name:   Mykobacteriophage_627
version:    8
date:   2014-09-30
owner:
    name:   Graham Hatfull
    email:  gfh@pitt.edu
    url:    https://www.biology.pitt.edu/person/graham-hatfull
description: >
    This database contains the 627 manually annotated Mycobacteriophages
    analyzed in Pope et al. 2015.
publications:
    1:
        doi:    10.1371/journal.pone.0118725
        pmid:   25742016
        title:  >
            Comparative genomics of Cluster O mycobacteriophages
        authors:    >
            Steven G Cresawn, Welkin H Pope, Deborah Jacobs-Sera, Charles A Bowman,
            Daniel A Russell, Rebekah M Dedrick, Tamarah Adair, Kirk R Anders, Sarah
            Ball, David Bollivar, Caroline Breitenberger, Sandra H Burnett, Kristen
            Butela, Deanna Byrnes, Sarah Carzo, Kathleen A Cornely, Trevor Cross,
            Richard L Daniels, David Dunbar, Ann M Findley, Chris R Gissendanner,
            Urszula P Golebiewska, Grant A Hartzog, J Robert Hatherill, Lee E Hughes,
            Chernoh S Jalloh, Carla De Los Santos, Kevin Ekanem, Sphindile L Khambule,
            Rodney A King, Christina King-Smith, Karen Klyczek, Greg P Krukonis,
            Christian Laing, Jonathan S Lapin, A Javier Lopez, Sipho M Mkhwanazi,
            Sally D Molloy, Deborah Moran, Vanisha Munsamy, Eddie Pacey, Ruth Plymale,
            Marianne Poxleitner, Nathan Reyna, Joel F Schildbach, Joseph Stukey,
            Sarah E Taylor, Vassie C Ware, Amanda L Wellmann, Daniel Westholm, Donna
            Wodarski, Michelle Zajko, Thabiso S Zikalala, Roger W Hendrix, Graham F
            Hatfull
        abstract:   >
            Mycobacteriophages--viruses of mycobacterial hosts--are genetically diverse but
            morphologically are all classified in the Caudovirales with double-stranded DNA and
            tails. We describe here a group of five closely related mycobacteriophages--Corndog,
            Catdawg, Dylan, Firecracker, and YungJamal--designated as Cluster O with long flexible
            tails but with unusual prolate capsids. Proteomic analysis of phage Corndog particles,
            Catdawg particles, and Corndog-infected cells confirms expression of half of the
            predicted gene products and indicates a non-canonical mechanism for translation of the
            Corndog tape measure protein. Bioinformatic analysis identifies 8-9 strongly predicted
            SigA promoters and all five Cluster O genomes contain more than 30 copies of a 17 bp
            repeat sequence with dyad symmetry located throughout the genomes. Comparison of the
            Cluster O phages provides insights into phage genome evolution including the processes
            of gene flux by horizontal genetic exchange.
    2:
        doi:    10.7554/eLife.06416
        pmid:   25919952
        title:  >
            Whole genome comparison of a large collection of mycobacteriophages
            reveals a continuum of phage genetic diversity
        authors:    >
            Welkin H Pope, Charles A Bowman, Daniel A Russell, Deborah Jacobs-Sera,
            David J Asai, Steven G Cresawn, William R Jacobs, Roger W Hendrix,
            Jeffrey G Lawrence, Graham F Hatfull, Science Education Alliance Phage
            Hunters Integrating Research and Education; Mycobacterial Genetics Course
        abstract:   >
            The bacteriophage population is large, dynamic, ancient, and genetically
            diverse. Limited genomic information shows that phage genomes are mosaic,
            and the genetic architecture of phage populations remains ill-defined.
            To understand the population structure of phages infecting a single host
            strain, we isolated, sequenced, and compared 627 phages of Mycobacterium
            smegmatis. Their genetic diversity is considerable, and there are 28
            distinct genomic types (clusters) with related nucleotide sequences.
            However, amino acid sequence comparisons show pervasive genomic mosaicism,
            and quantification of inter-cluster and intra-cluster relatedness reveals
            a continuum of genetic diversity, albeit with uneven representation of
            different phages. Furthermore, rarefaction analysis shows that the
            mycobacteriophage population is not closed, and there is a constant influx
            of genes from other sources. Phage isolation and analysis was performed by
            a large consortium of academic institutions, illustrating the substantial
            benefits of a disseminated, structured program involving large numbers of
            freshman undergraduates in scientific discovery.
resources: ~