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PMID: 19141593 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing.

Genome research ·Vol. 19 ·No. 4 ·2009-04-00 ·Pages 626-35

James SA, O'Kelly MJ, Carter DM, Davey RP, van Oudenaarden A, Roberts IN

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.

MeSH Terms
DNA, Fungal/genetics DNA, Ribosomal/genetics Gene Expression Regulation, Fungal Genome, Fungal Oligonucleotide Array Sequence Analysis Polymorphism, Single Nucleotide/genetics Repetitive Sequences, Nucleic Acid/genetics Saccharomyces cerevisiae/genetics,growth & development Sequence Analysis, DNA
Chemicals
DNA, Fungal DNA, Ribosomal
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
James Stephen A
National Collection of Yeast Cultures, Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom.
O'Kelly Michael J T
Carter David M
Davey Robert P
van Oudenaarden Alexander
Roberts Ian N
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.084517.108
Published
2009-04-00
Epub
2009-00-13
Pages
626-35
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2665781
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · BBS/E/F/00042258 · United Kingdom
Wellcome Trust · United Kingdom
External Links
PubMed source DOI: 10.1101/gr.084517.108 PMC Full Text View journal details
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