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PMID: 12743022 Published · ppublish English Comparative Study Journal Article

An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction.

Genome research ·Vol. 13 ·No. 6A ·2003-06-00 ·Pages 1123-32

Rocha EP

Abstract

An exhaustive search for shortly spaced repeats in 74 bacterial chromosomes reveals that they are much more numerous than is usually acknowledged. These repeats were divided into five classes: close repeats (CRs), tandem repeats (TRs), simple sequence repeats (SSRs), spaced interspersed direct repeats, and "others." CRs are widespread and constitute the most abundant class, particularly in coding sequences. The other classes are less frequent, but each individual element shows a higher potential for recombination, when the number of repeats and their distances are taken into account. SSRs and TRs are more frequent in pathogens, as expected given their role in contingency loci, but are also widespread in the other bacteria. The analysis of CRs shows that they have an important role in the evolution of genomes, namely by generating duplications and deletions. Several cases compatible with a significant role of small CRs in the formation of large repeats were detected. Also, gene deletion in Buchnera correlates with repeat density, suggesting that CRs may lead to sequence deletion in general and genome reductive evolution of obligatory intracellular bacteria in particular. The assembly of these results indicates that shortly spaced repeats are key players in the dynamics of genome evolution.

MeSH Terms
Chromosome Mapping Chromosomes, Bacterial/classification,genetics Clostridium/classification,genetics,pathogenicity DNA, Bacterial/classification,genetics Escherichia coli O157/classification,genetics,pathogenicity Gene Deletion Gene Duplication Genes, Bacterial/genetics Genome, Bacterial Haemophilus/classification,genetics,pathogenicity Interspersed Repetitive Sequences/genetics Methanosarcina/classification,genetics,pathogenicity Recombination, Genetic/genetics Virulence/genetics
Chemicals
DNA, Bacterial
Authors & Affiliations
1 authors, click to expand affiliations / ORCID
Rocha Eduardo P C
Unité Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France. [email protected]
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.966203
Email
[email protected]
Published
2003-06-00
Epub
2003-00-12
Pages
1123-32
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC403640
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.966203 PMC Full Text View journal details
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