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Low number of fixed somatic mutations in a long-lived oak tree

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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Fig. 1: Distribution of fixed somatic mutations in the Napoleon Oak.

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References

  1. Scofield, D. G. & Schultz, S. T. Proc. R. Soc. B 273, 275–282 (2006).

    Article  PubMed  Google Scholar 

  2. Ally., D., Ritland, K. & Otto, S. P. PLoS Biol. 8, e1000454 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  3. Bobiwash, K., Schultz, S. T. & Schoen, D. J. Heredity 111, 338–344 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Millet, J. L’architecture Des Arbres Des Régions Tempérées: Son Histoire, Ses Concepts, Ses Usages (MultiMondes, Quebec, 2012).

  5. Plomion, C. et al. Mol. Ecol. Resour. 16, 254–265 (2016).

    Article  CAS  PubMed  Google Scholar 

  6. McKenna, A. et al. Genome Res. 20, 1297–1303 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Iseli, C., Ambrosini, G., Bucher, P. & Jongeneel, C. V. PLoS One 2, e579 (2007).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Wolfe, K. H., Li, W. H. & Sharp, P. M. Proc. Natl Acad. Sci. USA 84, 9054–9058 (1987).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ossowski, S. et al. Science 327, 92–94 (2010).

    Article  CAS  PubMed  Google Scholar 

  10. Yang, S. et al. Nature 523, 463–467 (2015).

    Article  CAS  PubMed  Google Scholar 

  11. Scofield, D. G. Am. J. Bot. 93, 1740–1747 (2006).

    Article  PubMed  Google Scholar 

  12. Romberger, J. A., Hejnowicz, Z. & Hill, J. F. Plant Structure: Function and Development (Springer, Berlin, 1993).

  13. Kwiatkowska, D. J. Exp. Bot. 59, 187–201 (2008).

    Article  CAS  PubMed  Google Scholar 

  14. Burian, A., Barbier de Reuille, P. & Kuhlemeier, C. Curr. Biol. 26, 1385–1394 (2016).

    Article  CAS  PubMed  Google Scholar 

  15. Edwards, P. B., Wanjura, W. J., Brown, W. V. & Dearn, J. M. Nature 347, 434 (1990).

    Article  Google Scholar 

  16. Padovan, A., Lanfear, R., Keszei, A., Foley, W. J. & Külheim, C. BMC Plant Biol. 13, 29 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Watson, J. M. et al. Proc. Natl Acad. Sci. USA 113, 12226–12231 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Behjati, S. et al. Nature 513, 422–425 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Lodato, M. A. et al. Science 350, 94–98 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Van der Auwera, G. A. et al. Curr. Protoc. Bioinform. 43, 11.10.1–11.10.33 (2013).

    Google Scholar 

  21. Myers, E. W. & Miller, W. Comput. Appl. Biosci. 4, 11–17 (1988).

    CAS  PubMed  Google Scholar 

  22. Li, H. et al. Bioinformatics 25, 2078–2079 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

Download references

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

Authors and Affiliations

Authors

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.

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Correspondence to Philippe Reymond.

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The authors declare no competing financial interests.

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Supplementary Information

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

Life Sciences Reporting Summary

Supplementary Table 5

DNA repair genes

Supplementary Table 6

Arabidopsis DNA repair genes

Supplementary Table 7

Duplicated DNA repair genes

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Schmid-Siegert, E., Sarkar, N., Iseli, C. et al. Low number of fixed somatic mutations in a long-lived oak tree. Nature Plants 3, 926–929 (2017). https://doi.org/10.1038/s41477-017-0066-9

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