ArticleGenome biology2014
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 256 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
256 citing papers in PubMed, 512 citations in OpenAlex.
- Expanding the triangle of U: comparative analysis of the Hirschfeldia incana genome provides insights into chromosomal evolution, phylogenomics and high photosynthesis-related traits.Annals of botany · 2026Article
- T2T reference genome assembly provides insights into anthocyanin accumulation in broccoli.Horticulture research · 2026Article
- A fourth subgenome of the Camelina genus reveals gene dominance is influenced by chromosomal proximity.Nature communications · 2026Article
- Comparative Transcriptomic Analysis of Chlorophyll Metabolism in Broccoli Under Preharvest 1-MCP Application Versus Pre-Cooling Combined with Cold Chain Storage.Foods (Basel, Switzerland) · 2026Article
- A spontaneous termination mechanism of RNA polymerase V shapes the DNA methylation landscape in plants.The EMBO journal · 2026Article
- Highly accurate ab initio gene annotation with ANNEVO.Nature methods · 2026Article
- DNA methylation around transcription start sites is not globally associated with transcription in the grain of natural and synthetic hexaploid wheat.BMC plant biology · 2026Article
- Comprehensive phenomics and vegetative yield analysis of global kale (Brassica oleracea var. acephala) germplasm in controlled environment agriculture.BMC plant biology · 2026Article
- Genome-Wide Identification and Characterization of the Calmodulin-Binding Transcription Activators (CAMTA) Gene Family inPlants (Basel, Switzerland) · 2026Article
- Genome-based prediction of recombination within and between plant species: insights from Brassica oleracea recombinant populations and an interspecific tomato cross (Solanum lycopersicum × S. pimpinellifolium).BMC plant biology · 2026Article
- Genetic diversity, phylogenetic relationships, and marker development betweenFrontiers in plant science · 2026Article
- Genetic and Epigenetic Mechanisms Underpinning Biotic Stress Resilience ofPlants (Basel, Switzerland) · 2025Review
- AlloSHP: deconvoluting single homeologous polymorphism for phylogenetic analysis of allopolyploids.Plant methods · 2025Article
- Article
- Fine mapping of the dominant female sterility gene and novel model of hybrid seed production in cabbage (Brassica oleracea L. var. capitata).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Hybridization and gene expression: Beyond differentially expressed genes.Molecular ecology · 2025Review
- Recruitment, rewiring and deep conservation in flowering plant gene regulation.Nature plants · 2025Article
- Article
- Chromosome fusions shaped karyotype evolution and evolutionary relationships in the model family Brassicaceae.Nature communications · 2025Article
196 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
32 authors at 14 institutions in 5 countries.
Funding
Abstract
backgroundBrassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.
resultsWe generate an assembly representing 75% of the predicted B. oleracea genome using a hybrid Illumina/Roche 454 approach. Two dense genetic maps are generated to anchor almost 92% of the assembled scaffolds to nine pseudo-chromosomes. Over 50,000 genes are annotated and 40% of the genome predicted to be repetitive, thus contributing to the increased genome size of B. oleracea compared to its close relative B. rapa. A snapshot of both the leaf transcriptome and methylome allows comparisons to be made across the triplicated sub-genomes, which resulted from the most recent Brassiceae-specific polyploidy event.
conclusionsDifferential expression of the triplicated syntelogs and cytosine methylation levels across the sub-genomes suggest residual marks of the genome dominance that led to the current genome architecture. Although cytosine methylation does not correlate with individual gene dominance, the independent methylation patterns of triplicated copies suggest epigenetic mechanisms play a role in the functional diversification of duplicate genes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.