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High-quality genome and methylomes illustrate features underlying evolutionary success of oaks

Author

Listed:
  • Victoria L. Sork

    (University of California
    University of California)

  • Shawn J. Cokus

    (University of California)

  • Sorel T. Fitz-Gibbon

    (University of California)

  • Aleksey V. Zimin

    (Johns Hopkins University
    Johns Hopkins University)

  • Daniela Puiu

    (Johns Hopkins University)

  • Jesse A. Garcia

    (University of California)

  • Paul F. Gugger

    (University of Maryland Center for Environmental Science)

  • Claudia L. Henriquez

    (University of California)

  • Ying Zhen

    (University of California)

  • Kirk E. Lohmueller

    (University of California
    University of California)

  • Matteo Pellegrini

    (University of California)

  • Steven L. Salzberg

    (Johns Hopkins University
    Johns Hopkins University)

Abstract

The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼450 extant species. We present a high-quality de novo genome assembly of a California endemic oak, Quercus lobata, revealing features consistent with oak evolutionary success. Effective population size remained large throughout history despite declining since early Miocene. Analysis of 39,373 mapped protein-coding genes outlined copious duplications consistent with genetic and phenotypic diversity, both by retention of genes created during the ancient γ whole genome hexaploid duplication event and by tandem duplication within families, including numerous resistance genes and a very large block of duplicated DUF247 genes, which have been found to be associated with self-incompatibility in grasses. An additional surprising finding is that subcontext-specific patterns of DNA methylation associated with transposable elements reveal broadly-distributed heterochromatin in intergenic regions, similar to grasses. Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.

Suggested Citation

  • Victoria L. Sork & Shawn J. Cokus & Sorel T. Fitz-Gibbon & Aleksey V. Zimin & Daniela Puiu & Jesse A. Garcia & Paul F. Gugger & Claudia L. Henriquez & Ying Zhen & Kirk E. Lohmueller & Matteo Pellegrin, 2022. "High-quality genome and methylomes illustrate features underlying evolutionary success of oaks," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29584-y
    DOI: 10.1038/s41467-022-29584-y
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