Genome-wide variant discovery using sequence assembly, mapping and population-wide analysis

The transformation of DNA sequencing technologies has enabled more powerful and comprehensive genetic profiling of microbes. The sheer number of informative loci provided by genome-sequencing allows the investigation of structural variation and horizontal gene transfer as well as delivering novel insights into genetic origins, evolution and epidemiological history. Microbial genomes can be sequenced en masse at high coverage but have associated challenges of high mutation rates and low conservation of genome structure. Consequently, detecting changes in DNA sequences requires a nuanced approach specific to the organism, availability of similar genomes, and types of variation. Here, we outline the high power of genome-sequencing to detect a wide scope of polymorphism classes. Samples without related species on which to scaffold a genome sequence require specific assembly methods that can be enhanced by progressive procedures for improvement. Polymorphism identification depends on genome structure, and error rates in closely related specimens can be reduced by incorporating population-level information. The development of genome analysis platforms is hastening the optimization of variant discovery and has direct applications for pathogen surveillance. Robust variant screening facilitates more sensitive scrutiny of population history, including the origin and emergence of infectious agents, and a deeper understanding of the selective processes that shape microbial phenotypes. Background Microbial genomics is driven by the need to identify molecular markers and genetic switches associated with novel phenotypes. This is most extensively applied to address infectious disease and evolution but also is used for improving food, energy, water and biomolecule production (Suter et al., 2006). The core aim is to link the trait of interest to a defined cellular signature, principally a metabolic or regulatory change. Distinguishing phenotypes at a genetic level provides an enhanced resolution of the molecular events associated with natural variation due to the density of markers. Variability at the level of amino acids in peptides, repetitive DNA copy numbers and individual DNA nucleotides can provide sufficient power for discriminating traits: sample typing protocols have been developed on this basis (Wren, 2000). The most significant limitations for strain profiling are an adequate number of informative markers and the potential to overlook novel variation at other loci (Achtman, 2008). Although the first microbial genome sequence (RNA virus bacteriophage MS2) was completed in 1976 (Fiers et al., 1976), and the era of microbial genomics was proposed to have begun in 1995 (Rasko and Mongodin, 2005) with the bacterial genome of Haemophilus influenzae (Fleischmann et al., 1995), it was the recent development of DNA sequencing technologies more efficient than traditional capillary (Sanger) sequencing that made genome-sequencing accessible (Margulies et al., 2005). Since a 100-fold improvement developed for the Mycoplasma genitalium genome (Margulies et al., 2005), enhancements have continued and Genome SNP Analysis