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A survey of bacterial insertion sequences using IScan.

Andreas Wagner1, Christopher Lewis, Manuel Bichsel

  • 1Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27-J-54, CH-8057 Zurich, Switzerland. aw@bioc.uzh.ch

Nucleic Acids Research
|August 10, 2007
PubMed
Summary

IScan software identifies bacterial insertion sequences (ISs) and their elements across multiple genomes. Analysis suggests most ISs are recent, possibly persisting through horizontal transfer.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Bacterial insertion sequences (ISs) are mobile genetic elements crucial for genome evolution.
  • Consistent IS annotation across diverse bacterial genomes is essential for evolutionary studies.

Purpose of the Study:

  • To develop and apply an open-source software package, IScan, for accurate and flexible identification of bacterial ISs and their associated sequence elements.
  • To analyze the evolutionary dynamics and patterns of ISs in bacterial genomes.

Main Methods:

  • Development of the IScan software package for identifying ISs, inverted repeats, and target direct repeats.
  • Application of IScan to 438 completely sequenced bacterial genomes and 20 IS families.
  • Statistical analysis of sequence similarity among IS inverted repeats to identify functional ISs.

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Main Results:

  • ISs within individual bacterial genomes exhibit high similarity, with a mean synonymous divergence (K(s)) of 0.033.
  • The findings suggest that a majority of ISs have recently colonized bacterial genomes.
  • IS inverted repeat analysis can effectively enrich datasets for potentially functional IS elements.

Conclusions:

  • IScan provides a robust tool for comprehensive IS annotation in bacterial genomics.
  • The recent acquisition and potential reliance on horizontal transfer for persistence are key evolutionary characteristics of bacterial ISs.
  • IScan is poised to facilitate large-scale evolutionary and horizontal transfer analyses as genomic data expands.