Preferred Name
Madison Bendele
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International License.
Date of Graduation
5-15-2025
Semester of Graduation
Spring
Degree Name
Master of Science (MS)
Department
Department of Biology
First Advisor
Steven Cresawn
Abstract
The study of bacteriophages, the world's most numerous and genetically diverse biological entities, has led to many seminal discoveries in genetics, however their complex genomes and rampant horizontal genetic exchange (HGT) have left them understudied relative to other organisms. HGT induced by illegitimate recombination and subsequent natural selection adds layers of complexity to every phage genome, disrupting large syntenic regions with one or more horizontally inherited genes. This behavior complicates phage genomics and phylogenetics and has led to difficulty in unraveling operon structure and functional predictions of phage gene products.
In this study, we build upon prior work in clustering whole genomes and phage protein families ("phamilies") to confront the synteny and mosaicism issues head on by building and clustering a phage gene network. This network of gene clusters (GCLs) is the first of its kind for phages that infect hosts in the phylum Actinobacterium. This large, sparse, fully connected network can be visualized in several ways. Herein we utilize network graphs, gene cluster diagrams, and comparative genome maps to explore the utility of the clustered network for understanding synteny and mosaicism and the functional implications thereof for this important population of phages.
