name:   Staphylococcus_phage
version:    231
date:   2018-10-29
owner:
    name:   Graham Hatfull
    email:  gfh@pitt.edu
    url:    https://www.biology.pitt.edu/person/graham-hatfull
description: >
    This database contains the Staphylococcus phages analyzed in Oliveira et al 2019.
publications:
    1:
        doi:    10.1186/s12864-019-5647-8
        pmid:   31072320
        title:  >
            Staphylococci phages display vast genomic diversity and evolutionary relationships
        authors:    >
            Hugo Oliveira, Marta Sampaio, Luís D R Melo, Oscar Dias, Welkin H Pope,
            Graham F Hatfull, Joana Azeredo
        abstract:   >
            Bacteriophages are the most abundant and diverse entities in the biosphere, and this
            diversity is driven by constant predator-prey evolutionary dynamics and horizontal gene
            transfer. Phage genome sequences are under-sampled and therefore present an untapped
            and uncharacterized source of genetic diversity, typically characterized by highly
            mosaic genomes and no universal genes. To better understand the diversity and
            relationships among phages infecting human pathogens, we have analysed the complete
            genome sequences of 205 phages of Staphylococcus sp.
            These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies
            (phams) of related sequences; 745 of these are orphams and possess only a single gene.
            Based on shared gene content, these phages were grouped into four clusters (A, B, C and
            D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the
            genomes have mosaic architectures and individual genes with common ancestors are
            positioned in distinct genomic contexts in different clusters. The staphylococcal
            Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are
            often closely-linked to genes implicated in bacterial virulence determinants. There are
            four unusual endolysin organization strategies found in Staphylococcus phage genomes,
            with endolysins predicted to be encoded as single genes, two genes spliced, two genes
            adjacent and as a single gene with inter-lytic-domain secondary translational start
            site. Comparison of the endolysins reveals multi-domain modularity, with conservation
            of the SH3 cell wall binding domain.
            This study provides a high-resolution view of staphylococcal viral genetic diversity,
            and insights into their gene flux patterns within and across different phage groups
            (cluster and subclusters) providing insights into their evolution.
resources: ~