New tools for comparative genomics based on oligonucleotide compositional constraints and single nucleotide polymorphisms

Abstract

Tuberculosis is one of the leading causes of mortality globally. Although this disease has been around for many generations, treatment and management of the disease remains a daunting challenge. M. tb, is one of the most famous tuberculosis causing organisms, however there are many other mycobacterial strains and species that are also responsible for human mortality, globally. Not all mycobacterial species, however, are disease causing. It is only a few strains such as M. tb H37Rv, M. tb CDC1551, M. tb F11 and M. bovis which are responsible for causing disease. The rest are relatively harmless. What are the genetic differences between these virulent and avirulent strains that dictate a strain's behavior? The answers to these and many other questions lie hidden within the genomes of these organisms. Due to the great advances in DNA sequencing techniques, it is now now possible to more quickly and cheaply, sequence whole bacterial genomes in a single experimental run (High-throughput sequencing). Comparative genomics is therefore extremely relevant and important to be able to handle the dubious amounts of genomic data being poured into our public databases. Several comparative genomics environments already exist on the web today, however the goal of this project is to produce a web-based, comparative genomics environment which not only incorporates basic comparative genomics functions but also, novel tools such as the Seqword Genome Browser (SWGB) and the Mycobacterial Comparison Project (MCP). Using these tools, some interesting comparative genomics findings regarding certain strains of Mycobacteria are made. We reveal several genomic islands within M. avium and M. tb H37Rv. It is shown that certain genes which are usually found to be conserved among other bacteria, tend to be rather divergent among the mycobacteria. 'Mutational hotspots' containing many DNA replication genes are observed to have higher mutation rates relative to the rest of the genome which perhaps accounts for the slow-growth rate of these bacteria. By looking at the genetic profile of PE-PGRS genes in mycobacteria it was shown that M. tb H37Rv and M. tb F11 were actually closer for several genes than when compared to strain H37Ra. The finding was unexpected as H37Ra is known to be derived from H37Rv. These findings are extremely important in the area of TB research as it is of extreme importance to be able to trace areas of greater or lower selection within mycobacteria. Automated sequence comparison such as this is also important for tracking drug resistance markers and other features within mycobacteria so that more focused research can be carried out. The built system was tested and validated with mycobacteria, however, the system is flexible and designed with the intent of inclusion of any prokaryotic organism. It is hoped that systems such as these, and other advances in sequence comparison technology in the future, will provide the understanding needed to better control and cure diseases in the future.