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bioRxiv · 10.1101/2021.04.09.439191

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

Sork, V. L.·Cokus, S.·Fitz-Gibbon, S. T.·Zimin, A. V.·Puiu, D.·Garcia, J. A.·Gugger, P. F.·Henriquez, C. L.·Zhen, Y.·Lohmueller, K. E.·Pellegrini, M.·Salzberg, S. L.
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Abstract

The 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{gamma} 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.

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Sork, V. L., Cokus, S., Fitz-Gibbon, S. T., Zimin, A. V., Puiu, D., Garcia, J. A., Gugger, P. F., Henriquez, C. L., Zhen, Y., Lohmueller, K. E., Pellegrini, M., Salzberg, S. L.. 2021-04-11. High-quality genome and methylomes illustrate features underlying evolutionary success of oaks. https://doi.org/10.1101/2021.04.09.439191

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