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


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Article Info

DATE

2022-04-19

AUTHORS

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 Pellegrini, Steven L. Salzberg

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. More... »

PAGES

2047

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  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-022-29584-y

    DOI

    http://dx.doi.org/10.1038/s41467-022-29584-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1147209275

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/35440538


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    330 Department of Molecular, Cell, and Developmental Biology, University of California, 90095-7239, Los Angeles, CA, USA
    331 Institute of the Environment and Sustainability, University of California, 90095, Los Angeles, CA, USA
    332 rdf:type schema:Organization
    333 grid-institutes:grid.21107.35 schema:alternateName Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 21218, Baltimore, MD, USA
    334 Department of Biomedical Engineering, Johns Hopkins University, 21218, Baltimore, MD, USA
    335 Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, 21218, Baltimore, MD, USA
    336 schema:name Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, 21218, Baltimore, MD, USA
    337 Department of Biomedical Engineering, Johns Hopkins University, 21218, Baltimore, MD, USA
    338 Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, 21218, Baltimore, MD, USA
    339 rdf:type schema:Organization
    340 grid-institutes:grid.291951.7 schema:alternateName Appalachian Laboratory, University of Maryland Center for Environmental Science, 21532, Frostburg, MD, USA
    341 schema:name Appalachian Laboratory, University of Maryland Center for Environmental Science, 21532, Frostburg, MD, USA
    342 rdf:type schema:Organization
     




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