Research Publication Title

Complete Genome Annotation of Mycobacteriophage SheaKeira

Major

Biology

Faculty Mentor

Dr. Indiren Pillay

Keywords

bacteriophage, mycobacteriophage, genome annotation, novel phage, phage therapy, phage database

Abstract

Complete Genome Annotation of Mycobacteriophage SheaKeira Betsy Bartholf Just as eukaryotic cells are infected by a vast array of viruses, bacteria are infected by their own respective classification of viruses known as bacteriophage. These abundant phages display unusually-high genetic diversity ranging in size from 15 kilobasepairs to 500 kilobasepairs. The double-stranded DNA viruses that infect the genus Mycobacteria are known as mycobacteriophages. Because of their extensive genetic novelty, these phages are arranged into clusters and sub-clusters based on comparative genomic analysis and evolutionary relatedness. SheaKeira, a novel mycobacteriophage identified by previous members of the Pillay lab, is a member of cluster A, the largest group of bacteriophages, and sub-cluster A9. In this project, each gene in the genome of SheaKeira was assessed for the coding potential of its open reading frames (ORFs), the genes predicted within the genome based on codon potential, the presence of tRNAs and tmRNAs, and other distinctive features expressing the genetic novelty and evolutionary conservation of this phage. This annotation of SheaKeira’s genome, carried out using software such as GeneMark, Phamerator, Glimmer, and DNA Master, contains all of the corrections manually made to these genes, including modifying gene start sites based on Glimmer and GeneMark calls, annotating wrap-around genes, identifying tmRNA genes, and more. Most importantly, by BLASTing our phage’s genome against that of other closely-related mycobacteriophages, the functions of many of SheaKeira’s genes were elucidated. The goal of this annotation project was to successfully annotate the genome of novel bacteriophage SheaKeira for GenBank submission with hopes that it may assist in future mycobacteriophage studies.

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Complete Genome Annotation of Mycobacteriophage SheaKeira

Complete Genome Annotation of Mycobacteriophage SheaKeira Betsy Bartholf Just as eukaryotic cells are infected by a vast array of viruses, bacteria are infected by their own respective classification of viruses known as bacteriophage. These abundant phages display unusually-high genetic diversity ranging in size from 15 kilobasepairs to 500 kilobasepairs. The double-stranded DNA viruses that infect the genus Mycobacteria are known as mycobacteriophages. Because of their extensive genetic novelty, these phages are arranged into clusters and sub-clusters based on comparative genomic analysis and evolutionary relatedness. SheaKeira, a novel mycobacteriophage identified by previous members of the Pillay lab, is a member of cluster A, the largest group of bacteriophages, and sub-cluster A9. In this project, each gene in the genome of SheaKeira was assessed for the coding potential of its open reading frames (ORFs), the genes predicted within the genome based on codon potential, the presence of tRNAs and tmRNAs, and other distinctive features expressing the genetic novelty and evolutionary conservation of this phage. This annotation of SheaKeira’s genome, carried out using software such as GeneMark, Phamerator, Glimmer, and DNA Master, contains all of the corrections manually made to these genes, including modifying gene start sites based on Glimmer and GeneMark calls, annotating wrap-around genes, identifying tmRNA genes, and more. Most importantly, by BLASTing our phage’s genome against that of other closely-related mycobacteriophages, the functions of many of SheaKeira’s genes were elucidated. The goal of this annotation project was to successfully annotate the genome of novel bacteriophage SheaKeira for GenBank submission with hopes that it may assist in future mycobacteriophage studies.