Detection of Bacteriophages: Sequence-Based Systems
The invention of sequencing technologies has fundamentally changed molecular biology, including the way we look at bacteriophages. In addition to investigating bacteriophage plaques, electron micrographs, or the phenotypes of different mutants, we are now able to explore the entire genetic potential encoded in their genomes. As of July 2018, over 6,000 complete phage genome sequences were published in public databases, with over 28,000 partial sequences available.
In this chapter, we give an overview of the latest technologies that can be used to determine phage genome sequences, ranging from short-read platforms which generally give multiple gigabases of sequence data to long-read technologies which have the potential to sequence a bacteriophage genome in one single read. We then look at applications of sequencing technologies in detecting bacteriophages, from a single gene, over entire genomes, to the community level.
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