Computational Discovery and Analysis of rDNA Sequence Heterogeneity in Yeast

West, Claire Louise (2013) Computational Discovery and Analysis of rDNA Sequence Heterogeneity in Yeast. Doctoral thesis, University of East Anglia.

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Abstract

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.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Mia Reeves
Date Deposited: 12 Jun 2014 13:21
Last Modified: 12 Jun 2014 13:21
URI: https://ueaeprints.uea.ac.uk/id/eprint/48753
DOI:

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