Phage sub cluster A3 : A Divided Nation?

1. Phage sub cluster A3 : A Divided Nation? Gabby Field, Matt Sutter, and Megan Kreitzman Summary of results Both of methods of research that we used created unique groups within the A3 phage sub cluster. However these groups differ from each other as well as with the hypothesized groups. Abstract The purpose behind our research was to determine if the current phage sub clusters A3 should be separated into two more sub clusters from the current A3 phages. Data The split Tree data created two unique groups. The blue group consist of Misomonster, Phoxy, Spike509, Methuselah, Norbert, Popcicle, Veracruz, and 205870. The red group is Epicphail, Maniac, Microwolf, Jobu, Phantastic, Rockstar, HelDan, JHC117, Marquart, and Vix. Figure 1: Split Tree of Integrase Gene Conclusions/Discussion Based on these results, we believe that the A3 sub cluster should not be divided. The data that we found does not support the hypothesized groups. What would you do differently if you were to repeat this project? This research can be furthered by creating dot plots, comparing average nucleotide identity, making SplitsTree analysis of the whole genome, and identifying stoperator sequences of the current A3 phages. These two methods only show part of the picture, but that does not take away from the data we gathered. Introduction Two new groups have been hypothesized using Phamerator map alignment of the A3 phages. Phages in group 1 are Veracruz, Rockstar, Popcicle, Phantastic, Norbert, and Heldan. Phages in group 2 are Bxz2, EpicPhail, GinkoMaracino, JHC117, Jobu08, Mainiac, MarQuardt, Methuselah, Microwolf, Misomonster, and Phoxy. We used split trees and virtual gels to determine if these two groups should be created. Data The virtual gels generated from Case It created 3 groups. The first group did not digest with anything. The second group digested with EcoR1 yielding 4 bands. The third group digested with EcoR1 yielding only 3 bands. Methods The first method we used was a split tree. We downloaded each A3 phage from phagesdb.org. The phage sequences were aligned using MEGA software. Once the sequences are aligned, it shows the way the A3 phage are similar and different. The second method was creating virtual gels with DNA from the A3 phages. The sequences that were collected from phagesdb.org are put into Case It software. Each A3 phage sequence is digested in a virtual gel with Hind111, EcoR1, Cla1, BamH1, Undigested DNA, and a 1 Kb ladder. References 1. Dr. Grahm Hatful, et. All. The Microbacteriophage Database. http://phagesdb.org. 2. Steven G Cresawn, et. All.12 May 2011. Phamerator: a Bioinformatic tool for Comparative bacteriophage Genomics. BioMed Central Bioinformatics. 3. Case It software (v6.06 beta) Karen Klyczek and Mark Bergland, University of Wisconsin-River Falls, October 2011 Figure 1: Split Tree of Integrase Gene Acknowledgements Dr. Alfred Bonilla, Dr. Kim Mogen, Dr. Karen Klyczek, the UW-River Falls, Biology department, and the HHMI Phage Hunters Program. Virtual Gel of Joebu08, Maniac, Marquart, Methuselah, Micrwolf, and Misomoster Virtual gel of Spike 509, Bxz2, Epic Fail, GingkoMarachino, and JHC117 Virtual Gel of HellDan, Norbert, Phantastic, Popsicle, Rockstar, Veracruz, and Vix