Refining the Genomic Annotation of Mangled: Marine Phage from Host Bacterium Vibrio alginolyticus
Department
Biological Sciences
Faculty Advisor
Mauricio Rodriguez-Lanetty
Start Date
1-10-2020 9:00 AM
End Date
1-10-2020 10:00 AM
Abstract
Mangled, a marine phage hosted by the bioluminescent bacterium Vibrio alginolyticus, was isolated by students of the SEA-PHAGES program at Florida International University after its discovery in a South Florida mangrove. The identification of Mangled is of special importance due to its designation as a marine phage, an area of phage genomics that is yet to be fully understood. Additionally, the gram-negative bacterium that is its host has been deemed to be medically important due to its affiliation with infectious diseases such as vibriosis, wound infections, and otitis, suggesting potential implications in regards to phage therapy. Mangled has been sequenced and annotated for start sites and functional calls using programs such as Phages DB, PECAAN, HHPred , and NCBI Blast. Overall, it has a genome that is 41,638 base pairs long consisting of a total of 77 genes with a gc content of 43.5 percent. In this project, a secondary functional analysis will be completed to gain insight into the genome's auxiliary metabolic genes, which are proteins that are thought to increase overall phage fitness in regard to metabolism and infection. Specifically, Gene 25 (NinB), Gene 55 (Proteosome Subunit Alpha Type-2), and Gene 72 (Chitin Binding Domain) has been cross examined with other phages and bacterium in order to perform phylogenetic analysis that has helped in verifying the identity of these genes as well as has provided a deeper understanding of the distinctive characteristics this newly-discovered phaged may possess. The data collection process consisted of two methodologies: searching for similar gene sequences on NCBI Blast, aligning those specific protein sequences on PromalSD, and creating a tree on IQ tree, as well as blasting the raw gene sequences on NCBI Blast and creating a phylogenetic tree directly from there. Ultimately, the information collected serves to close the gaps of understanding that are present within the field of marine phage genomics.
File Type
Event
Refining the Genomic Annotation of Mangled: Marine Phage from Host Bacterium Vibrio alginolyticus
Mangled, a marine phage hosted by the bioluminescent bacterium Vibrio alginolyticus, was isolated by students of the SEA-PHAGES program at Florida International University after its discovery in a South Florida mangrove. The identification of Mangled is of special importance due to its designation as a marine phage, an area of phage genomics that is yet to be fully understood. Additionally, the gram-negative bacterium that is its host has been deemed to be medically important due to its affiliation with infectious diseases such as vibriosis, wound infections, and otitis, suggesting potential implications in regards to phage therapy. Mangled has been sequenced and annotated for start sites and functional calls using programs such as Phages DB, PECAAN, HHPred , and NCBI Blast. Overall, it has a genome that is 41,638 base pairs long consisting of a total of 77 genes with a gc content of 43.5 percent. In this project, a secondary functional analysis will be completed to gain insight into the genome's auxiliary metabolic genes, which are proteins that are thought to increase overall phage fitness in regard to metabolism and infection. Specifically, Gene 25 (NinB), Gene 55 (Proteosome Subunit Alpha Type-2), and Gene 72 (Chitin Binding Domain) has been cross examined with other phages and bacterium in order to perform phylogenetic analysis that has helped in verifying the identity of these genes as well as has provided a deeper understanding of the distinctive characteristics this newly-discovered phaged may possess. The data collection process consisted of two methodologies: searching for similar gene sequences on NCBI Blast, aligning those specific protein sequences on PromalSD, and creating a tree on IQ tree, as well as blasting the raw gene sequences on NCBI Blast and creating a phylogenetic tree directly from there. Ultimately, the information collected serves to close the gaps of understanding that are present within the field of marine phage genomics.