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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
Published on: June 11, 2015
Reticulate representation of evolutionary and functional relationships between phage genomes
Gipsi Lima-Mendez1, Jacques Van Helden, Ariane Toussaint
1Service de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Bruxelles, Belgium. gipsi@scmbb.ulb.ac.be
Molecular Biology and Evolution
|February 1, 2008
Summary
Bacteriophage classification is evolving beyond traditional methods due to mosaic genomes. A new gene-content based reticulate classification framework reveals phage relationships and evolutionary modules.
Area of Science:
- Virology
- Bioinformatics
- Computational Biology
Background:
- Bacteriophage genomes exhibit mosaicism, driven by horizontal gene exchange, challenging traditional classification systems.
- Existing classification methods based on morphology and nucleic acid type are inconsistent with genomic data, leading to unclassifiable phages.
- The genomic era necessitates new approaches to classify bacteriophages, accommodating their mosaic nature and evolutionary dynamics.
Purpose of the Study:
- To propose a novel framework for bacteriophage classification based on gene content, addressing the limitations of traditional and tree-based methods.
- To develop a reticulate classification system that reflects the complex evolutionary relationships and mosaicism in phage genomes.
- To identify and characterize evolutionary cohesive modules within phage genomes and their functional implications.
Main Methods:
- Constructed a weighted graph where nodes represent phages and edges represent shared gene content.
- Applied graph topology measures (clustering coefficient, closeness, betweenness) to analyze phage relationships and distinguish phage types.
- Utilized a 2-step clustering method to generate a reticulate classification and clustered genes by phylogenetic profiles to define evolutionary modules.
Main Results:
- The gene-content based graph successfully grouped most double-stranded DNA phages into a single component.
- Graph topology measures differentiated temperate, virulent, and chimeric phages.
- Identified distinct evolutionary modules in virulent and temperate phages, revealing differences in their functional organization and providing a basis for higher-level classification.
Conclusions:
- A reticulate classification framework based on gene content offers a dynamic and automatic method for representing bacteriophage relationships.
- This approach accommodates phage mosaicism and can be extended to incorporate newly sequenced genomes and other genetic elements.
- The identified evolutionary modules provide insights into the functional organization and evolutionary history of bacteriophages.
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