Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing - PubMed (original) (raw)

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

Stephen A James et al. Genome Res. 2009 Apr.

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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Figures

Figure 1.

Figure 1.

Distribution of (base substitution-only) polymorphisms, occurring in 100-bp bins, in the S. cerevisiae rDNA array derived from the combined sequence data of 34 different strains of S. cerevisiae (Table 1; Supplemental Table 1).

Figure 2.

Figure 2.

Distribution of (base substitution-only) polymorphisms, occurring in 20-bp bins, across the 2.28-kb IGS region. The approximate locations of the 5S rRNA gene, the RFB site, E-pro, and rARS are shown, along with the number of polymorphisms (in parentheses) identified in each _cis_-acting functional element. A trend line (dotted line) has also been added to show the polymorphism distribution if the 149 detected sites were evenly distributed across this region (i.e., at a frequency of ∼1.3 sites per 20 nucleotides).

Figure 3.

Figure 3.

Distribution plot of rDNA pSNP frequency (occupancy ratio) values grouped in bins of 10% increments.

Figure 4.

Figure 4.

Maximum frequency (occupancy ratio) distribution plots of polymorphisms found in the RFB site, nucleotide positions 6913 (1) to 7030 (118) (A), and the rARS, nucleotide positions 8473 (1) to 8579 (107) (B).

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