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MBE Advance Access published online on November 24, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msi057
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted November 2, 2004

Research Article

Survey of Simple Sequence Repeats in Completed Fungal Genomes

Haydar Karaoglu 1, Crystal Man Ying Lee 2, and Wieland Meyer 3*

1 School of Molecular and Microbial Biosciences, University of Sydney, Sydney, Australia; Molecular Mycology Research Laboratory, CIDM, Westmead Hospital, Westmead, Australia
2 Molecular Mycology Research Laboratory, CIDM, Westmead Hospital, Westmead, Australia
3 Molecular Mycology Research Laboratory, CIDM, Westmead Hospital, Westmead, Australia; Department of Medicine, Western Clinical School, The University of Sydney, Australia

* To whom correspondence should be addressed.
Wieland Meyer, E-mail: w.meyer{at}usyd.edu.au


  Abstract

The use of simple sequence repeats or microsatellites as genetic markers has become very popular due to their abundance and length variation between different individuals. SSRs are tandem repeat units of one to six base pairs that are found abundantly in many prokaryotic and eukaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced fungal genomes. We analysed and compared the occurrences, relative abundance, relative density, most common and longest SSRs in nine taxonomically different fungal species: Aspergillus nidulans, Cryptococcus neoformans, Encephalitozoon cuniculi, Fusarium graminearum, Magnaporthe grisea, Neurospora crassa, Schizosaccharomyces pombe, and Ustilago maydis. Our analysis revealed that, in all of the genomes studied, the occurrence, abundance, and relative density of SSRs varied, and was not influenced by the genome sizes. No correlation between relative abundance and the genomes sizes was observed but it was shown that N. crassa, the largest genome analysed had the highest relative abundance of SSRs. In most genomes, mono-, di- and trinucleotide repeats were more abundant than the longer repeated SSRs. Generally in each organism, the occurrence, relative abundance and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. Our analysis showed that the relative abundance of SSRs in fungi is low compared to the human genome, and that longer SSRs in fungi are rare. In addition to providing new information concerning the abundance of SSRs for each of these fungi, the results provide a general source of molecular markers that could be useful for a variety of applications such as population genetics and strain identification of fungal organisms.

Keywords: Simple Sequence Repeat; Microsatellite; Fungi.
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