ArticleGenome research2009
Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 96 citations in OpenAlex.
- Chromosome-scale assembly of yeast genomes using enzyme-free, dense optical genome mapping.Nature communications · 2026Article
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast.Nucleus (Austin, Tex.) · 2025Article
- CompletebioRxiv : the preprint server for biology · 2025Article
- Chromosomal-level assembly of Magnusiomyces clavatus: novel genetic insights on an emerging fungal pathogen.G3 (Bethesda, Md.) · 2025Article
- Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans.PLoS genetics · 2025Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Article
- Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.G3 (Bethesda, Md.) · 2024Article
- Article
- A comparative analysis of chloroplast genomes revealed the chloroplast heteroplasmy ofFrontiers in pharmacology · 2024Article
- Ribosomal DNA Copy Number Variation is Coupled with DNA Methylation Changes at the 45S rDNA Locus.Epigenetics · 2023Article
- Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast.Genome biology and evolution · 2023Article
- Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?Heredity · 2023Review
- Intrageneric Relationship of Datnioides (Lobotiformes) Inferred from the Complete Nuclear Ribosomal DNA Operon.Biochemical genetics · 2023Article
- Can nuclear aquatic environmental DNA be a genetic marker for the accurate estimation of species abundance?Die Naturwissenschaften · 2022Article
- Genomic architecture of 5S rDNA cluster and its variations within and between species.BMC genomics · 2022Article
- Using High-Throughput Amplicon Sequencing to Evaluate Intragenomic Variation and Accuracy in Species Identification ofJournal of fungi (Basel, Switzerland) · 2021Article
- Challenges and Approaches to Genotyping Repetitive DNA.G3 (Bethesda, Md.) · 2020Article
- Australia: A Continent Without Native Powdery Mildews? The First Comprehensive Catalog Indicates Recent Introductions and Multiple Host Range Expansion Events, and Leads to the Re-discovery ofFrontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Ribosomal DNA (rDNA) plays a key role in ribosome biogenesis, encoding genes for the structural RNA components of this important cellular organelle. These genes are vital for efficient functioning of the cellular protein synthesis machinery and as such are highly conserved and normally present in high copy numbers. In the baker's yeast Saccharomyces cerevisiae, there are more than 100 rDNA repeats located at a single locus on chromosome XII. Stability and sequence homogeneity of the rDNA array is essential for function, and this is achieved primarily by the mechanism of gene conversion. Detecting variation within these arrays is extremely problematic due to their large size and repetitive structure. In an attempt to address this, we have analyzed over 35 Mbp of rDNA sequence obtained from whole-genome shotgun sequencing (WGSS) of 34 strains of S. cerevisiae. Contrary to expectation, we find significant rDNA sequence variation exists within individual genomes. Many of the detected polymorphisms are not fully resolved. For this type of sequence variation, we introduce the term partial single nucleotide polymorphism, or pSNP. Comparative analysis of the complete data set reveals that different S. cerevisiae genomes possess different patterns of rDNA polymorphism, with much of the variation located within the rapidly evolving nontranscribed intergenic spacer (IGS) region. Furthermore, we find that strains known to have either structured or mosaic/hybrid genomes can be distinguished from one another based on rDNA pSNP number, indicating that pSNP dynamics may provide a reliable new measure of genome origin and stability.
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Registered trials
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