Lateral Gene Transfer in Operons and Its Effects on Neighbouring Genes

Abstract

<p>Prokaryotes evolve, in part, by lateral gene transfer (LGT). This transfer of genetic material is likely important in the evolution of operons, a group of genes that are transcribed as a single mRNA. Genes that are transferred may then be integrated into genomes by homologous recombination. In this thesis, it was proposed that homologous recombination is the mechanism of integration of laterally transferred genes into operons. To investigate this proposal, a phylogenetic tree of Bacillus was inferred using DNA sequence alignments. LGT was inferred using a parsimony algorithm, and operons were inferred using OperonDB. Homologous recombination breakpoints were identified by permutation tests, <em>GENECONV</em> and maximum chi square algorithm. The results indicate that there is evidence for integration of functionally annotated genes into operons by homologous recombination. There are several laterally transferred genes that have recombination breakpoints before the start codon or after the stop codon of the genes. It was also proposed in this thesis that LGT causes an increase in the rate of evolution of genes that are neighbours of laterally transferred genes. To investigate this proposal, genes that are neighbours of laterally transferred genes in Bacillus were identified. These genes were classified as upstream or downstream genes to the LGT event. Genes that are not neighbours of laterally transferred genes were also identified as a control. Selection and the rate of evolution was studied using maximum likelihood models implemented in CodeML of PAML. Genes under positive selection were inferred using likelihood ratio tests. The results indicate that only a few neighbouring genes were under positive selection, and the rate of evolution of the neighbouring genes was slightly higher than that of the non-neighbouring genes. The high rates of evolution of the neighbouring genes are likely due to relaxed selection on the neighbouring genes.</p>