A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

Larson, Drew A.; Staton, Margaret E.; Kapoor, Beant; Islam‐Faridi, Nurul; Zhebentyayeva, Tetyana; Fan, Shenghua; Stork, Jozsef; Thomas, Austin; Ahmed, Alaa S.; Stanton, Elizabeth C.; Houston, Allan; Schlarbaum, Scott E.; Hahn, Matthew W.; Carlson, John E.; Abbott, Albert G.; DeBolt, Seth; Nelson, C. Dana

doi:10.1111/nph.20463

Title: A haplotype‐resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks

Journal Article · 10 February 2025 · New Phytologist

DOI: https://doi.org/10.1111/nph.20463 · OSTI ID:2514483

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Department of Biology Indiana University Bloomington IN 47405 USA
Department of Entomology and Plant Pathology University of Tennessee Knoxville TN 37996 USA
USDA Forest Service, Southern Research Station College Station TX 77843 USA, Department of Ecology and Conservation Biology Texas A&,M University College Station TX 77843 USA
Department of Forestry and Natural Resources University of Kentucky Lexington KY 40546 USA
Department of Horticulture University of Kentucky Lexington KY 40546 USA
Oak Ridge Institute for Science and Education (ORISE) USDA Forest Service, Southern Research Station Lexington KY 40546 USA
Genome Science and Technology University of Tennessee Knoxville TN 37996 USA
School of Natural Resources University of Tennessee Knoxville TN 37996 USA
Department of Biology Indiana University Bloomington IN 47405 USA, Department of Computer Science Indiana University Bloomington IN 47405 USA
Department of Ecosystem Science and Management Pennsylvania State University University Park PA 16802 USA
Department of Forestry and Natural Resources University of Kentucky Lexington KY 40546 USA, Abbott Tree Farm and Research Consultants Cape Vincent NY 13618 USA
Department of Horticulture University of Kentucky Lexington KY 40546 USA, James B. Beam Institute for Kentucky Spirits University of Kentucky Lexington KY 40546 USA
USDA Forest Service, Southern Research Station Lexington KY 40546 USA

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus , certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus . Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus .

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Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0014664

OSTI ID:: 2514483

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 1 Vol. 246; ISSN 0028-646X

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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