Abstract

Because plants do not possess a defined germline, deleterious somatic mutations can be passed to gametes, and a large number of cell divisions separating zygote from gamete formation may lead to many mutations in long-lived plants. We sequenced the genome of two terminal branches of a 234-year-old oak tree and found several fixed somatic single-nucleotide variants whose sequential appearance in the tree could be traced along nested sectors of younger branches. Our data suggest that stem cells of shoot meristems in trees are robustly protected from the accumulation of mutations.

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Acknowledgements

This work was funded by the University of Lausanne through a supportive grant from the University rectorate and by the Swiss National Science Foundation (Agora Grant CRAGI3_145652). The Pacific Biosciences RS II sequencing was performed at the Lausanne Genomic Technologies Facility (GTF). The purchase of the GTF’s RS II instrument was financed in part by the Loterie Romande through the Fondation pour la Recherche en Médecine Génétique. We thank K. Harshman, J. Weber and M. Dupasquier from the GTF for sequencing. We thank C. Kuhlemeier for sharing unpublished results, J. Tercier for tree-ring analysis, Transistor communication for graphical production of the 3D oak, Woodtli + Leuba SA for sample collection, N. Guex for advice on SNV identification and J.-J. Strahm and M. Bonetti for providing oak images.

Author information

Author notes

  1. Emanuel Schmid-Siegert, Namrata Sarkar, Christian Iseli, Christian Fankhauser, Christian S. Hardtke, Laurent Keller, John R. Pannell, Alexandre Reymond, Marc Robinson-Rechavi and Ioannis Xenarios contributed equally to this work.

Affiliations

  1. Vital-IT Competence Center, Swiss Institute of Bioinformatics, Lausanne, Switzerland

    • Emanuel Schmid-Siegert
    • , Christian Iseli
    • , Sandra Calderon
    • , Marco Pagni
    •  & Ioannis Xenarios
  2. Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland

    • Namrata Sarkar
    • , Jacqueline Chrast
    • , Frédéric Schütz
    • , Christian Fankhauser
    • , Alexandre Reymond
    •  & Ioannis Xenarios
  3. Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland

    • Namrata Sarkar
    • , Laurent Keller
    • , John R. Pannell
    •  & Marc Robinson-Rechavi
  4. Evolutionary Bioinformatics Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland

    • Namrata Sarkar
    •  & Marc Robinson-Rechavi
  5. Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland

    • Caroline Gouhier-Darimont
    • , Pietro Cattaneo
    • , Christian S. Hardtke
    •  & Philippe Reymond
  6. Fasteris SA, Plan-les-Ouates, Switzerland

    • Laurent Farinelli
  7. Swiss-Prot group, Swiss Institute of Bioinformatics, Geneva, Switzerland

    • Michel Schneider
    •  & Ioannis Xenarios
  8. Risk Analysis Group, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland

    • Jérémie Voumard
    •  & Michel Jaboyedoff

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Contributions

L.F. sequenced the genome. E.S.-S., S.C. and M.P. assembled and annotated the genome. N.S., E.S.-S. and C.I. identified SNVs. C.G.-D. and J.C. extracted DNA and confirmed SNVs. E.S.-S. and M.R.-R. analysed genome duplication. P.C. produced cross-sections of oak apical meristems. M.S. established a list of DNA repair genes. F.S. provided statistical help with the analyses. J.V. and M.J. produced a 3D model of the oak tree. C.H., C.F., L.K., I.X., M.R.-R., J.P., A.R. and P.R. conceived the project and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Philippe Reymond.

Electronic supplementary material

  1. Supplementary Information

    Supplementary Figures 1–9, Supplementary Tables 1–4, Supplementary Methods, Supplementary Discussion

  2. Life Sciences Reporting Summary

  3. Supplementary Table 5

    DNA repair genes

  4. Supplementary Table 6

    Arabidopsis DNA repair genes

  5. Supplementary Table 7

    Duplicated DNA repair genes