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; Steven L Salzberg

doi:10.1038/s41467-022-29584-y

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

Nat Commun. 2022 Apr 19;13(1):2047. doi: 10.1038/s41467-022-29584-y.

Authors

Victoria L Sork^#^{1

2}, Shawn J Cokus^#³, Sorel T Fitz-Gibbon^#⁴, Aleksey V Zimin^{5

6}, Daniela Puiu⁵, Jesse A Garcia⁴, Paul F Gugger⁷, Claudia L Henriquez⁴, Ying Zhen⁴, Kirk E Lohmueller^{4

8}, Matteo Pellegrini³, Steven L Salzberg^{5

9}

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA. vlsork@ucla.edu.
² Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA. vlsork@ucla.edu.
³ Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095-7239, USA.
⁴ Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095-1438, USA.
⁵ Center for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
⁶ Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA.
⁷ Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21532, USA.
⁸ Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
⁹ Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, 21218, USA.

^# Contributed equally.

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.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Biological Evolution
DNA Methylation / genetics
Epigenome
Evolution, Molecular
Humans
Quercus* / genetics

Abstract

Publication types

MeSH terms

Grants and funding