Evolutionary dynamics of intergenic sites, pan-genomes, and introgression in bacteria

  • Harry Thorpe

Student thesis: Doctoral ThesisPhD


Bacterial genomes evolve under strong selective constraints. They are compact, gene dense, and contain little extraneous DNA. They are also diverse; individuals from the same species frequently differ substantially in gene content from each other. The work presented in this thesis has investigated the diversity of bacterial species and the selective forces which shape their genomes. A focus has been given to regions of the genome which are poorly understood, particularly intergenic sites. Intergenic sites are shown to be under widespread purifying selection which varies according to divergence time, the class of regulatory element, and distance from gene borders. This is complemented by work on Rho-independent terminator sequences which shows that compensatory evolution is widespread in many species. A detailed analysis of H. pylori introgression shows that selection acts to moderate the uptake of DNA from different sources. Additionally, analyses of pan-genomes incorporating intergenic regions were performed, and a new tool, Piggy, was introduced to facilitate these analyses. This enabled the interaction between genes and their cognate intergenic regions to be analysed, and genes with divergent upstream intergenic regions were shown to be more differentially expressed than those without in S. aureus. This work has provided new insights into the evolutionary dynamics of these poorly understood but vital components of bacterial genomes.
Date of Award17 May 2018
Original languageEnglish
Awarding Institution
  • University of Bath
SupervisorEdward Feil (Supervisor) & Laurence Hurst (Supervisor)


  • Bacteria
  • Genomics
  • Bioinformatics

Cite this