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Is the pan-genome also a pan-selectome?
Francisco Rodriguez-Valera1, David W Ussery2
1Departmento de Producción Vegetal y Microbiología, Universidad Miguel Hernandez, San Juan de Alicante, 03550, Spain.
F1000Research
|December 24, 2013
Summary
Prokaryotic populations comprise diverse "meta-clones" sharing a core genome but varying in flexible genes. Phages maintain this diversity by preventing resource monopolization, acting as natural selection units alongside these polyclonal assemblages.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Comparative genomics reveals prokaryotes possess a core genome and a flexible genome.
- Flexible genome regions are crucial for surface structures and niche adaptation.
- Metagenomics shows natural prokaryotic populations are meta-clonal, varying in flexible gene content.
Purpose of the Study:
- To explore the role of phages in maintaining prokaryotic meta-clonal diversity.
- To define the evolutionary significance of the core and flexible genome components.
- To identify natural selection units in prokaryotic populations.
Main Methods:
- Comparative genomics analysis of prokaryotic genomes.
- Metagenomic data analysis of natural prokaryotic populations.
- Phylogenetic analysis of phage-host interactions.
Main Results:
- Prokaryotic populations consist of meta-clones with shared core genomes and diverse flexible genomes.
- Flexible genome regions are implicated in phage recognition and niche exploitation.
- Phages actively regulate meta-clonal diversity by preventing resource monopolization.
Conclusions:
- The interplay between polyclonal prokaryotic assemblages and their predatory phages constitutes a fundamental unit of natural selection.
- Phage predation is a key mechanism driving and maintaining microbial diversity in natural environments.
- Understanding genome plasticity and phage dynamics is crucial for microbial ecology and evolution.
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