Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Research article

Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites

Robert Kofler1*, Christian Schlötterer2, Evita Luschützky3 and Tamas Lelley1

Author Affiliations

1 University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology IFA-Tulln, Institute of Biotechnology in Plant Production, Konrad Lorenz Straße 20, 3430 Tulln, Austria

2 Institut für Popluationsgenetik, Veterinärmedizinische Universitat Wien, Josef Baumann Gasse 1, 1210 Wien, Austria

3 Umweltbundesamt, Spittelauer Lände 5, 1090 Wien, Austria

For all author emails, please log on.

BMC Genomics 2008, 9:612  doi:10.1186/1471-2164-9-612

Published: 17 December 2008



Compound microsatellites are a special variation of microsatellites in which two or more individual microsatellites are found directly adjacent to each other. Until now, such composite microsatellites have not been investigated in a comprehensive manner.


Our in silico survey of microsatellite clustering in genomes of Homo sapiens, Maccaca mulatta, Mus musculus, Rattus norvegicus, Ornithorhynchus anatinus, Gallus gallus, Danio rerio and Drosophila melanogaster revealed an unexpected high abundance of compound microsatellites. About 4 – 25% of all microsatellites could be categorized as compound microsatellites. Compound microsatellites are approximately 15 times more frequent than expected under the assumption of a random distribution of microsatellites. Interestingly, microsatellites do not only tend to cluster but the adjacent repeat types of compound microsatellites have very similar motifs: in most cases (>90%) these motifs differ only by a single mutation (base substitution or indel). We propose that the majority of the compound microsatellites originates by duplication of imperfections in a microsatellite tract. This process occurs mostly at the end of a microsatellite, leading to a new repeat type and a potential microsatellite repeat track.


Our findings suggest a more dynamic picture of microsatellite evolution than previously believed. Imperfections within microsatellites might not only cause the "death" of microsatellites they might also result in their "birth".