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Staphylococci phages display vast genomic diversity and evolutionary relationships
Hugo Oliveira1, Marta Sampaio2, Luís D R Melo2
1CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal. hugooliveira@deb.uminho.pt.
BMC Genomics
|May 11, 2019
Summary
Bacteriophage genomes reveal extensive genetic diversity in Staphylococcus phages, uncovering novel gene families and evolutionary patterns. This research enhances our understanding of viral evolution and gene flux in bacterial pathogens.
Area of Science:
- Microbiology
- Virology
- Genomics
Background:
- Bacteriophages are highly diverse and abundant, driven by evolution and gene transfer.
- Phage genomes are under-sampled, representing a source of uncharacterized genetic diversity.
- Analysis of 205 Staphylococcus phages provides insight into their genetic makeup.
Purpose of the Study:
- To analyze the complete genome sequences of 205 Staphylococcus phages.
- To understand the diversity and relationships among these phages.
- To investigate phage gene flux and evolutionary patterns.
Main Methods:
- Whole-genome sequencing of 205 Staphylococcus phages.
- Bioinformatic analysis of predicted proteins and gene families (phams).
- Phylogenetic analysis to group phages into clusters and subclusters based on shared gene content.
Main Results:
- 20,579 proteins sorted into 2,139 phamilies (phams), with 745 orphams.
- Phages grouped into four clusters (A, B, C, D) and 27 subclusters.
- Mosaic genome architectures observed, with conserved genes in varied genomic contexts.
- Staphylococcal Cluster B siphoviridae predicted as temperate, with integration cassettes linked to virulence genes.
- Four endolysin organization strategies identified, showing modularity and conserved SH3 domains.
Conclusions:
- High-resolution view of staphylococcal viral genetic diversity.
- Insights into gene flux patterns within and across phage groups.
- Enhanced understanding of phage evolution and adaptation.
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