ArticleNature communications2022
High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 76 citations in OpenAlex.
- 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
- Applying Both Landscape Genomic and Ecological Niche Model Predictions to Inform Conservation Strategies of a California Foundational Oak Species.Molecular ecology · 2026Article
- A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana.G3 (Bethesda, Md.) · 2026Article
- Landscape Genomic Analyses ofEvolutionary applications · 2026Article
- Population genomics of Quercus gilva provides insights into the conservation of fengshui forests.Communications biology · 2026Article
- Drought-associated genes exhibit high constitutive expression in Quercus douglasii, a drought-tolerant California oak.G3 (Bethesda, Md.) · 2026Article
- quercusTOA: integrating functional annotations and comparative genomics across oak lineages.Frontiers in bioinformatics · 2026Article
- Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae).BMC plant biology · 2025Article
- Pan-Genome Analysis Reveals Local Adaptation to Climate Driven by Introgression in Oak Species.Molecular biology and evolution · 2025Article
- A haplotype-resolved reference genome of Quercus alba sheds light on the evolutionary history of oaks.The New phytologist · 2025Article
- Genomic insights into ecological adaptation of oaks revealed by phylogenomic analysis of multiple species.Plant diversity · 2025Article
- Comparison of Conservation Strategies for California Channel Island Oak (Evolutionary applications · 2024Article
- Unravelling DNA methylation dynamics during developmental stages in Quercus ilex subsp. ballota [Desf.] Samp.BMC plant biology · 2024Article
- Genome-wide characterization and analysis of rice DUF247 gene family.BMC genomics · 2024Article
- Karyotype and LTR-RTs analysis provide insights into oak genomic evolution.BMC genomics · 2024Article
- Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology.Evolutionary applications · 2024Article
- The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.The Journal of heredity · 2024Article
- Distinct ancient structural polymorphisms control heterodichogamy in walnuts and hickories.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar.BMC biology · 2024Article
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
Abstract
The genus Quercus, which emerged ∼55 million years ago during globally warm temperatures, diversified into ∼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 γ 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.