Kot, Witold Piotr4; Vogensen, Finn Kvist5; Sørensen, Søren Johannes6; Hansen, Lars H.6
1 Microbiology, Department of Biology, Faculty of Science, Københavns Universitet2 Microbiology and Fermentation, Department of Food Science, Faculty of Science, Københavns Universitet3 Food Microbiology, Department of Food Science, Faculty of Life Sciences, Københavns Universitet4 Food Microbiology, Department of Food Science, Faculty of Life Sciences, Københavns Universitet5 Microbiology and Fermentation, Department of Food Science, Faculty of Science, Københavns Universitet6 Microbiology, Department of Biology, Faculty of Science, Københavns Universitet
Bacteriophages (phages) coexist with bacteria in all environments and influence microbial diversity, evolution and industrial production processes. As a result of this major impact of phages on microbes, tools that allow rapid characterization of phages are needed. Today, one of the most powerful methods for characterization of phages is determination of the whole genome using high throughput sequencing approaches. Here a direct plaque sequencing (DPS) is described, which is a rapid method that allows easy full genome sequencing of DNA-containing phages using the Nextera XT™ kit. A combination of host-DNA removal followed by purification and concentration of the viral DNA, allowed the construction of Illumina-compatible sequencing libraries using the Nextera™ XT technology directly from single phage plaques without any whole genome amplification step. This method was tested on three Caudovirales phages; ϕ29 Podoviridae, P113g Siphoviridae and T4 Myovirdae, which are representative of >96% of all known phages, and were sequenced using the Illumina MiSeq platform. Successful de novo assembly of the viral genomes was possible.
Journal of Virological Methods, 2014, Vol 196, p. 152-156