ArticleThe plant genome2022
Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach.
Article in The plant genome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 20 citations in OpenAlex.
- Genome architecture modulates 35S and 5S rDNA homogenization in Asteraceae.The Plant journal : for cell and molecular biology · 2026Article
- Dynamic evolution and hierarchical regulation of rDNA in polyploid oat.The Plant journal : for cell and molecular biology · 2026Article
- Efficient site-specific gene addition using R2 retrotransposons in tobacco and rice.Nature biotechnology · 2026Article
- Optimized R2 retroelement complexes for DNA insertion into plant genomes.Nature biotechnology · 2026Article
- Article
- Nucleolar dominance arises in Spartina homoploid hybrids and persists after allopolyploidization.The Plant journal : for cell and molecular biology · 2026Article
- Regulation of nucleolar dominance through allopolyploidization of hexaploid wheat.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A telomere-to-telomere genome assembly coupled with multi-omic data provides insights into the evolution of hexaploid bread wheat.Nature genetics · 2025Article
- Are cereal grasses a single genetic system?Nature plants · 2024Article
- The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics.Molecular biology and evolution · 2024Article
- Insight into chromatin compaction and spatial organization in rice interphase nuclei.Frontiers in plant science · 2024Article
- Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Heredity · 2023Review
- Ribosome heterogeneity and specialization of Plasmodium parasites.PLoS pathogens · 2023Article
- Flow Sorting-Assisted Optical Mapping.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Uniparental expression of ribosomal RNA in ×Frontiers in plant science · 2023Article
- Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome.Plant biotechnology journal · 2022Article
- A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.GigaScience · 2022Article
- Fine structure and transcription dynamics of bread wheat ribosomal DNA loci deciphered by a multi-omics approach.The plant genome · 2022Article
- Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes.Frontiers in plant science · 2021Review
- Personal Perspectives on Plant Ribosomal RNA Genes Research: From Precursor-rRNA to Molecular Evolution.Frontiers in plant science · 2021Review
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Three out of four RNA components of ribosomes are encoded by 45S ribosomal DNA (rDNA) loci, which are organized as long head-to-tail tandem arrays of nearly identical units, spanning several megabases of sequence. Due to this structure, the rDNA loci are the major sources of gaps in genome assemblies, and gene copy number, sequence composition, and expression status of particular arrays remain elusive, especially in complex genomes harboring multiple loci. Here we conducted a multi-omics study to decipher the 45S rDNA loci in hexaploid bread wheat. Coupling chromosomal genomics with optical mapping, we reconstructed individual rDNA arrays, enabling locus-specific analyses of transcription activity and methylation status from RNA- and bisulfite-sequencing data. We estimated a total of 6,650 rDNA units in the bread wheat genome, with approximately 2,321, 3,910, 253, and 50 gene copies located in short arms of chromosomes 1B, 6B, 5D, and 1A, respectively. Only 1B and 6B loci contributed substantially to rRNA transcription at a roughly 2:1 ratio. The ratio varied among five tissues analyzed (embryo, coleoptile, root tip, primary leaf, mature leaf), being the highest (2.64:1) in mature leaf and lowest (1.72:1) in coleoptile. Cytosine methylation was considerably higher in CHG context in the silenced 5D locus as compared with the active 1B and 6B loci. In conclusion, a fine genomic organization and tissue-specific expression of rDNA loci were deciphered, for the first time, in a complex polyploid species. The results are discussed in the context of wheat evolution and transcription regulation.
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