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Evolution of REP diversity: a comparative study.

Jaroslav Nunvar1, Irena Licha, Bohdan Schneider

  • 1Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague 2, Czech Republic. nunvar@natur.cuni.cz

BMC Genomics
|June 14, 2013
PubMed
Summary
This summary is machine-generated.

Repetitive extragenic palindromic (REP) elements are abundant in Pseudomonas and Stenotrophomonas genomes, showing dynamic evolution and species-specific distribution. Their high copy numbers suggest a beneficial role in bacterial long-term fitness.

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Area of Science:

  • Bacterial genomics
  • Molecular evolution
  • Genomic repeat elements

Background:

  • Repetitive extragenic palindromic (REP) elements are abundant bacterial genomic repeats with significant roles in host physiology.
  • Analysis of REP element diversity and evolution provides insights into bacterial genome dynamics.

Purpose of the Study:

  • To analyze the phylogenetic distribution of REP classes in Pseudomonas fluorescens and Stenotrophomonas sp.
  • To assess intraspecific REP diversity and understand long-term REP evolution.

Main Methods:

  • Phylogenetic analysis of REP element distribution across 63 Pseudomonas fluorescens strains and 10 Stenotrophomonas strains.
  • Identification of REP classes based on proximity to REP-associated tyrosine transposase (RAYT) genes.

Main Results:

  • Twenty-two and thirteen unique REP classes were identified in fluorescent pseudomonads and stenotrophomonads, respectively.
  • REP element abundances varied significantly, generally correlating with host phylogeny and RAYT gene presence.
  • Fluorescent pseudomonads exhibited higher REP copy numbers (hundreds to over a thousand) compared to stenotrophomonads (tens to hundreds).

Conclusions:

  • REP elements are dynamic genomic components in fluorescent pseudomonads and stenotrophomonads, with ongoing diversification and proliferation.
  • High REP numbers are likely maintained due to beneficial effects on host long-term fitness.
  • REP elements offer a model system for studying interactions between repetitive elements, mobilizers, and bacterial hosts.