“Giant” phages are bacterial viruses with genomes >200kb with hundreds of genes. The greater level of genetic and structural complexity of giant phages is poorly defined because the functions of many genes are unknown. My research focused on the giant phage SPN3US which infects the foodborne pathogen Salmonella enterica. Early studies indicated that SPN3US had potential to create a genetic model system which could be used to assign functions to novel giant phage genes. Since the number of giant phage genomes in GenBank has recently increased dramatically, my research focused on reassessing our hypothesis. My research showed that ~41% of 280 giant phage genomes are genetically related to SPN3US, sharing between 55-251 homologous genes. The number of homologs shared with SPN3US by any giant phage generally correlated with new taxonomic assignments. My analysis of 255 SPN3US amber mutants revealed that 76 SPN3US genes are essential. These essential SPN3US genes were among the most highly conserved genes across the related phages, indicating that they likely represent the core set of genes needed to form a giant phage particle. For future studies, these amber mutants can be used to define specific gene functionality in SPN3US and general functionality in this expanding group of giant phages. This knowledge would be valuable because many giant phages have applications in the control of multi-drug resistant bacteria.

Library of Congress Subject Headings

Bacteriophages; Genomics

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Julia A. Thomas

Advisor/Committee Member

Gary Skuse

Advisor/Committee Member

Michael V. Osier


RIT – Main Campus

Plan Codes