| Summary: | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>Our <it>in silico </it>survey of microsatellite clustering in genomes of <it>Homo sapiens</it>, <it>Maccaca mulatta</it>, <it>Mus musculus</it>, <it>Rattus norvegicus</it>, <it>Ornithorhynchus anatinus</it>, <it>Gallus gallus</it>, <it>Danio rerio </it>and <it>Drosophila melanogaster </it>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.</p> <p>Conclusion</p> <p>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".</p>
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