Computational Discovery and Analysis of rDNA Sequence Heterogeneity in Yeast

Ribosomal RNA genes, known as ribosomal DNA or rDNA, are commonly found in tandem arrays of hundreds of repeating units. The sequences of each unit in an array were thought to be near-identical but it is now known that frequent mutations may occur, causing heterogeneity amongst units. Opposing these divergent mutational processes, unit sequences are homogenised through concerted evolutionary processes such as unequal sister chromatid exchange (USCE) and gene conversion (GC). In this study Perl software has been used to uncover rDNA sequence variation in the yeast Saccharomyces paradoxus, using data derived from the Saccharomyces Genome Resequencing Project. This analysis, in conjunction with a reanalysis of the Saccharomyces cerevisiae data from the same project, has provided detailed information regarding rDNA sequence heterogeneity in two contrasting, yet closelyrelated yeast species. Additionally, the rDNA flanking sequences of four yeast strains have been characterised via an analysis of new next generation sequencing reads, adding to our knowledge of concerted evolutionary processes in these genomic regions. Partial Single Nucleotide Polymorphisms (pSNPs) within these datasets are shown to reflect genome mosaicism within a population, and to identify strains with signs of genome hybridisation undetectable by other means. This information provides further insights into the dynamics of the rDNA region in the two yeast species. In particular, examination of the percentage occupancies of pSNPs reveals U-shaped distributions which differ between the two species. Further investigations of rDNA evolutionary dynamics through the development of two Java simulation tools (SIMPLEX and CONCERTINA), which model USCE and GC events, follow the fate of both single and multiple pSNPs in one or more rDNA arrays. Initial simulations show the distribution of pSNPs varies depending upon the balance between mutations and concerted evolutionary events, and provide a framework to investigate the mechanisms involved in altered rDNA dynamics in various cellular processes.

Name dc:type.qualificationname

phd

Level dc:type.qualificationlevel

doctoral

Grantor dc:publisher.institution

University of East Anglia

Year dc:date.issued

2013

Author dc:creator

• West, Claire Louise

Language dc:language

en