Phylogeny and evolution of prokaryotic genomes

As potentially the first organisms to originate from earth, prokaryotes had a profound impact on the formation of the biosphere on earth. With the availability of increasing amount of genomic sequences, researchers are able to address many basic evolutionary questions that have puzzled biologists for centuries. My thesis was designed to study two important aspects of prokaryotic genomes: horizontal gene transfer and the evolution of noncoding sequences. It is well known that prokaryotic genomes have experienced horizontal transfer and incorporation of foreign genetic information. However, to what extent such horizontal gene transfer (HGT) affects the core genealogical history of organisms remains controversial. Here, we re-examine this question by assessing the extent of HGT among core orthologous genes using a novel statistical method based on statistical comparisons of tree topology. We apply the method to forty microbial genomes in the Clusters of Orthologous Groups (COG) database over a curated set of 297 orthologous gene clusters and we detect significant HGT events in 33 out of 297 clusters over a wide range of functional categories. Estimates of positions of HGT events suggest a low mean genome-specific rate of HGT (2.0%) among the orthologous genes, which is in general agreement with other quantitative estimates of HGT. Noncoding elements have drawn much attention due to their great impact on organismal phenotype. However, there is no systematic study currently available that examines evolutionary patterns within prokaryotic noncoding regions. Using 225 completely sequenced prokaryotic genomes, we are able to obtain a set of well-delimited noncoding sequences and study their evolutionary characteristics. We examine the relationship between noncoding content with genome size, operon formation and pseudogene rate. We also design a novel algorithm to address the challenges in aligning noncoding sequences, using which we construct homologous noncoding clusters. Noncoding sequences reveal a low level of conservation. The conserved noncoding elements are predominantly located at immediate upstream and downstream of coding regions. Many of them display modular architecture, with hub-modules enriched with known transcription factor binding sites. Finally, we create a web resource for the scientific community to search for regulatory elements, and to further explore the evolution of noncoding regions in prokaryotes