Applications of optical DNA mapping in microbiology – BioTechniques.com

Diana Bogas1, Lena Nyberg2, Rui Pacheco1, Nuno F. Azevedo3, Jason P. Beech4, Margarita Gomila5, Jorge Lalucat5, Clia M. Manaia1, Olga C. Nunes3, Jonas O. Tegenfeldt4, and Fredrik Westerlund2

1Universidade Catlica Portuguesa, CBQF - Centro de Biotecnologia e Qumica Fina Laboratrio Associado, Escola Superior de Biotecnologia, Porto, Portugal 2Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden 3LEPABE Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculdade de Engenharia, Universidade do Porto, Porto, Portugal 4NanoLund and Department of Physics, Lund University, Lund, Sweden 5Microbiology, Biology Department, Universitat de les Illes Balears, Palma de Mallorca, Balearic Islands, Spain

BioTechniques, Vol. 62, No. 6, June 2017, pp. 255267

Abstract

Optical mapping (OM) has been used in microbiology for the past 20 years, initially as a technique to facilitate DNA sequencebased studies; however, with decreases in DNA sequencing costs and increases in sequence output from automated sequencing platforms, OM has grown into an important auxiliary tool for genome assembly and comparison. Currently, there are a number of new and exciting applications for OM in the field of microbiology, including investigation of disease outbreaks, identification of specific genes of clinical and/or epidemiological relevance, and the possibility of single-cell analysis when combined with cell-sorting approaches. In addition, designing lab-on-a-chip systems based on OM is now feasible and will allow the integrated and automated microbiological analysis of biological fluids. Here, we review the basic technology of OM, detail the current state of the art of the field, and look ahead to possible future developments in OM technology for microbiological applications.

Optical mapping (OM) is a technique capable of imaging single DNA molecules (Figure 1; Box 1). The use of OM in microbiology started in the 1990s as an auxiliary technique that, combined with Sanger nucleotide sequencing, supported reliable and cost-effective bacterial genome mapping (1). In 1999, Lin et al. (2) reported the first de novo shotgun OM-generated map of a microorganism, Deinococcus radiodurans. This map aided genome assembly (sequencing) as well as the discovery of new episomes and contributed to the elucidation of recombination mechanisms in this organism. Over the years, OM methods have been optimized, increasing the resolution and allowing smaller DNA fragments to be differentiated (generally in the kilobase range). While OM cannot fully replace most of the already established methods, it has been demonstrated that it is a good complementary or auxiliary method for two major applications: (i) comparative genome profiling, based on the detection of structural genome variations, with applications in microbial typing; and, more recently, (ii) assembly and validation of whole-genome sequencing using high-throughput sequencing methods (Table 1). OM-based maps can be compared in silico with known sequences or, conversely, can be used as scaffolds for de novo assembly. These applications led to the recognition of OM restriction fragment mapping as a tool for rapidly identifying and/or characterizing microorganisms, motivating use of the technology for the development of commercial products (e.g., http://opgen.com; http://bionanogenomics.com/; http://www.genomicvision.com/).

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Applications of optical DNA mapping in microbiology - BioTechniques.com