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Modern comparative and composition-based approaches – the state of the art
Following the publication of the first two complete genome sequences of Haemophilus influenza (Fleischmann et al., 1995) and Mycoplasma genitalium (Fraser et al., 1995) in 1995, a total of 6342 bacteria have reportedly been completely sequenced and become publicly available in the Genomes OnLine Database (GOLD), accessed September the 5th 2013 (Kyrpides N. C., 1999). The increase in numbers of sequenced bacterial genomes from 2 in 1995 to 6342 in 2013 has been made possible by the advances in high-throughput sequencing technologies i.e. Roche-454 (Margulies et al., 2005), Solexa – Illumina (Fedurco et al.,2006), ABI SOLiD (Shendure et al., 2005) and Pacific Biosciences (Eid et al., 2009).
The high-throughput projects have provided fast and cost effective methodologies that allow sequencing of large DNA stretches which span entire genomes in a single run. These advancements indicate how the concept of genome sequencing has evolved ever since the times of Gilbert & Maxam (1973) and Sanger & Coulson (1975), when researchers were only interested in getting single runs that allowed reading of 200-300 nucleotides. During the conventional sequencing days, sequencing was costly and a single bacterial genome sequence was delivered in months or even years (Loman et al., 2012).
The relatively inexpensive sequencing technologies have been producing large quantities of data by the day and opened up new perspectives in the field of genomics (Metzker, 2005). In addition to the reported number of completely sequenced genomes as mentioned above, 12189 more bacterial genomes are currently indicated as ongoing in GOLD, accessed September the 5th 2013 (Kyrpides N. C., 1999). The numbers mentioned earlier do not include the entire amount of available bacterial genomes and those of ongoing sequencing projects taking place in the other research facilities, as many do not make it onto GOLD.
These great numbers of bacteria are sequenced in order to study processes by which they evolve and understand their range of functions. Several of these bacteria are used to study their virulence properties towards humans, plants and animals and also their importance in industrial use i.e. bioremediation. Metagenomics, the study that focuses on the genomicanalysis of genetic material recovered directly from communities in environmental samples also contributes towards the increase in number of sequenced bacteria and make it possible to study differences in genomes of organisms which are difficult to culture. Collectively these genomes are beneficial for comparative genomics studies as they make it feasible to study large groups of (related and unrelated) bacteria with the aim of providing a broader picture of genomic diversity. It is generally believed that the important information which underlies the differences between highly virulent and avirulent strains may be read in their genomes as these may be due to DNA replication and repair based events (Karlin et al., 1997). Such analysis may be conducted by utilizing the available data to study and compare sets of strains and variants of the same species to get insight into their genomic evolutionary changes and identify factors which influence pathogenicity, persistence in host environments and, drug resistance. These also allow studying genomes in a comparative approach in order to understand the evolutionary events which are the most important on the level of microevolution. This review chapter will provide a brief overview of analytical approaches and studies conducted on the vast amounts of completely sequenced bacteria to gain insight into their genomic diversity and adaptation to different environments with the influence of microevolutionary events
Chapter 1: Modern comparative and composition based approaches – the state of the
art
1.1 Introduction
1.2 Bacterial microevolution and fitness traits
1.3 Genomic fragments acquired through horizontal transfer events
1.4 Features and detection of Genomic Islands.
1.5 Online Genomic Islands resources
1.6 Research objective.
1.7 Aims
1.8 List of Manuscripts.
Chapter 2: Optimization and practical use of composition based approaches towards
identification of horizontally transferred genomic islands
2.1 Introduction .
2.2 Materials and Methods
2.3 Results and Discussion
2.4 SWGIS parametric optimization
2.5 Case study of SWGIS failures and problem solving strategies
2.6 Conclusion.
Chapter 3: Analyses and visualization of genomic islands using composition based
approaches .
3.1 Introduction .
3.2 Materials and Methods
3.3 Results and Discussion.
3.4 Conclusion
Chapter 4: Mainstreams of horizontal gene exchange in enterobacteria: consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011
4.1 Abstract .
4.2 Introduction .
4.3 Materials and Methods
4.4 Results .
4.5 Genomic islands of the pathogenicity plasmids of the EAHEC strains .
4.6 Discussion
4.7 Conclusion
Chapter 5: Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and
TB
Chapter 6: Concluding Discussion
Bibliography
7 Appendices
