ArticleThe New phytologist2025
A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks.
Article in The New phytologist, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Multi-organ single-cell transcriptomic atlas identifies QrIAA14 as a candidate negative regulator of adventitious root development in Quercus robur.PLoS genetics · 2026Article
- Chromosome-Level Genome Assembly and Comparative Genomic Analysis ofPlants (Basel, Switzerland) · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana.G3 (Bethesda, Md.) · 2026Article
- quercusTOA: integrating functional annotations and comparative genomics across oak lineages.Frontiers in bioinformatics · 2026Article
- Decoding drought tolerance from a genomic approach in Castanea sativa Mill.The plant genome · 2025Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
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Authors and funding
17 authors.
Funding
Abstract
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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