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DNA Research 2005 12(4):221-233; doi:10.1093/dnares/dsi009
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Characterization of Mononucleotide Repeats in Sequenced Prokaryotic Genomes

Tom Coenye* and Peter Vandamme

Laboratorium voor Microbiologie, Universiteit Gent K.L. Ledeganckstraat 35, B-9000 Gent, Belgium

The increasing availability of prokaryotic genome sequences has shown that simple sequence repeats (SSRs) are widespread in prokaryotes and that there is extensive variation in their length, number and distribution. Considering their potential importance in generating genomic diversity, we determined the distribution of a specific group of SSRs, mononucleotide repeats of size between 5 and 13 nt, in 157 sequenced prokaryotic genomes. The data obtained in the present study show that (i) a large number of mononucleotide SSRs is present in all prokaryotic genomes investigated, (ii) shorter repeats are much more abundant than longer repeats, and (iii) in the majority of the genomes, longer mononucleotide SSRs are excluded from coding regions although we identified several organisms where mononucleotide SSRs are not excluded from the coding regions. We also observed that some genomes contain more mononucleotide SSRs than expected, while others contain significantly less. Bacterial genomes that contain much less mononucleotide SSRs than expected are generally larger and more GC-rich, while bacterial genomes that contain much more mononucleotide SSRs than expected are in general smaller and more AT-rich. Finally, we also noted that genomes that contain a high fraction of horizontally transferred genes have a lower mononucleotide SSR density and that A and T are generally overrepresented in mononucleotide SSRs.

Key words: mononucleotide repeats; simple sequence repeats; comparative genomics; genome evolution

*To whom correspondence should be addressed. Tel. +32-9-2645128, Fax. +32-9-2645092, Email: Tom.Coenye{at}UGent.be

Communicated by Naotaka Ogasawara


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