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

The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features relevant to its evolutionary success. The genus Quercus, which emerged similar to 55 million years ago during globally warm temperatures, diversified into similar to 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 gamma 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.

Automated summary

The genus Quercus, which has diversified into over 450 species, plays dominant roles in ecosystems. This study presents a genome and methylome for a California endemic oak, Quercus lobata, and identifies evolutionary features that contribute to its success. The analysis reveals genetic and phenotypic diversity through duplications of protein-coding genes and methylation patterns associated with transposable elements.