The genome of E. coli is typically about 5.0 Mb and contains about 4200 genes. But E. coli genomes can vary from about 4 – 6 Mb among different strains. Recent analysis has shown, that regardless of a strain’s phylogenetic origins, the genomes of E. coli strains isolated from poultry raised for commercial meat production have, on average, genome sizes significantly larger than strains from any other source. This increase in genome size is particularly noticeable among E. coli belonging to phylogroup A, one of eight E. coli ‘subspecies’ and a phylogroup that is prevalent in commercial poultry. Preliminary evidence indicates that the increased genome size is not only due to the acquisition of mobile-genetic elements such as plasmids or bacteriophage, but also due to the gain of chromosomal genes from distantly related strains of E. coli and perhaps also from other species.
This study will aim to determine how these large E. coli genomes evolved. The research will determine, relative to the nearest phylogenetic neighbours of these strains, what fraction of the increase in genome size is due to the acquisition of mobile elements and chromosomal genes. Other questions to be addressed will be; the phylogenetic origins of the acquired genes; the number of independent gene acquisition events; and where in the chromosome these genes are located? This is a bioinformatics based project that will make use of a variety of tools and will expoit a large collection of whole genome sequence data.