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

Author:

Sork Victoria L.ORCID,Cokus Shawn J.,Fitz-Gibbon Sorel T.ORCID,Zimin Aleksey V.ORCID,Puiu DanielaORCID,Garcia Jesse A.ORCID,Gugger Paul F.ORCID,Henriquez Claudia L.,Zhen Ying,Lohmueller Kirk E.ORCID,Pellegrini MatteoORCID,Salzberg Steven L.ORCID

Abstract

AbstractThe genus Quercus, which emerged ~55 million years ago during globally warm temperatures, diversified into ~450 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 the 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 the numerous resistance genes and also unexpected candidate genes for an incompatibility system involving multiple non-self-recognition genes. 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 (another highly successful taxon). Collectively, these features promote genetic and phenotypic variation that would facilitate adaptability to changing environments.

Publisher

Cold Spring Harbor Laboratory

Reference94 articles.

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3. Denk, T. , Grimm, G. W. , Manos, P. S. , Deng, M. & Hipp, A. L. in Oaks Physiological Ecology. Exploring the Functional Diversity of Genus Quercus L. Vol. 7 Tree Physiology (eds E. Gil-Pelegrín , J. Peguero-Pina , & D. Sancho-Knapik ) (Springer, 2017).

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