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

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 and Steven L. Salzberg
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Victoria L. Sork: University of California
Shawn J. Cokus: University of California
Sorel T. Fitz-Gibbon: University of California
Aleksey V. Zimin: 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
Matteo Pellegrini: University of California
Steven L. Salzberg: Johns Hopkins University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-29584-y

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