In Silico Genomic Annotation of Kady, a Novel Bacteriophage Isolated from Soil

Maxwell, Danielle, Madeleine Reardon, Joshua Thomson, and Jacob Kagey

The purpose of this research project was to isolate, name, sequence, and analyze a newly-discovered mycobacteriophage.  A mycobacteriophage is a virus that destroys a bacterial cell by taking over the internal machinery of the host bacterium.  In our study, we discovered a novel, lytic, Siphoviridae mycobacteriophage named Kady.  Kady’s known bacterial host is Mycobacterium smegmatius, but there could be other bacterial hosts for it as well.  Kady was isolated from an enriched soil sample in the fall and was later sent to a sequencing facility to have its DNA analyzed. The sequenced file of Kady’s DNA provided us with the data needed to further annotate Kady’s genome.  We used bioinformatics tools, such as DNA Master, a genome annotation software that predicts a bacteriophage’s gene location, as the basis for our gene annotation studies.  We also utilized several additional software programs to cross-analyze the genomic data with other sources and with similar species of bacteriophage.  GeneMark and Glimmer were useful at determining the coding potential for various start codons along Kady’s genome.  Phamerator, Starterator, and BLAST analysis tools were efficient at comparing the genome of Kady and closely related bacteriophage to identify similarities and differences between the genomes.  These software programs collectively identified eighty-nine potential genes in Kady’s genome, though we only annotated fourty-six of these genes.  After comparing Kady’s genome to genetically similar mycobacteriophage, we altered some of the genes within Kady’s genome.  We changed the start codon, deleted a gene, or predicted a frameshift for several of Kady’s genes based on sufficient data from these software programs.  However, the function of the 89 identified genes has yet to be determined.