Cyanophage Genomic DNA Extraction

Twelve cyanophages were isolated (Waterbury and Valois, 1993 (link); Sullivan et al., 2003 (link); Sullivan et al., 2008 (link)), then concentrated and purified for genomic DNA extraction either by CsCl purification (details in Lindell et al., 2004 (link)) or using a Lambda Wizard DNA kit (Promega Corp., Madison, WI) directly on phage lysates. This kit precipitates phage particles using a polyethylene glycol solution, followed by DNA extraction using a diatomaceous earth-based resin (Promega Corp., Madison, WI). Total DNA yields were consistently higher using the Wizard DNA kit than using CsCl-purified particles (1–2 µg from 250 ml of lysate versus nanograms from 2 l of lysate). Although host DNA contamination was significant (ranged 11.4–77.5% of total reads) in the Wizard DNA kit preps due to the less rigorous purification, host reads could be filtered out during phage genome assembly. These methods are described in detail elsewhere (Henn et al., 2010 (link)).