Genomic Annotation of Bacteriophages Ashballer and Bombitas
Session Title
Poster Session 1
Faculty Mentor
Kristi M. Westover, Ph.D.| Victoria J. Frost Ph.D.
College
College of Arts and Sciences
Department
Biology
Abstract
In the bioinformatics semester of SEA-PHAGES, our goal was to annotate the genomes of bacteriophages Ashballer (52,231 bp) and Bombitas (110,129 bp), members of subcluster A1 and cluster J, respectively. DNA Master, used for initial manual annotation of Ashballer, provided putative start site locations of open reading frames as well as statistics associated with the ribosomal binding assessment for these starts. Evaluating whether the open reading frames have biological functions was based on homology comparisons at the protein level with HHPred, NCBI’s BLASTp, and Phamerator. Bombitas was annotated using PECAAN, a software program which auto-implements all of the above described evidence. Both phages showed synteny (shared genes in similar locations and relative position on their genomes) with other phages in their clusters. Mosaicism, due to recombination events, sequence loss and gain, was also evident. 61% of Ashballer’s rightward-transcribed genes have predicted functions, while only 17% of the leftwards-transcribed genes do. Annotation of Bombitas displayed a similar trend. It is noticeable that a higher percentage of rightward-transcribed genes often code for structural proteins in phages genomes. Determining the putative function of each phage gene can provide further insight into possible interactions with host bacteria. The third component of the SEA-program is SEA-GENES. This next step will help characterize those genes with putative functions as well as those where homology comparisons provided no evidence of function.
Course Assignment
BIOL 271 – Westover
Previously Presented/Performed?
Winthrop University Showcase of Undergraduate Research and Creative Endeavors, Rock Hill, SC, April 2023.
Type of Presentation
Poster presentation
Grant Support?
Supported by HHMI SEA-PHAGES Discovery, Howard Hughes Medical Institute, 2016
Start Date
15-4-2023 12:00 PM
Genomic Annotation of Bacteriophages Ashballer and Bombitas
In the bioinformatics semester of SEA-PHAGES, our goal was to annotate the genomes of bacteriophages Ashballer (52,231 bp) and Bombitas (110,129 bp), members of subcluster A1 and cluster J, respectively. DNA Master, used for initial manual annotation of Ashballer, provided putative start site locations of open reading frames as well as statistics associated with the ribosomal binding assessment for these starts. Evaluating whether the open reading frames have biological functions was based on homology comparisons at the protein level with HHPred, NCBI’s BLASTp, and Phamerator. Bombitas was annotated using PECAAN, a software program which auto-implements all of the above described evidence. Both phages showed synteny (shared genes in similar locations and relative position on their genomes) with other phages in their clusters. Mosaicism, due to recombination events, sequence loss and gain, was also evident. 61% of Ashballer’s rightward-transcribed genes have predicted functions, while only 17% of the leftwards-transcribed genes do. Annotation of Bombitas displayed a similar trend. It is noticeable that a higher percentage of rightward-transcribed genes often code for structural proteins in phages genomes. Determining the putative function of each phage gene can provide further insight into possible interactions with host bacteria. The third component of the SEA-program is SEA-GENES. This next step will help characterize those genes with putative functions as well as those where homology comparisons provided no evidence of function.
