ArticleBMC genomics2015
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 53 citations in OpenAlex.
- In Situ GWAS in Two Range-Edge Populations of European Beech (Fagus sylvatica L.) Identify Genetic Factors of Adaptation to Climate Change.Molecular ecology · 2026Article
- Forward genetic screening of mutants of the wild diploid ancestor Nicotiana sylvestris identifies aspartate oxidase 2 as a key gene for nicotine biosynthesis in cultivated allotetraploid tobacco (Nicotiana tabacum).The Plant journal : for cell and molecular biology · 2026Article
- Response of Pedunculate Oak (Plants (Basel, Switzerland) · 2025Review
- Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae).Annals of botany · 2024Article
- Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur.BMC genomics · 2024Article
- Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology.BMC plant biology · 2023Article
- OakRootRNADB-a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur).Database : the journal of biological databases and curation · 2022Article
- Multiomics Molecular Research into the Recalcitrant and OrphanInternational journal of molecular sciences · 2022Review
- Current status and trends in forest genomics.Forestry research · 2022Review
- Quercus species divergence is driven by natural selection on evolutionarily less integrated traits.Heredity · 2021Article
- Genome-Wide Identification of Epigenetic Regulators inInternational journal of molecular sciences · 2020Article
- ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability inFrontiers in plant science · 2020Article
- From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.BMC genomics · 2019Article
- Proteomics, Holm Oak (International journal of molecular sciences · 2019Review
- Gene expression analysis of bud burst process in European hazelnut (Physiology and molecular biology of plants : an international journal of functional plant biology · 2019Article
- Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome.PloS one · 2019Article
- How Quercus ilex L. saplings face combined salt and ozone stress: a transcriptome analysis.BMC genomics · 2018Article
- Oak genome reveals facets of long lifespan.Nature plants · 2018Article
- Hardwood Tree Genomics: Unlocking Woody Plant Biology.Frontiers in plant science · 2018Article
- Extensive recent secondary contacts between four European white oak species.The New phytologist · 2017Article
Corrections and comments
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Authors and funding
27 authors at 9 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection.
resultsThe assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment.
conclusionIn addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
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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.