Unique genes found in J Cluster’s ThreeRngTarJay

Jones, Wayman, Briana Murdock, Stephanie B. Conant, Jonathan S. Finkel, and Jacob D. Kagey

Bacteriophages are a revived virus that are helping scientists to begin to reimagine how we treat infection. These “phages” specifically target bacterial infections like influenza in a way that won’t be deleterious to the body. This is a great alternative to antibiotics because it can destroy surface level biofilm that drugs cannot penetrate. This pervasive strength can be traced in the genes of each phage, which contain other interesting characteristics. J-Cluster Bacteriophages’ genomes are mosaic in structure, which leads to fascinating research on functionality. Over time a phage may incorporate many different genes like antibiotic immunity from bacteria, other phages, etc. and will always contain a unique genome that does not completely match others. During our research, we examined many of the genes that expressed these functionalities. ThreeRngTarJay, a phage in the J-Cluster, was found in front of Shiple Hall on the campus of the University of Detroit Mercy. This phage exhibited turbid plaque morphologies that were described as “targets” and was discovered to be a Siphoviridae by using TEM. These plaques were then isolated, purified and sent to Pittsburg University to be sequenced. It was then archived in phagesdb.org and blasted using DNA Master. Our research with this sequence involved annotating a “50-60 gene” section of the genome, which involved the use of GLIMMER and GeneMark to judge for coding potential, and DNA Master to check for gene complications and compare alignment ratio and E-scores of multiple genes to predict whether a gene is correctly represented by DNA Master. The information learned from these programs led us to unique genes (80, 101-102, 79, 93-92). These include, gene overlap, long ORF values, multiple starts, and unusual gaps. Through the annotation of each of the genes in this section, we could predict which genes were deletions and the correct start codons.