigan State University, East Lansing, MI, USA

    Seung Y. Rhee

  44. Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA

    Seung Y. Rhee

  45. Department of Biology, University of Oxford, Oxford, UK

    Thomas A. Richards

  46. Stowers Institute for Medical Research, Kansas City, MO, USA

    Tatjana Sauka-Spengler

  47. Radcliffe Department of Medicine, University of Oxford, Oxford, UK

    Tatjana Sauka-Spengler

  48. Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany

    Lauren M. Saunders

  49. Department of Biology, KU Leuven, Leuven, Belgium

    Eve Seuntjens

  50. Living Systems Institute, University of Exeter, Exeter, UK

    Jordi Solana

  51. Department of Biosciences, University of Exeter, Exeter, UK

    Jordi Solana

  52. European Molecular Biology Laboratory—European Bioinformatics Institute, Hinxton, UK

    Yuyao Song

  53. Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria

    Ulrich Technau

  54. Department of Bioengineering, Stanford University, Stanford, CA, USA

    Bo Wang

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  1. Arnau Sebé-Pedrós
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Consortia

Biodiversity Cell Atlas meeting participants

  • Stein Aerts
  • , John Archibald
  • , Detlev Arendt
  • , Maria Ina Arnone
  • , Mark Blaxter
  • , Phillip Cleves
  • , Susana M. Coelho
  • , Mafalda Dias
  • , Casey Dunn
  • , Anamaria Elek
  • , Jonathan Frazer
  • , Toni Gabaldón
  • , Jesse Gillis
  • , Xavier Grau-Bové
  • , Roderic Guigó
  • , Oliver Hobert
  • , Jaime Huerta-Cepas
  • , Manuel Irimia
  • , Allon Klein
  • , Mara K. N. Lawniczak
  • , Harris Lewin
  • , Christopher J. Lowe
  • , Heather Marlow
  • , Jacob M. Musser
  • , László G. Nagy
  • , Sebastián R. Najle
  • , Lior Pachter
  • , Sadye Paez
  • , Irene Papatheodorou
  • , Michael J. Passalacqua
  • , Nikolaus Rajewsky
  • , Seung Y. Rhee
  • , Thomas A. Richards
  • , Tatjana Sauka-Spengler
  • , Lauren M. Saunders
  • , Arnau Sebé-Pedrós
  • , Eve Seuntjens
  • , Jordi Solana
  • , Yuyao Song
  • , Amos Tanay
  • , Ulrich Technau
  •  & Bo Wang

Contributions

A.S.-P., A.T., M.K.N.L. and D.A. wrote the paper based on discussions, comments and edits from S.A., J.A., M.I.A., M.B., P.C., S.M.C., M.D., C.D., A.E., J.F., T.G., J.G., X.G.-B., R.G., O.H., J.H.-C., M.I., A.K., H.L., C.J.L., H.M., J.M.M., L.G.N. S.R.N., L.P., S.P., I.P., M.J.P., N.R., S.Y.R., T.A.R., T.S.-S., L.M.S., E.S., J.S., Y.S., U.T. and B.W.

Corresponding author

Correspondence to Arnau Sebé-Pedrós.

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Supplementary information

Supplementary Table 1

BCA single-cell dataset reporting checklist and recommended quality controls.

Full list of participants Biodiversity Cell Atlas meeting participants.

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Sebé-Pedrós, A., Tanay, A., Lawniczak, M.K.N. et al. The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution. Nature 645, 877–885 (2025). https://doi.org/10.1038/s41586-025-09312-4

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