The In Silico Annotation of the A3 Mycobacteriophage Fred313

Patel, Payal, John Sherwood, Stephanie B. Conant, Jonathan S. Finkel, and Jacob D. Kagey

Bacteriophage are viruses that infect and kill bacteria by using the bacteria to replicate themselves before building up inside the bacteria and lysing the bacteria. Bacteriophage can be used in what is called phage therapy which is a therapeutic use of bacteriophage to attack and eliminate harmful bacteria that infect humans. Mycobacteriophage Fred313 is a novel bacteriophage isolated in the fall of 2015 from Chesterfield, Michigan. Fred 313 was isolated with 8 other phages as a part of the HHMI SEA-Phages program at University of Detroit Mercy. Fred313 was isolated using mycobacterium smegmatis mc2 155 as a host in an enriched soil sample from Chesterfield, Michigan. Fred313 was characterized as a lytic bacteriophage and purified using a series of streak plates and titer assays. Electron microscopy was used to identify Fred313 as a siphoviridae phage. Once purified, DNA was taken from Fred313 and sent to the University of Pittsburgh for DNA sequencing. Here we present the In Silico genomic annotation of this A3 sub-cluster bacteriophage. The genome of Fred313 was found to contain 50,053 base pairs with 10 base pair 3’ sticky overhangs. Genemark and GLIMMER were used to auto-annotate the genome and these were entered in DNA Master. This auto-annotation was then checked using In Silico methods. Auto-annotation predicted 84 predicted protein encoding genes as well as 2 tRNA. After In Silico annotation, there were found to be 83 predicted protein encoding genes, as well as 1 false positive in the auto-annotation. There were also 2 predicted tRNA and 1 predicted frameshift at genes 20 and 21. Functional assignments were then added to 26 gene predictions using BLAST data and HHPred software. The purpose of this project is to add Fred313 to a growing database of annotated bacteriophage to help understand the genetic diversity and evolution of the bacteriophage population.