Exploring the boundaries of shallow
phylogeny in the YESS group and the
dynamics of gene cluster and operon
formation in bacterial genomes.
PhD thesis, National University of Ireland Maynooth.
In this thesis I look at two different problems in bacterial genomic analysis. The first
involves reconstructing the evolutionary history between a group of closely related
bacteria. I addressed whether or not it is possible to separate such genomes into different
genera, species and strains. Specifically, I addressed how different approaches such as
the use of 16S rRNA phylogenetic trees, phylogenetic supertrees and concatenation of
individual genes in order to construct phylogenetic trees compare with one another.
What effect will problems associated with resolving shallow-phylogeny have on
recovering a tree of life? Ultimately I show that for the group of genomes involved,
different methods and data produce different results and that the true tree, if a tree-like
structure does indeed exist for these genomes, is unrecoverable using such approaches.
In the second part of my thesis I examine the phenomenon of gene clustering in bacterial
genomes. I present a software program, GenClust, for the identification, analysis and
visualisation of gene clusters. I show how GenClust can be used to recover and analyse
clusters of genes involved in amino acid biosynthesis across a large !-proteobacterial
dataset. Finally, I examine models of gene cluster and operon formation and test them
with real data, using a combined approach of comparing clusters on both structural
similarity and the underlying phylogenetic signals of the clustered genes. I provide a
hypothesis for the selective forces driving cluster and operon formation in bacterial
||shallow phylogeny; YESS group; gene cluster; operon formation; bacterial genomes;
||Faculty of Science and Engineering > Biology
||19 Nov 2010 11:43
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