Exploring the boundaries of shallow phylogeny in the YESS group and the dynamics of gene cluster and operon formation in bacterial genomes

摘要: 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. addressed whether or not it is possible to separate such genomes into different genera, species and strains. Specifically, how approaches as the use 16S rRNA phylogenetic trees, supertrees concatenation of individual genes order construct trees compare with one another. What effect will associated resolving shallow-phylogeny have on recovering tree life? Ultimately show that for involved, different methods data produce results true tree, if tree-like structure does indeed exist these genomes, unrecoverable using approaches. In second part my examine phenomenon gene clustering bacterial genomes. present software program, GenClust, identification, analysis and visualisation clusters. GenClust can be used recover analyse clusters involved amino acid biosynthesis across large !-proteobacterial dataset. Finally, models cluster operon formation test them with real data, combined approach comparing clusters on both structural similarity underlying signals clustered genes. provide a hypothesis selective forces driving